Progressive Loss of Function in a Limb Enhancer during Snake Evolution
The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long...
Saved in:
| Published in | Cell Vol. 167; no. 3; pp. 633 - 642.e11 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
20.10.2016
Elsevier |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0092-8674 1097-4172 1097-4172 |
| DOI | 10.1016/j.cell.2016.09.028 |
Cover
| Abstract | The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution.
[Display omitted]
[Display omitted]
•Activity of the critical ZRS limb enhancer is highly conserved across vertebrates•ZRS enhancer has progressively lost its function during snake evolution•Snake-specific nucleotide changes contributed to the loss of ZRS enhancer function•Resurrection of snake enhancer function in vivo
Morphological disappearance of limbs in snakes is associated with sequence changes disrupting the function of a critical limb enhancer. |
|---|---|
| AbstractList | The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of
Sonic hedgehog (Shh)
. Transgenic mouse reporter assays revealed that the
in vivo
activity pattern of the enhancer is conserved across a wide range of vertebrates including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full
in vivo
function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution.
Increased rate of molecular evolution and progressive loss of function for a critical limb enhancer in snakes explains morphological disappearance of limbs The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP.The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP. The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution.[Display omitted] The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. In this paper, we identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. [Display omitted] [Display omitted] •Activity of the critical ZRS limb enhancer is highly conserved across vertebrates•ZRS enhancer has progressively lost its function during snake evolution•Snake-specific nucleotide changes contributed to the loss of ZRS enhancer function•Resurrection of snake enhancer function in vivo Morphological disappearance of limbs in snakes is associated with sequence changes disrupting the function of a critical limb enhancer. The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP. |
| Author | Mannion, Brandon J. Tissières, Virginie Lee, Elizabeth A. Afzal, Veena Osterwalder, Marco Kato, Momoe Melo, Uirá S. Rubin, Edward M. Barozzi, Iros Pickle, Catherine S. Pennacchio, Len A. Kamneva, Olga K. Akiyama, Jennifer A. Visel, Axel Garvin, Tyler H. Dickel, Diane E. Plajzer-Frick, Ingrid Lopez-Rios, Javier Kvon, Evgeny Z. |
| AuthorAffiliation | 4 U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA 1 MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA 3 Department of Biomedicine, University of Basel, 4058 Basel, Switzerland 5 School of Natural Sciences, University of California, Merced, CA 95343, USA 2 Department of Biology, Stanford University, Stanford, CA 94305, USA |
| AuthorAffiliation_xml | – name: 1 MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – name: 5 School of Natural Sciences, University of California, Merced, CA 95343, USA – name: 4 U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA – name: 3 Department of Biomedicine, University of Basel, 4058 Basel, Switzerland – name: 2 Department of Biology, Stanford University, Stanford, CA 94305, USA |
| Author_xml | – sequence: 1 givenname: Evgeny Z. surname: Kvon fullname: Kvon, Evgeny Z. organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 2 givenname: Olga K. surname: Kamneva fullname: Kamneva, Olga K. organization: Department of Biology, Stanford University, Stanford, CA 94305, USA – sequence: 3 givenname: Uirá S. surname: Melo fullname: Melo, Uirá S. organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 4 givenname: Iros surname: Barozzi fullname: Barozzi, Iros organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 5 givenname: Marco surname: Osterwalder fullname: Osterwalder, Marco organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 6 givenname: Brandon J. surname: Mannion fullname: Mannion, Brandon J. organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 7 givenname: Virginie surname: Tissières fullname: Tissières, Virginie organization: Department of Biomedicine, University of Basel, 4058 Basel, Switzerland – sequence: 8 givenname: Catherine S. surname: Pickle fullname: Pickle, Catherine S. organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 9 givenname: Ingrid surname: Plajzer-Frick fullname: Plajzer-Frick, Ingrid organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 10 givenname: Elizabeth A. surname: Lee fullname: Lee, Elizabeth A. organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 11 givenname: Momoe surname: Kato fullname: Kato, Momoe organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 12 givenname: Tyler H. surname: Garvin fullname: Garvin, Tyler H. organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 13 givenname: Jennifer A. surname: Akiyama fullname: Akiyama, Jennifer A. organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 14 givenname: Veena surname: Afzal fullname: Afzal, Veena organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 15 givenname: Javier surname: Lopez-Rios fullname: Lopez-Rios, Javier organization: Department of Biomedicine, University of Basel, 4058 Basel, Switzerland – sequence: 16 givenname: Edward M. surname: Rubin fullname: Rubin, Edward M. organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 17 givenname: Diane E. surname: Dickel fullname: Dickel, Diane E. organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 18 givenname: Len A. surname: Pennacchio fullname: Pennacchio, Len A. email: lapennacchio@lbl.gov organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA – sequence: 19 givenname: Axel surname: Visel fullname: Visel, Axel email: avisel@lbl.gov organization: MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/27768887$$D View this record in MEDLINE/PubMed https://www.osti.gov/biblio/1398431$$D View this record in Osti.gov |
| BookMark | eNqFkV9rFDEUxYNU7Lb6BXyQwSdfZkwy-QsilLJrCwsK6nPIZO7uZp1NajKz4Lc347aiPtSnBHLOuTfnd4HOQgyA0EuCG4KJeLtvHAxDQ8u9wbrBVD1BC4K1rBmR9AwtMNa0VkKyc3SR8x5jrDjnz9A5lVIopeQCrT6luE2Qsz9CtY45V3FTrabgRh9D5UNlq7U_dNUy7GxwkKp-Sj5sq8_BfoNqeYzDNCufo6cbO2R4cX9eoq-r5Zfrm3r98cPt9dW6dlyRsQYmVC8cKLJxBMBRDBsutdCSWE6tanvZdoJ3rHNasE66jlEO1GlHHIhOt5fo_Sn3buoO0DsIY7KDuUv-YNMPE603f78EvzPbeDScKcYpKwGvTwExj95k50dwOxdDADca0mrFWlJEb-6npPh9gjyag89z1zZAnLKhpUnaMiLEf6VEtUxrrn6lvvpz999LP8AoAnUSuFRAJNiYsp6d6y1f8YMh2Mzczd7MA8zM3WBtCvdipf9YH9IfNb07maAQO3pIcx9QKPc-zXX00T9m_wkH48Z_ |
| CitedBy_id | crossref_primary_10_1016_j_gde_2017_03_004 crossref_primary_10_7554_eLife_84118 crossref_primary_10_1016_j_cub_2020_12_043 crossref_primary_10_1016_j_isci_2024_109304 crossref_primary_10_1111_dgd_12668 crossref_primary_10_1016_j_celrep_2021_109896 crossref_primary_10_1038_s41556_024_01435_6 crossref_primary_10_1073_pnas_2322692121 crossref_primary_10_1016_j_aaf_2020_07_009 crossref_primary_10_1007_s11427_022_2233_x crossref_primary_10_1016_j_tig_2017_11_007 crossref_primary_10_1038_s41422_020_0308_7 crossref_primary_10_1002_dvdy_646 crossref_primary_10_1016_j_neuron_2024_08_002 crossref_primary_10_1016_j_cub_2016_10_018 crossref_primary_10_3389_fcell_2023_1135519 crossref_primary_10_1038_s41588_021_00812_3 crossref_primary_10_1093_cz_zoz057 crossref_primary_10_1016_j_celrep_2019_10_102 crossref_primary_10_1016_j_ydbio_2019_11_015 crossref_primary_10_1186_s40104_022_00726_y crossref_primary_10_3390_jcdd7040044 crossref_primary_10_1242_dev_159764 crossref_primary_10_1017_S0963180119000860 crossref_primary_10_1016_j_ygeno_2022_110292 crossref_primary_10_3389_fmolb_2021_711710 crossref_primary_10_1093_molbev_msy125 crossref_primary_10_1134_S0031030123110096 crossref_primary_10_1093_gbe_evad166 crossref_primary_10_1016_j_celrep_2017_07_037 crossref_primary_10_1093_sysbio_syx058 crossref_primary_10_1016_j_cbpa_2023_111415 crossref_primary_10_3389_fcell_2023_1247361 crossref_primary_10_1002_jez_b_23096 crossref_primary_10_1016_j_ydbio_2018_09_008 crossref_primary_10_1038_s41586_024_07830_1 crossref_primary_10_1016_j_devcel_2021_02_016 crossref_primary_10_3389_fimmu_2021_659761 crossref_primary_10_7554_eLife_38555 crossref_primary_10_1126_sciadv_ade6529 crossref_primary_10_1016_j_jmb_2019_09_010 crossref_primary_10_1038_s41467_024_52380_9 crossref_primary_10_1002_dvdy_308 crossref_primary_10_1016_j_toxcx_2020_100053 crossref_primary_10_1111_joa_12707 crossref_primary_10_1093_molbev_msz300 crossref_primary_10_3390_md17070426 crossref_primary_10_1186_s13059_023_02856_6 crossref_primary_10_1186_s12711_022_00754_2 crossref_primary_10_1093_molbev_msae239 crossref_primary_10_1093_nar_gkab841 crossref_primary_10_1002_ece3_8226 crossref_primary_10_1126_science_abm7993 crossref_primary_10_1101_gr_277715_123 crossref_primary_10_3389_fgene_2021_642975 crossref_primary_10_1186_s12860_020_00270_5 crossref_primary_10_1038_s41467_021_25810_1 crossref_primary_10_1186_s41065_017_0040_6 crossref_primary_10_1038_nature25461 crossref_primary_10_1002_dvg_23077 crossref_primary_10_1016_j_celrep_2021_110280 crossref_primary_10_1111_dgd_12901 crossref_primary_10_1002_dvg_23078 crossref_primary_10_1007_s00438_021_01775_0 crossref_primary_10_1007_s00253_023_12524_1 crossref_primary_10_1038_s41586_023_06548_w crossref_primary_10_1002_dvdy_288 crossref_primary_10_1111_eva_12939 crossref_primary_10_1016_j_ydbio_2017_02_001 crossref_primary_10_1038_s41467_024_55500_7 crossref_primary_10_1038_s41418_023_01207_z crossref_primary_10_1126_sciadv_add0695 crossref_primary_10_1038_s41588_019_0559_8 crossref_primary_10_1093_molbev_msaa212 crossref_primary_10_1007_s11427_023_2362_5 crossref_primary_10_1093_molbev_msaa331 crossref_primary_10_1186_s13227_016_0063_5 crossref_primary_10_1093_gbe_evac159 crossref_primary_10_1186_s12859_018_2343_7 crossref_primary_10_1126_science_aay1645 crossref_primary_10_1093_nar_gkae940 crossref_primary_10_1073_pnas_1719798115 crossref_primary_10_1016_j_ydbio_2019_06_015 crossref_primary_10_1007_s11427_020_1748_0 crossref_primary_10_1038_s41467_022_31848_6 crossref_primary_10_1002_dvg_23052 crossref_primary_10_3389_fcell_2017_00023 crossref_primary_10_1242_dev_204275 crossref_primary_10_1186_s12864_022_08450_7 crossref_primary_10_1126_science_abl8621 crossref_primary_10_1186_s12864_022_09024_3 crossref_primary_10_3389_fped_2022_797978 crossref_primary_10_1111_evo_13651 crossref_primary_10_1134_S1990519X22060086 crossref_primary_10_1016_j_celrep_2018_02_008 crossref_primary_10_1016_j_jia_2024_05_005 crossref_primary_10_1093_molbev_msad188 crossref_primary_10_1126_sciadv_aba7261 crossref_primary_10_1002_jez_b_23103 crossref_primary_10_1534_genetics_120_303626 crossref_primary_10_3389_fcell_2017_00014 crossref_primary_10_1038_s41576_019_0128_0 crossref_primary_10_1093_icb_icx092 crossref_primary_10_1242_dev_203077 crossref_primary_10_1016_j_jmb_2019_10_017 crossref_primary_10_3390_ani11020444 crossref_primary_10_1038_s41588_024_01681_2 crossref_primary_10_1186_s12864_021_07925_3 crossref_primary_10_1186_s12915_023_01535_z crossref_primary_10_1016_j_ydbio_2016_11_005 crossref_primary_10_1038_nrg_2016_149 crossref_primary_10_1073_pnas_1719885115 crossref_primary_10_1093_bioinformatics_btab684 crossref_primary_10_1007_s42977_022_00136_1 crossref_primary_10_1093_sysbio_syz050 crossref_primary_10_1111_tpj_14985 crossref_primary_10_1101_gad_310367_117 crossref_primary_10_1016_j_ebiom_2024_105026 crossref_primary_10_3390_biomedicines12112505 crossref_primary_10_1038_s41598_017_15999_x crossref_primary_10_1038_s41598_024_68608_z crossref_primary_10_1016_j_apsb_2022_11_015 crossref_primary_10_1126_science_adf8009 crossref_primary_10_1101_gr_277784_123 crossref_primary_10_1093_gbe_evac108 crossref_primary_10_3390_ijms25010343 crossref_primary_10_1371_journal_pone_0281297 crossref_primary_10_1093_jhered_esac061 crossref_primary_10_1002_dvdy_24676 crossref_primary_10_1038_s41467_018_07122_z crossref_primary_10_1590_1678_4685_gmb_2022_0384 crossref_primary_10_1038_nrg_2016_167 crossref_primary_10_1002_dvdy_31 crossref_primary_10_1038_s41586_023_06922_8 crossref_primary_10_1093_nar_gky741 crossref_primary_10_1038_538430e crossref_primary_10_1136_jmedgenet_2019_106369 crossref_primary_10_1073_pnas_2204716119 crossref_primary_10_1242_dev_202610 crossref_primary_10_1038_s41576_021_00398_w crossref_primary_10_12688_openreseurope_13795_2 crossref_primary_10_1093_zoolinnean_zlz098 crossref_primary_10_1038_s41586_019_1312_2 crossref_primary_10_1016_j_gde_2017_09_004 crossref_primary_10_12688_openreseurope_13795_1 crossref_primary_10_1016_j_cell_2023_05_030 crossref_primary_10_1093_molbev_msy191 crossref_primary_10_1670_19_002 crossref_primary_10_3389_fgene_2021_775205 crossref_primary_10_1098_rspb_2022_1928 crossref_primary_10_1101_gr_272468_120 crossref_primary_10_1111_dgd_12952 crossref_primary_10_1038_s41467_017_02788_3 crossref_primary_10_1186_s12860_023_00474_5 crossref_primary_10_1016_j_stem_2022_06_006 crossref_primary_10_1016_j_devcel_2022_12_003 crossref_primary_10_1002_dneu_22891 crossref_primary_10_1016_j_tree_2024_07_005 crossref_primary_10_1093_gbe_evaa118 crossref_primary_10_1242_dev_202032 crossref_primary_10_1139_gen_2020_0104 crossref_primary_10_1016_j_cell_2020_02_031 crossref_primary_10_1093_nar_gkx1074 crossref_primary_10_2139_ssrn_4186258 crossref_primary_10_1016_j_cell_2016_10_007 crossref_primary_10_1016_j_cell_2017_12_017 crossref_primary_10_1016_j_semcdb_2019_04_003 crossref_primary_10_1038_s41588_018_0080_5 crossref_primary_10_1371_journal_pgen_1011174 crossref_primary_10_1002_dvdy_447 crossref_primary_10_3390_genes11020140 crossref_primary_10_1073_pnas_2421990122 crossref_primary_10_1016_j_cell_2020_06_037 crossref_primary_10_1038_s41586_023_05868_1 crossref_primary_10_1038_s41598_018_32565_1 crossref_primary_10_1038_s41588_023_01424_9 crossref_primary_10_1007_s40610_020_00131_2 crossref_primary_10_1093_gbe_evab103 crossref_primary_10_1002_dvdy_677 crossref_primary_10_1016_j_gde_2021_02_005 crossref_primary_10_3099_0027_4100_163_2_47 crossref_primary_10_1038_s41576_018_0007_0 crossref_primary_10_1093_molbev_msab150 crossref_primary_10_1016_j_xinn_2025_100798 crossref_primary_10_1002_ece3_11117 crossref_primary_10_3389_fphys_2018_00278 crossref_primary_10_1016_j_ygeno_2021_06_028 crossref_primary_10_1016_j_job_2019_08_001 crossref_primary_10_1038_s41598_019_51730_8 crossref_primary_10_1371_journal_pgen_1007573 crossref_primary_10_3390_jdb6020013 crossref_primary_10_1126_science_abn3263 crossref_primary_10_1002_2211_5463_13581 crossref_primary_10_1186_s13227_025_00239_5 crossref_primary_10_1101_cshperspect_a037226 crossref_primary_10_1093_molbev_msad102 crossref_primary_10_1073_pnas_2011531117 crossref_primary_10_1038_s41467_024_53009_7 crossref_primary_10_1126_sciadv_abg5968 crossref_primary_10_1016_j_stem_2024_12_011 crossref_primary_10_1534_g3_120_401777 crossref_primary_10_1038_s41559_017_0377_2 crossref_primary_10_1016_j_bbagrm_2022_194839 crossref_primary_10_1093_gbe_evae274 crossref_primary_10_1242_jeb_206433 crossref_primary_10_1002_cbf_3582 crossref_primary_10_1038_s41467_019_10532_2 crossref_primary_10_1038_s41598_017_12532_y crossref_primary_10_1038_s41592_024_02260_3 crossref_primary_10_1073_pnas_1900672116 |
| Cites_doi | 10.1101/pdb.prot5170 10.1038/416527a 10.1242/dev.02395 10.1038/nature08789 10.1093/nar/gkl822 10.1038/nrg2681 10.1002/dvdy.22535 10.1038/ng.3537 10.1242/dev.095430 10.1016/j.cell.2012.12.009 10.1038/nrg2063 10.1016/j.molcel.2010.05.004 10.1016/j.cell.2008.06.030 10.1186/1471-2148-13-93 10.1016/j.cell.2015.08.036 10.1038/ng.2991 10.1038/nature10944 10.1126/science.1182213 10.1111/ele.12620 10.1038/ng.808 10.1038/nature13289 10.1242/dev.02529 10.1126/science.287.5460.2010 10.1242/dev.01613 10.1016/j.semcdb.2015.12.018 10.1038/ng.3497 10.1016/j.devcel.2015.09.003 10.1126/science.1241006 10.1093/molbev/mst010 10.1038/nature05436 10.1098/rstb.2012.0357 10.1093/bioinformatics/btr064 10.1126/science.165.3891.349 10.1093/oxfordjournals.molbev.a026334 10.1016/j.cell.2012.04.029 10.1038/nature13496 10.1038/484046a 10.1073/pnas.1300592110 10.1073/pnas.1314475110 10.7554/eLife.16087 10.1016/j.cell.2015.01.006 10.1038/nature04413 10.1073/pnas.1314702110 10.1126/science.1090005 10.1126/science.1159974 10.1016/j.cell.2013.05.056 10.1038/nmeth.1318 10.1073/pnas.93.17.9067 10.1073/pnas.1420208112 10.1038/nmeth.2109 10.1093/hmg/ddm370 10.1038/nature07730 10.1038/ng.650 10.1016/0092-8674(93)90627-3 10.1038/nature05295 10.1007/s00335-033-2317-5 10.1016/j.cell.2013.08.022 10.1038/nature14042 10.1093/hmg/ddg180 10.1242/dev.105.4.707 10.1126/science.1260943 10.1038/nrg3095 10.1016/j.ympev.2005.07.016 10.1038/5096 10.1242/dev.00473 10.1093/sysbio/syq010 10.1038/nature12027 10.1038/nature09774 10.1093/bioinformatics/17.12.1246 10.1016/j.devcel.2011.12.010 10.1038/ng.1006 10.1038/ng.3009 10.1126/science.aaa9208 10.1093/nar/gku410 10.1387/ijdb.150060at 10.1016/j.gde.2007.07.006 10.1038/20944 10.1101/gad.1620408 10.1101/gad.12.20.3156 10.1186/s12862-015-0358-5 10.1038/nature03648 10.1016/j.cell.2015.12.007 10.1016/j.cell.2013.04.025 10.1038/nprot.2014.134 |
| ContentType | Journal Article |
| Copyright | 2016 Elsevier Inc. Copyright © 2016 Elsevier Inc. All rights reserved. |
| Copyright_xml | – notice: 2016 Elsevier Inc. – notice: Copyright © 2016 Elsevier Inc. All rights reserved. |
| CorporateAuthor | Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States) |
| CorporateAuthor_xml | – name: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States) |
| DBID | 6I. AAFTH AAYXX CITATION CGR CUY CVF ECM EIF NPM 7X8 7S9 L.6 OTOTI 5PM |
| DOI | 10.1016/j.cell.2016.09.028 |
| DatabaseName | ScienceDirect Open Access Titles Elsevier:ScienceDirect:Open Access CrossRef Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic AGRICOLA AGRICOLA - Academic OSTI.GOV PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic AGRICOLA AGRICOLA - Academic |
| DatabaseTitleList | MEDLINE - Academic AGRICOLA MEDLINE |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: EIF name: MEDLINE url: https://proxy.k.utb.cz/login?url=https://www.webofscience.com/wos/medline/basic-search sourceTypes: Index Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 1097-4172 |
| EndPage | 642.e11 |
| ExternalDocumentID | PMC5484524 1398431 27768887 10_1016_j_cell_2016_09_028 S0092867416313101 |
| Genre | Research Support, Non-U.S. Gov't Journal Article Research Support, N.I.H., Extramural |
| GrantInformation_xml | – fundername: NHGRI NIH HHS grantid: U54 HG006997 – fundername: NHGRI NIH HHS grantid: R01 HG003988 – fundername: NIDCR NIH HHS grantid: U01 DE024427 |
| GroupedDBID | --- --K -DZ -ET -~X 0R~ 0WA 1RT 1~5 29B 2FS 2WC 3EH 4.4 457 4G. 53G 5GY 5RE 62- 6I. 6J9 7-5 85S AACTN AAEDW AAFTH AAFWJ AAIAV AAKRW AAKUH AAUCE AAVLU AAXJY AAXUO ABCQX ABJNI ABMAC ABMWF ABOCM ABVKL ACGFO ACGFS ACNCT ADBBV ADEZE ADJPV AEFWE AENEX AEXQZ AFTJW AGHSJ AGKMS AHHHB AIDAL AITUG ALKID ALMA_UNASSIGNED_HOLDINGS AMRAJ ASPBG AVWKF AZFZN BAWUL CS3 DIK DU5 E3Z EBS EJD F5P FCP FDB FIRID HH5 IH2 IHE IXB J1W JIG K-O KOO KQ8 L7B LX5 M3Z M41 N9A NCXOZ O-L O9- OK1 P2P RCE RIG RNS ROL RPZ SCP SDG SDP SES SSZ TAE TN5 TR2 TWZ UKR UPT VQA WH7 WQ6 YZZ ZA5 ZCA .-4 .55 .GJ .HR 1CY 1VV 2KS 3O- 5VS 6TJ 9M8 AAEDT AAHBH AAIKJ AALRI AAMRU AAQFI AAQXK AAYJJ AAYWO AAYXX ABDGV ABDPE ABEFU ABWVN ACRPL ACVFH ADCNI ADMUD ADNMO ADVLN ADXHL AETEA AEUPX AFPUW AGCQF AGHFR AGQPQ AI. AIGII AKAPO AKBMS AKRWK AKYEP APXCP CITATION FEDTE FGOYB G-2 HVGLF HZ~ H~9 MVM OHT OMK OZT PUQ R2- UBW UHB VH1 X7M YYP YYQ ZGI ZHY ZKB ZY4 0SF CGR CUY CVF ECM EIF NPM 7X8 EFKBS 7S9 L.6 ABPTK ABQIS AFUVZ AKALU OTOTI 5PM |
| ID | FETCH-LOGICAL-c581t-e468d6ce81fc1eec20ef5796971a52a83d73b65b4bc964b7cb425e2c9c1ce6b93 |
| IEDL.DBID | IXB |
| ISSN | 0092-8674 1097-4172 |
| IngestDate | Thu Aug 21 17:51:07 EDT 2025 Fri May 19 01:20:39 EDT 2023 Fri Sep 05 10:10:03 EDT 2025 Fri Sep 05 03:38:20 EDT 2025 Thu Jan 02 23:11:13 EST 2025 Tue Jul 01 02:16:56 EDT 2025 Thu Apr 24 23:05:49 EDT 2025 Fri Feb 23 02:30:34 EST 2024 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 3 |
| Keywords | limb development evo-devo genome editing enhancer Sonic hedgehog (Shh) CRISPR/Cas9 cis-regulatory element morphological evolution snakes ZRS |
| Language | English |
| License | This article is made available under the Elsevier license. Copyright © 2016 Elsevier Inc. All rights reserved. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c581t-e468d6ce81fc1eec20ef5796971a52a83d73b65b4bc964b7cb425e2c9c1ce6b93 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 AC02-05CH11231 USDOE Office of Science (SC) Lead Contact |
| OpenAccessLink | https://www.sciencedirect.com/science/article/pii/S0092867416313101 |
| PMID | 27768887 |
| PQID | 1834995831 |
| PQPubID | 23479 |
| PageCount | 10 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_5484524 osti_scitechconnect_1398431 proquest_miscellaneous_2000234166 proquest_miscellaneous_1834995831 pubmed_primary_27768887 crossref_citationtrail_10_1016_j_cell_2016_09_028 crossref_primary_10_1016_j_cell_2016_09_028 elsevier_sciencedirect_doi_10_1016_j_cell_2016_09_028 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2016-10-20 |
| PublicationDateYYYYMMDD | 2016-10-20 |
| PublicationDate_xml | – month: 10 year: 2016 text: 2016-10-20 day: 20 |
| PublicationDecade | 2010 |
| PublicationPlace | United States |
| PublicationPlace_xml | – name: United States |
| PublicationTitle | Cell |
| PublicationTitleAlternate | Cell |
| PublicationYear | 2016 |
| Publisher | Elsevier Inc Elsevier |
| Publisher_xml | – name: Elsevier Inc – name: Elsevier |
| References | Cotney, Leng, Yin, Reilly, DeMare, Emera, Ayoub, Rakic, Noonan (bib16) 2013; 154 Wittkopp, Kalay (bib79) 2011; 13 Yang, Wang, Shivalila, Cheng, Shi, Jaenisch (bib83) 2013; 154 Apesteguía, Zaher (bib3) 2006; 440 Heinz, Benner, Spann, Bertolino, Lin, Laslo, Cheng, Murre, Singh, Glass (bib33) 2010; 38 Cretekos, Wang, Green, Martin, Rasweiler, Behringer (bib17) 2008; 22 Jones, Grabherr, Chan, Russell, Mauceli, Johnson, Swofford, Pirun, Zody, White (bib40) 2012; 484 Montague, Cruz, Gagnon, Church, Valen (bib56) 2014; 42 Ovchinnikov (bib57) 2009 Cohn, Tickle (bib14) 1999; 399 Romanes (bib65) 1892 Sekine, Ohuchi, Fujiwara, Yamasaki, Yoshizawa, Sato, Yagishita, Matsui, Koga, Itoh, Kato (bib68) 1999; 21 Tchernov, Rieppel, Zaher, Polcyn, Jacobs (bib71) 2000; 287 Hoekstra (bib35) 2012; 484 Hill, Lettice (bib34) 2013; 368 Lawson, Slowinski, Crother, Burbrink (bib45) 2005; 37 Darriba, Taboada, Doallo, Posada (bib19) 2012; 9 Infante, Mihala, Park, Wang, Johnson, Lauderdale, Menke (bib38) 2015; 35 Martill, Tischlinger, Longrich (bib52) 2015; 349 Carroll (bib10) 2008; 134 Lopez-Rios (bib50) 2016; 49 Panman, Galli, Lagarde, Michos, Soete, Zuniga, Zeller (bib58) 2006; 133 Castresana (bib12) 2000; 17 Wang, Yang, Shivalila, Dawlaty, Cheng, Zhang, Jaenisch (bib78) 2013; 153 Prabhakar, Visel, Akiyama, Shoukry, Lewis, Holt, Plajzer-Frick, Morrison, Fitzpatrick, Afzal (bib60) 2008; 321 Wright, Lyons, Brandley, Hillis (bib81) 2015; 324 Zeller, López-Ríos, Zuniga (bib86) 2009; 10 Lettice, Williamson, Wiltshire, Peluso, Devenney, Hill, Essafi, Hagman, Mort, Grimes (bib48) 2012; 22 Guerreiro, Gitto, Nóvoa, Codourey, Nguyen Huynh, Gonzalez, Milinkovitch, Mallo, Duboule (bib29) 2016; 5 Ullate-Agote, Milinkovitch, Tzika (bib72) 2014; 58 Reilly, Yin, Ayoub, Emera, Leng, Cotney, Sarro, Rakic, Noonan (bib64) 2015; 347 Guenther, Tasic, Luo, Bedell, Kingsley (bib27) 2014; 46 Katoh, Standley (bib41) 2013; 30 Rallis, Bruneau, Del Buono, Seidman, Seidman, Nissim, Tabin, Logan (bib63) 2003; 130 Shimodaira, Hasegawa (bib69) 2001; 17 Eckalbar, Schlebusch, Mason, Gill, Parker, Booker, Nishizaki, Muswamba-Nday, Terhune, Nevonen (bib22) 2016; 48 Guindon, Dufayard, Lefort, Anisimova, Hordijk, Gascuel (bib30) 2010; 59 Bronson, Plaehn, Kluckman, Hagaman, Maeda, Smithies (bib8) 1996; 93 Capellini, Di Giacomo, Salsi, Brendolan, Ferretti, Srivastava, Zappavigna, Selleri (bib9) 2006; 133 Blow, McCulley, Li, Zhang, Akiyama, Holt, Plajzer-Frick, Shoukry, Wright, Chen (bib6) 2010; 42 Lettice, Heaney, Purdie, Li, de Beer, Oostra, Goode, Elgar, Hill, de Graaff (bib46) 2003; 12 Lettice, Williamson, Devenney, Kilanowski, Dorin, Hill (bib49) 2014; 141 Villar, Berthelot, Aldridge, Rayner, Lukk, Pignatelli, Park, Deaville, Erichsen, Jasinska (bib74) 2015; 160 Britten, Davidson (bib7) 1969; 165 Chan, Marks, Jones, Villarreal, Shapiro, Brady, Southwick, Absher, Grimwood, Schmutz (bib13) 2010; 327 Gibson, Young, Chuang, Venter, Hutchison, Smith (bib25) 2009; 6 Xiao, Xie, Cao, Yu, Xing, Chen, Musselman, Xie, West, Lewin (bib82) 2012; 149 May, Blow, Kaplan, McCulley, Jensen, Akiyama, Holt, Plajzer-Frick, Shoukry, Wright (bib53) 2011; 44 Head, Polly (bib32) 2015; 520 Lopez-Rios, Duchesne, Speziale, Andrey, Peterson, Germann, Ünal, Liu, Floriot, Barbey (bib51) 2014; 511 Acemel, Tena, Irastorza-Azcarate, Marlétaz, Gómez-Marín, de la Calle-Mustienes, Bertrand, Diaz, Aldea, Aury (bib1) 2016; 48 Lettice, Hill, Devenney, Hill (bib47) 2008; 17 Vonk, Casewell, Henkel, Heimberg, Jansen, McCleary, Kerkkamp, Vos, Guerreiro, Calvete (bib77) 2013; 110 He, Bardet, Patton, Purvis, Johnston, Paulson, Gogol, Stark, Zeitlinger (bib31) 2011; 43 Jolma, Yan, Whitington, Toivonen, Nitta, Rastas, Morgunova, Enge, Taipale, Wei (bib39) 2013; 152 Castoe, de Koning, Hall, Card, Schield, Fujita, Ruggiero, Degner, Daza, Gu (bib11) 2013; 110 Gehrke, Schneider, de la Calle-Mustienes, Tena, Gomez-Marin, Chandran, Nakamura, Braasch, Postlethwait, Gómez-Skarmeta (bib24) 2015; 112 Hsiang, Field, Webster, Behlke, Davis, Racicot, Gauthier (bib36) 2015; 15 Echelard, Epstein, St-Jacques, Shen, Mohler, McMahon, McMahon (bib21) 1993; 75 Pyron, Burbrink, Wiens (bib62) 2013; 13 VanderMeer, Ahituv (bib73) 2011; 240 Kmita, Tarchini, Zàkàny, Logan, Tabin, Duboule (bib43) 2005; 435 Sagai, Hosoya, Mizushina, Tamura, Shiroishi (bib67) 2005; 132 Amemiya, Alföldi, Lee, Fan, Philippe, Maccallum, Braasch, Manousaki, Schneider, Rohner (bib2) 2013; 496 Indjeian, Kingman, Jones, Guenther, Grimwood, Schmutz, Myers, Kingsley (bib37) 2016; 164 Arnold, Gerlach, Spies, Matts, Sytnikova, Pagani, Lau, Stark (bib4) 2014; 46 Prescott, Srinivasan, Marchetto, Grishina, Narvaiza, Selleri, Gage, Swigut, Wysocka (bib61) 2015; 163 King, Wilson (bib42) 1975; 188 Esquerré, Scott Keogh (bib23) 2016; 19 Yang, Wang, Jaenisch (bib84) 2014; 9 Attanasio, Nord, Zhu, Blow, Li, Liberton, Morrison, Plajzer-Frick, Holt, Hosseini (bib5) 2013; 342 Visel, Blow, Li, Zhang, Akiyama, Holt, Plajzer-Frick, Shoukry, Wright, Chen (bib76) 2009; 457 Di-Poï, Montoya-Burgos, Miller, Pourquié, Milinkovitch, Duboule (bib20) 2010; 464 Dahn, Davis, Pappano, Shubin (bib18) 2007; 445 McLean, Reno, Pollen, Bassan, Capellini, Guenther, Indjeian, Lim, Menke, Schaar (bib54) 2011; 471 Zeller, Zuniga (bib85) 2007; 17 Min, Danilenko, Scully, Bolon, Ring, Tarpley, DeRose, Simonet (bib55) 1998; 12 Pennacchio, Ahituv, Moses, Prabhakar, Nobrega, Shoukry, Minovitsky, Dubchak, Holt, Lewis (bib59) 2006; 444 Visel, Minovitsky, Dubchak, Pennacchio (bib75) 2007; 35 Cooper, Sears, Uygur, Maier, Baczkowski, Brosnahan, Antczak, Skidmore, Tabin (bib15) 2014; 511 Guerreiro, Nunes, Woltering, Casaca, Nóvoa, Vinagre, Hunter, Duboule, Mallo (bib28) 2013; 110 Grant, Bailey, Noble (bib26) 2011; 27 Kothary, Clapoff, Darling, Perry, Moran, Rossant (bib44) 1989; 105 Sagai, Masuya, Tamura, Shimizu, Yada, Wakana, Gondo, Noda, Shiroishi (bib66) 2004; 15 Tanaka, Münsterberg, Anderson, Prescott, Hazon, Tickle (bib70) 2002; 416 Wray (bib80) 2007; 8 Chan (10.1016/j.cell.2016.09.028_bib13) 2010; 327 Yang (10.1016/j.cell.2016.09.028_bib84) 2014; 9 Montague (10.1016/j.cell.2016.09.028_bib56) 2014; 42 Grant (10.1016/j.cell.2016.09.028_bib26) 2011; 27 Esquerré (10.1016/j.cell.2016.09.028_bib23) 2016; 19 Romanes (10.1016/j.cell.2016.09.028_bib65) 1892 Indjeian (10.1016/j.cell.2016.09.028_bib37) 2016; 164 Jones (10.1016/j.cell.2016.09.028_bib40) 2012; 484 Lettice (10.1016/j.cell.2016.09.028_bib46) 2003; 12 Arnold (10.1016/j.cell.2016.09.028_bib4) 2014; 46 Infante (10.1016/j.cell.2016.09.028_bib38) 2015; 35 Katoh (10.1016/j.cell.2016.09.028_bib41) 2013; 30 Pennacchio (10.1016/j.cell.2016.09.028_bib59) 2006; 444 McLean (10.1016/j.cell.2016.09.028_bib54) 2011; 471 Echelard (10.1016/j.cell.2016.09.028_bib21) 1993; 75 VanderMeer (10.1016/j.cell.2016.09.028_bib73) 2011; 240 Head (10.1016/j.cell.2016.09.028_bib32) 2015; 520 Bronson (10.1016/j.cell.2016.09.028_bib8) 1996; 93 Zeller (10.1016/j.cell.2016.09.028_bib85) 2007; 17 Wray (10.1016/j.cell.2016.09.028_bib80) 2007; 8 Kmita (10.1016/j.cell.2016.09.028_bib43) 2005; 435 Martill (10.1016/j.cell.2016.09.028_bib52) 2015; 349 Attanasio (10.1016/j.cell.2016.09.028_bib5) 2013; 342 Lettice (10.1016/j.cell.2016.09.028_bib47) 2008; 17 Lettice (10.1016/j.cell.2016.09.028_bib49) 2014; 141 Lopez-Rios (10.1016/j.cell.2016.09.028_bib50) 2016; 49 Castresana (10.1016/j.cell.2016.09.028_bib12) 2000; 17 Darriba (10.1016/j.cell.2016.09.028_bib19) 2012; 9 Gibson (10.1016/j.cell.2016.09.028_bib25) 2009; 6 Tanaka (10.1016/j.cell.2016.09.028_bib70) 2002; 416 Amemiya (10.1016/j.cell.2016.09.028_bib2) 2013; 496 Kothary (10.1016/j.cell.2016.09.028_bib44) 1989; 105 Jolma (10.1016/j.cell.2016.09.028_bib39) 2013; 152 Vonk (10.1016/j.cell.2016.09.028_bib77) 2013; 110 Di-Poï (10.1016/j.cell.2016.09.028_bib20) 2010; 464 Cohn (10.1016/j.cell.2016.09.028_bib14) 1999; 399 Hill (10.1016/j.cell.2016.09.028_bib34) 2013; 368 Hoekstra (10.1016/j.cell.2016.09.028_bib35) 2012; 484 Reilly (10.1016/j.cell.2016.09.028_bib64) 2015; 347 Tchernov (10.1016/j.cell.2016.09.028_bib71) 2000; 287 Villar (10.1016/j.cell.2016.09.028_bib74) 2015; 160 Wang (10.1016/j.cell.2016.09.028_bib78) 2013; 153 Guindon (10.1016/j.cell.2016.09.028_bib30) 2010; 59 Apesteguía (10.1016/j.cell.2016.09.028_bib3) 2006; 440 Zeller (10.1016/j.cell.2016.09.028_bib86) 2009; 10 Cotney (10.1016/j.cell.2016.09.028_bib16) 2013; 154 Yang (10.1016/j.cell.2016.09.028_bib83) 2013; 154 Dahn (10.1016/j.cell.2016.09.028_bib18) 2007; 445 Visel (10.1016/j.cell.2016.09.028_bib75) 2007; 35 Lopez-Rios (10.1016/j.cell.2016.09.028_bib51) 2014; 511 Gehrke (10.1016/j.cell.2016.09.028_bib24) 2015; 112 Hsiang (10.1016/j.cell.2016.09.028_bib36) 2015; 15 Cooper (10.1016/j.cell.2016.09.028_bib15) 2014; 511 Wright (10.1016/j.cell.2016.09.028_bib81) 2015; 324 King (10.1016/j.cell.2016.09.028_bib42) 1975; 188 Sagai (10.1016/j.cell.2016.09.028_bib66) 2004; 15 May (10.1016/j.cell.2016.09.028_bib53) 2011; 44 Visel (10.1016/j.cell.2016.09.028_bib76) 2009; 457 Britten (10.1016/j.cell.2016.09.028_bib7) 1969; 165 Eckalbar (10.1016/j.cell.2016.09.028_bib22) 2016; 48 Panman (10.1016/j.cell.2016.09.028_bib58) 2006; 133 Lawson (10.1016/j.cell.2016.09.028_bib45) 2005; 37 Guenther (10.1016/j.cell.2016.09.028_bib27) 2014; 46 Capellini (10.1016/j.cell.2016.09.028_bib9) 2006; 133 Guerreiro (10.1016/j.cell.2016.09.028_bib28) 2013; 110 Castoe (10.1016/j.cell.2016.09.028_bib11) 2013; 110 Ullate-Agote (10.1016/j.cell.2016.09.028_bib72) 2014; 58 Wittkopp (10.1016/j.cell.2016.09.028_bib79) 2011; 13 Prabhakar (10.1016/j.cell.2016.09.028_bib60) 2008; 321 Min (10.1016/j.cell.2016.09.028_bib55) 1998; 12 Pyron (10.1016/j.cell.2016.09.028_bib62) 2013; 13 Prescott (10.1016/j.cell.2016.09.028_bib61) 2015; 163 Heinz (10.1016/j.cell.2016.09.028_bib33) 2010; 38 Ovchinnikov (10.1016/j.cell.2016.09.028_bib57) 2009 Guerreiro (10.1016/j.cell.2016.09.028_bib29) 2016; 5 Cretekos (10.1016/j.cell.2016.09.028_bib17) 2008; 22 He (10.1016/j.cell.2016.09.028_bib31) 2011; 43 Sagai (10.1016/j.cell.2016.09.028_bib67) 2005; 132 Blow (10.1016/j.cell.2016.09.028_bib6) 2010; 42 Sekine (10.1016/j.cell.2016.09.028_bib68) 1999; 21 Rallis (10.1016/j.cell.2016.09.028_bib63) 2003; 130 Acemel (10.1016/j.cell.2016.09.028_bib1) 2016; 48 Lettice (10.1016/j.cell.2016.09.028_bib48) 2012; 22 Shimodaira (10.1016/j.cell.2016.09.028_bib69) 2001; 17 Xiao (10.1016/j.cell.2016.09.028_bib82) 2012; 149 Carroll (10.1016/j.cell.2016.09.028_bib10) 2008; 134 25058643 - Nat Protoc. 2014 Aug;9(8):1956-68 20147105 - Cold Spring Harb Protoc. 2009 Mar;2009(3):pdb.prot5170 24880339 - Nat Genet. 2014 Jul;46(7):748-52 23627680 - BMC Evol Biol. 2013 Apr 29;13:93 18772437 - Science. 2008 Sep 5;321(5894):1346-50 22143240 - Nat Rev Genet. 2011 Dec 06;13(1):59-69 26227660 - J Exp Zool B Mol Dev Evol. 2015 Sep;324(6):504-16 26206932 - Science. 2015 Jul 24;349(6246):416-9 2557196 - Development. 1989 Apr;105(4):707-14 25535365 - Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):803-8 26829752 - Nat Genet. 2016 Mar;48(3):336-41 5789433 - Science. 1969 Jul 25;165(3891):349-57 8799155 - Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):9067-72 7916661 - Cell. 1993 Dec 31;75(7):1417-30 15677727 - Development. 2005 Feb;132(4):797-803 24297902 - Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20645-50 22340503 - Dev Cell. 2012 Feb 14;22(2):459-67 27019111 - Nat Genet. 2016 May;48(5):528-36 23674686 - Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10682-6 11751242 - Bioinformatics. 2001 Dec;17(12):1246-7 23332764 - Cell. 2013 Jan 17;152(1-2):327-39 26365491 - Cell. 2015 Sep 24;163(1):68-83 26762695 - Semin Cell Dev Biol. 2016 Jan;49:116-24 17304246 - Nat Rev Genet. 2007 Mar;8(3):206-16 16908629 - Development. 2006 Sep;133(17 ):3419-28 21330290 - Bioinformatics. 2011 Apr 1;27(7):1017-8 16625194 - Nature. 2006 Apr 20;440(7087):1037-40 18156157 - Hum Mol Genet. 2008 Apr 1;17(7):978-85 9784490 - Genes Dev. 1998 Oct 15;12(20):3156-61 23650631 - Philos Trans R Soc Lond B Biol Sci. 2013 May 06;368(1620):20120357 20525638 - Syst Biol. 2010 May;59(3):307-21 24159046 - Science. 2013 Oct 25;342(6157):1241006 25539083 - Nature. 2015 Apr 2;520(7545):86-9 22481358 - Nature. 2012 Apr 04;484(7392):55-61 16172004 - Mol Phylogenet Evol. 2005 Nov;37(2):581-601 15973411 - Nature. 2005 Jun 23;435(7045):1113-6 22847109 - Nat Methods. 2012 Jul 30;9(8):772 23598338 - Nature. 2013 Apr 18;496(7445):311-6 16672333 - Development. 2006 Jun;133(11):2263-73 10720326 - Science. 2000 Mar 17;287(5460):2010-2 20203609 - Nature. 2010 Mar 4;464(7285):99-103 24715461 - Development. 2014 Apr;141(8):1715-25 23329690 - Mol Biol Evol. 2013 Apr;30(4):772-80 23643243 - Cell. 2013 May 9;153(4):910-8 10365960 - Nature. 1999 Jun 3;399(6735):474-9 9916808 - Nat Genet. 1999 Jan;21(1):138-41 26439399 - Dev Cell. 2015 Oct 12;35(1):107-19 17086198 - Nature. 2006 Nov 23;444(7118):499-502 27923134 - Curr Biol. 2016 Dec 5;26(23):R1237-R1240 21478888 - Nat Genet. 2011 May;43(5):414-20 22138689 - Nat Genet. 2011 Dec 04;44(1):89-93 14727139 - Mamm Genome. 2004 Jan;15(1):23-34 1090005 - Science. 1975 Apr 11;188(4184):107-16 18198333 - Genes Dev. 2008 Jan 15;22(2):141-51 25745175 - Science. 2015 Mar 6;347(6226):1155-9 26154328 - Int J Dev Biol. 2014;58(10-12):881-8 27476854 - Elife. 2016 Aug 01;5:null 24297900 - Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20651-6 23827682 - Cell. 2013 Jul 3;154(1):185-96 21509892 - Dev Dyn. 2011 May;240(5):920-30 17130149 - Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92 25635462 - Cell. 2015 Jan 29;160(3):554-66 25989795 - BMC Evol Biol. 2015 May 20;15:87 24861617 - Nucleic Acids Res. 2014 Jul;42(Web Server issue):W401-7 27264195 - Ecol Lett. 2016 Jul;19(7):800-9 21390129 - Nature. 2011 Mar 10;471(7337):216-9 12837695 - Hum Mol Genet. 2003 Jul 15;12 (14 ):1725-35 26774823 - Cell. 2016 Jan 14;164(1-2):45-56 24908250 - Nat Genet. 2014 Jul;46(7):685-92 12736217 - Development. 2003 Jun;130(12):2741-51 19363495 - Nat Methods. 2009 May;6(5):343-5 20513432 - Mol Cell. 2010 May 28;38(4):576-89 17714931 - Curr Opin Genet Dev. 2007 Oct;17(5):428-34 27768881 - Cell. 2016 Oct 20;167(3):598-600 20007865 - Science. 2010 Jan 15;327(5963):302-5 18614008 - Cell. 2008 Jul 11;134(1):25-36 17187056 - Nature. 2007 Jan 18;445(7125):311-4 24990742 - Nature. 2014 Jul 3;511(7507):41-5 22682255 - Cell. 2012 Jun 8;149(6):1381-92 19212405 - Nature. 2009 Feb 12;457(7231):854-8 10742046 - Mol Biol Evol. 2000 Apr;17(4):540-52 22481355 - Nature. 2012 Apr 04;484(7392):46-7 24990743 - Nature. 2014 Jul 3;511(7507):46-51 11932743 - Nature. 2002 Apr 4;416(6880):527-31 20729851 - Nat Genet. 2010 Sep;42(9):806-10 19920852 - Nat Rev Genet. 2009 Dec;10(12):845-58 23992847 - Cell. 2013 Sep 12;154(6):1370-9 |
| References_xml | – volume: 511 start-page: 41 year: 2014 end-page: 45 ident: bib15 article-title: Patterning and post-patterning modes of evolutionary digit loss in mammals publication-title: Nature – volume: 416 start-page: 527 year: 2002 end-page: 531 ident: bib70 article-title: Fin development in a cartilaginous fish and the origin of vertebrate limbs publication-title: Nature – volume: 38 start-page: 576 year: 2010 end-page: 589 ident: bib33 article-title: Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities publication-title: Mol. Cell – volume: 165 start-page: 349 year: 1969 end-page: 357 ident: bib7 article-title: Gene regulation for higher cells: A theory publication-title: Science – volume: 37 start-page: 581 year: 2005 end-page: 601 ident: bib45 article-title: Phylogeny of the Colubroidea (Serpentes): New evidence from mitochondrial and nuclear genes publication-title: Mol. Phylogenet. Evol. – volume: 347 start-page: 1155 year: 2015 end-page: 1159 ident: bib64 article-title: Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis publication-title: Science – volume: 43 start-page: 414 year: 2011 end-page: 420 ident: bib31 article-title: High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species publication-title: Nat. Genet. – volume: 10 start-page: 845 year: 2009 end-page: 858 ident: bib86 article-title: Vertebrate limb bud development: Moving towards integrative analysis of organogenesis publication-title: Nat. Rev. Genet. – volume: 163 start-page: 68 year: 2015 end-page: 83 ident: bib61 article-title: Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest publication-title: Cell – volume: 349 start-page: 416 year: 2015 end-page: 419 ident: bib52 article-title: EVOLUTION. A four-legged snake from the Early Cretaceous of Gondwana publication-title: Science – volume: 42 start-page: W401 year: 2014 end-page: W407 ident: bib56 article-title: CHOPCHOP: A CRISPR/Cas9 and TALEN web tool for genome editing publication-title: Nucleic Acids Res. – volume: 399 start-page: 474 year: 1999 end-page: 479 ident: bib14 article-title: Developmental basis of limblessness and axial patterning in snakes publication-title: Nature – volume: 141 start-page: 1715 year: 2014 end-page: 1725 ident: bib49 article-title: Development of five digits is controlled by a bipartite long-range cis-regulator publication-title: Development – volume: 17 start-page: 540 year: 2000 end-page: 552 ident: bib12 article-title: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis publication-title: Mol. Biol. Evol. – year: 1892 ident: bib65 article-title: Darwin and after Darwin: An Exposition of the Darwinian Theory and a Discussion of post-Darwinian Questions – volume: 457 start-page: 854 year: 2009 end-page: 858 ident: bib76 article-title: ChIP-seq accurately predicts tissue-specific activity of enhancers publication-title: Nature – volume: 324 start-page: 504 year: 2015 end-page: 516 ident: bib81 article-title: Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states. J. Exp. Zool. B Mol publication-title: Dev. Evol. – volume: 134 start-page: 25 year: 2008 end-page: 36 ident: bib10 article-title: Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution publication-title: Cell – volume: 133 start-page: 3419 year: 2006 end-page: 3428 ident: bib58 article-title: Differential regulation of gene expression in the digit forming area of the mouse limb bud by SHH and gremlin 1/FGF-mediated epithelial-mesenchymal signalling publication-title: Development – volume: 13 start-page: 59 year: 2011 end-page: 69 ident: bib79 article-title: Cis-regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence publication-title: Nat. Rev. Genet. – volume: 164 start-page: 45 year: 2016 end-page: 56 ident: bib37 article-title: Evolving new skeletal traits by cis-regulatory changes in bone morphogenetic proteins publication-title: Cell – volume: 444 start-page: 499 year: 2006 end-page: 502 ident: bib59 article-title: In vivo enhancer analysis of human conserved non-coding sequences publication-title: Nature – volume: 17 start-page: 428 year: 2007 end-page: 434 ident: bib85 article-title: Shh and Gremlin1 chromosomal landscapes in development and disease publication-title: Curr. Opin. Genet. Dev. – volume: 93 start-page: 9067 year: 1996 end-page: 9072 ident: bib8 article-title: Single-copy transgenic mice with chosen-site integration publication-title: Proc. Natl. Acad. Sci. USA – volume: 44 start-page: 89 year: 2011 end-page: 93 ident: bib53 article-title: Large-scale discovery of enhancers from human heart tissue publication-title: Nat. Genet. – volume: 21 start-page: 138 year: 1999 end-page: 141 ident: bib68 article-title: Fgf10 is essential for limb and lung formation publication-title: Nat. Genet. – volume: 75 start-page: 1417 year: 1993 end-page: 1430 ident: bib21 article-title: Sonic hedgehog, a member of a family of putative signaling molecules, is implicated in the regulation of CNS polarity publication-title: Cell – volume: 5 start-page: 347 year: 2016 ident: bib29 article-title: Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan publication-title: eLife – year: 2009 ident: bib57 article-title: Alcian blue/alizarin red staining of cartilage and bone in mouse publication-title: Cold Spring Harb. Protoc. – volume: 440 start-page: 1037 year: 2006 end-page: 1040 ident: bib3 article-title: A Cretaceous terrestrial snake with robust hindlimbs and a sacrum publication-title: Nature – volume: 112 start-page: 803 year: 2015 end-page: 808 ident: bib24 article-title: Deep conservation of wrist and digit enhancers in fish publication-title: Proc. Natl. Acad. Sci. USA – volume: 8 start-page: 206 year: 2007 end-page: 216 ident: bib80 article-title: The evolutionary significance of cis-regulatory mutations publication-title: Nat. Rev. Genet. – volume: 6 start-page: 343 year: 2009 end-page: 345 ident: bib25 article-title: Enzymatic assembly of DNA molecules up to several hundred kilobases publication-title: Nat. Methods – volume: 27 start-page: 1017 year: 2011 end-page: 1018 ident: bib26 article-title: FIMO: Scanning for occurrences of a given motif publication-title: Bioinformatics – volume: 342 start-page: 1241006 year: 2013 ident: bib5 article-title: Fine tuning of craniofacial morphology by distant-acting enhancers publication-title: Science – volume: 484 start-page: 46 year: 2012 end-page: 47 ident: bib35 article-title: Genomics: Stickleback is the catch of the day publication-title: Nature – volume: 133 start-page: 2263 year: 2006 end-page: 2273 ident: bib9 article-title: Pbx1/Pbx2 requirement for distal limb patterning is mediated by the hierarchical control of Hox gene spatial distribution and Shh expression publication-title: Development – volume: 22 start-page: 141 year: 2008 end-page: 151 ident: bib17 article-title: Regulatory divergence modifies limb length between mammals publication-title: Genes Dev. – volume: 46 start-page: 748 year: 2014 end-page: 752 ident: bib27 article-title: A molecular basis for classic blond hair color in Europeans publication-title: Nat. Genet. – volume: 435 start-page: 1113 year: 2005 end-page: 1116 ident: bib43 article-title: Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function publication-title: Nature – volume: 35 start-page: 107 year: 2015 end-page: 119 ident: bib38 article-title: Shared enhancer activity in the limbs and phallus and functional divergence of a limb-genital cis-regulatory element in snakes publication-title: Dev. Cell – volume: 9 start-page: 1956 year: 2014 end-page: 1968 ident: bib84 article-title: Generating genetically modified mice using CRISPR/Cas-mediated genome engineering publication-title: Nat. Protoc. – volume: 484 start-page: 55 year: 2012 end-page: 61 ident: bib40 article-title: The genomic basis of adaptive evolution in threespine sticklebacks publication-title: Nature – volume: 49 start-page: 116 year: 2016 end-page: 124 ident: bib50 article-title: The many lives of SHH in limb development and evolution publication-title: Semin. Cell Dev. Biol. – volume: 15 start-page: 87 year: 2015 ident: bib36 article-title: The origin of snakes: Revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record publication-title: BMC Evol. Biol. – volume: 9 start-page: 772 year: 2012 ident: bib19 article-title: jModelTest 2: More models, new heuristics and parallel computing publication-title: Nat. Methods – volume: 48 start-page: 528 year: 2016 end-page: 536 ident: bib22 article-title: Transcriptomic and epigenomic characterization of the developing bat wing publication-title: Nat. Genet. – volume: 132 start-page: 797 year: 2005 end-page: 803 ident: bib67 article-title: Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb publication-title: Development – volume: 58 start-page: 881 year: 2014 end-page: 888 ident: bib72 article-title: The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates publication-title: Int. J. Dev. Biol. – volume: 188 start-page: 107 year: 1975 end-page: 116 ident: bib42 article-title: Evolution at two levels in humans and chimpanzees publication-title: Science – volume: 15 start-page: 23 year: 2004 end-page: 34 ident: bib66 article-title: Phylogenetic conservation of a limb-specific, cis-acting regulator of Sonic hedgehog ( Shh) publication-title: Mamm. Genome – volume: 110 start-page: 20651 year: 2013 end-page: 20656 ident: bib77 article-title: The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system publication-title: Proc. Natl. Acad. Sci. USA – volume: 154 start-page: 1370 year: 2013 end-page: 1379 ident: bib83 article-title: One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering publication-title: Cell – volume: 368 start-page: 20120357 year: 2013 ident: bib34 article-title: Alterations to the remote control of Shh gene expression cause congenital abnormalities publication-title: Philos. Trans. R. Soc. Lond. B Biol. Sci. – volume: 327 start-page: 302 year: 2010 end-page: 305 ident: bib13 article-title: Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer publication-title: Science – volume: 496 start-page: 311 year: 2013 end-page: 316 ident: bib2 article-title: The African coelacanth genome provides insights into tetrapod evolution publication-title: Nature – volume: 321 start-page: 1346 year: 2008 end-page: 1350 ident: bib60 article-title: Human-specific gain of function in a developmental enhancer publication-title: Science – volume: 110 start-page: 20645 year: 2013 end-page: 20650 ident: bib11 article-title: The Burmese python genome reveals the molecular basis for extreme adaptation in snakes publication-title: Proc. Natl. Acad. Sci. USA – volume: 152 start-page: 327 year: 2013 end-page: 339 ident: bib39 article-title: DNA-binding specificities of human transcription factors publication-title: Cell – volume: 511 start-page: 46 year: 2014 end-page: 51 ident: bib51 article-title: Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs publication-title: Nature – volume: 105 start-page: 707 year: 1989 end-page: 714 ident: bib44 article-title: Inducible expression of an hsp68-lacZ hybrid gene in transgenic mice publication-title: Development – volume: 42 start-page: 806 year: 2010 end-page: 810 ident: bib6 article-title: ChIP-Seq identification of weakly conserved heart enhancers publication-title: Nat. Genet. – volume: 17 start-page: 1246 year: 2001 end-page: 1247 ident: bib69 article-title: CONSEL: For assessing the confidence of phylogenetic tree selection publication-title: Bioinformatics – volume: 13 start-page: 93 year: 2013 ident: bib62 article-title: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes publication-title: BMC Evol. Biol. – volume: 154 start-page: 185 year: 2013 end-page: 196 ident: bib16 article-title: The evolution of lineage-specific regulatory activities in the human embryonic limb publication-title: Cell – volume: 46 start-page: 685 year: 2014 end-page: 692 ident: bib4 article-title: Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution publication-title: Nat. Genet. – volume: 19 start-page: 800 year: 2016 end-page: 809 ident: bib23 article-title: Parallel selective pressures drive convergent diversification of phenotypes in pythons and boas publication-title: Ecol. Lett. – volume: 160 start-page: 554 year: 2015 end-page: 566 ident: bib74 article-title: Enhancer evolution across 20 mammalian species publication-title: Cell – volume: 287 start-page: 2010 year: 2000 end-page: 2012 ident: bib71 article-title: A fossil snake with limbs publication-title: Science – volume: 59 start-page: 307 year: 2010 end-page: 321 ident: bib30 article-title: New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0 publication-title: Syst. Biol. – volume: 17 start-page: 978 year: 2008 end-page: 985 ident: bib47 article-title: Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly publication-title: Hum. Mol. Genet. – volume: 48 start-page: 336 year: 2016 end-page: 341 ident: bib1 article-title: A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation publication-title: Nat. Genet. – volume: 35 start-page: D88 year: 2007 end-page: D92 ident: bib75 article-title: VISTA Enhancer Browser—A database of tissue-specific human enhancers publication-title: Nucleic Acids Res. – volume: 240 start-page: 920 year: 2011 end-page: 930 ident: bib73 article-title: cis-regulatory mutations are a genetic cause of human limb malformations publication-title: Dev. Dyn. – volume: 130 start-page: 2741 year: 2003 end-page: 2751 ident: bib63 article-title: Tbx5 is required for forelimb bud formation and continued outgrowth publication-title: Development – volume: 149 start-page: 1381 year: 2012 end-page: 1392 ident: bib82 article-title: Comparative epigenomic annotation of regulatory DNA publication-title: Cell – volume: 110 start-page: 10682 year: 2013 end-page: 10686 ident: bib28 article-title: Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine publication-title: Proc. Natl. Acad. Sci. USA – volume: 153 start-page: 910 year: 2013 end-page: 918 ident: bib78 article-title: One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering publication-title: Cell – volume: 471 start-page: 216 year: 2011 end-page: 219 ident: bib54 article-title: Human-specific loss of regulatory DNA and the evolution of human-specific traits publication-title: Nature – volume: 12 start-page: 1725 year: 2003 end-page: 1735 ident: bib46 article-title: A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly publication-title: Hum. Mol. Genet. – volume: 520 start-page: 86 year: 2015 end-page: 89 ident: bib32 article-title: Evolution of the snake body form reveals homoplasy in amniote Hox gene function publication-title: Nature – volume: 30 start-page: 772 year: 2013 end-page: 780 ident: bib41 article-title: MAFFT multiple sequence alignment software version 7: Improvements in performance and usability publication-title: Mol. Biol. Evol. – volume: 22 start-page: 459 year: 2012 end-page: 467 ident: bib48 article-title: Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly publication-title: Dev. Cell – volume: 445 start-page: 311 year: 2007 end-page: 314 ident: bib18 article-title: Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning publication-title: Nature – volume: 464 start-page: 99 year: 2010 end-page: 103 ident: bib20 article-title: Changes in Hox genes’ structure and function during the evolution of the squamate body plan publication-title: Nature – volume: 12 start-page: 3156 year: 1998 end-page: 3161 ident: bib55 article-title: Fgf-10 is required for both limb and lung development and exhibits striking functional similarity to Drosophila branchless publication-title: Genes Dev. – year: 2009 ident: 10.1016/j.cell.2016.09.028_bib57 article-title: Alcian blue/alizarin red staining of cartilage and bone in mouse publication-title: Cold Spring Harb. Protoc. doi: 10.1101/pdb.prot5170 – volume: 416 start-page: 527 year: 2002 ident: 10.1016/j.cell.2016.09.028_bib70 article-title: Fin development in a cartilaginous fish and the origin of vertebrate limbs publication-title: Nature doi: 10.1038/416527a – volume: 133 start-page: 2263 year: 2006 ident: 10.1016/j.cell.2016.09.028_bib9 article-title: Pbx1/Pbx2 requirement for distal limb patterning is mediated by the hierarchical control of Hox gene spatial distribution and Shh expression publication-title: Development doi: 10.1242/dev.02395 – volume: 464 start-page: 99 year: 2010 ident: 10.1016/j.cell.2016.09.028_bib20 article-title: Changes in Hox genes’ structure and function during the evolution of the squamate body plan publication-title: Nature doi: 10.1038/nature08789 – volume: 35 start-page: D88 year: 2007 ident: 10.1016/j.cell.2016.09.028_bib75 article-title: VISTA Enhancer Browser—A database of tissue-specific human enhancers publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkl822 – volume: 10 start-page: 845 year: 2009 ident: 10.1016/j.cell.2016.09.028_bib86 article-title: Vertebrate limb bud development: Moving towards integrative analysis of organogenesis publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2681 – volume: 240 start-page: 920 year: 2011 ident: 10.1016/j.cell.2016.09.028_bib73 article-title: cis-regulatory mutations are a genetic cause of human limb malformations publication-title: Dev. Dyn. doi: 10.1002/dvdy.22535 – volume: 48 start-page: 528 year: 2016 ident: 10.1016/j.cell.2016.09.028_bib22 article-title: Transcriptomic and epigenomic characterization of the developing bat wing publication-title: Nat. Genet. doi: 10.1038/ng.3537 – volume: 141 start-page: 1715 year: 2014 ident: 10.1016/j.cell.2016.09.028_bib49 article-title: Development of five digits is controlled by a bipartite long-range cis-regulator publication-title: Development doi: 10.1242/dev.095430 – volume: 152 start-page: 327 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib39 article-title: DNA-binding specificities of human transcription factors publication-title: Cell doi: 10.1016/j.cell.2012.12.009 – volume: 8 start-page: 206 year: 2007 ident: 10.1016/j.cell.2016.09.028_bib80 article-title: The evolutionary significance of cis-regulatory mutations publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2063 – volume: 38 start-page: 576 year: 2010 ident: 10.1016/j.cell.2016.09.028_bib33 article-title: Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities publication-title: Mol. Cell doi: 10.1016/j.molcel.2010.05.004 – volume: 134 start-page: 25 year: 2008 ident: 10.1016/j.cell.2016.09.028_bib10 article-title: Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution publication-title: Cell doi: 10.1016/j.cell.2008.06.030 – volume: 13 start-page: 93 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib62 article-title: A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes publication-title: BMC Evol. Biol. doi: 10.1186/1471-2148-13-93 – volume: 163 start-page: 68 year: 2015 ident: 10.1016/j.cell.2016.09.028_bib61 article-title: Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest publication-title: Cell doi: 10.1016/j.cell.2015.08.036 – volume: 46 start-page: 748 year: 2014 ident: 10.1016/j.cell.2016.09.028_bib27 article-title: A molecular basis for classic blond hair color in Europeans publication-title: Nat. Genet. doi: 10.1038/ng.2991 – volume: 484 start-page: 55 year: 2012 ident: 10.1016/j.cell.2016.09.028_bib40 article-title: The genomic basis of adaptive evolution in threespine sticklebacks publication-title: Nature doi: 10.1038/nature10944 – volume: 327 start-page: 302 year: 2010 ident: 10.1016/j.cell.2016.09.028_bib13 article-title: Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer publication-title: Science doi: 10.1126/science.1182213 – volume: 19 start-page: 800 year: 2016 ident: 10.1016/j.cell.2016.09.028_bib23 article-title: Parallel selective pressures drive convergent diversification of phenotypes in pythons and boas publication-title: Ecol. Lett. doi: 10.1111/ele.12620 – volume: 43 start-page: 414 year: 2011 ident: 10.1016/j.cell.2016.09.028_bib31 article-title: High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species publication-title: Nat. Genet. doi: 10.1038/ng.808 – volume: 511 start-page: 46 year: 2014 ident: 10.1016/j.cell.2016.09.028_bib51 article-title: Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs publication-title: Nature doi: 10.1038/nature13289 – volume: 133 start-page: 3419 year: 2006 ident: 10.1016/j.cell.2016.09.028_bib58 article-title: Differential regulation of gene expression in the digit forming area of the mouse limb bud by SHH and gremlin 1/FGF-mediated epithelial-mesenchymal signalling publication-title: Development doi: 10.1242/dev.02529 – volume: 287 start-page: 2010 year: 2000 ident: 10.1016/j.cell.2016.09.028_bib71 article-title: A fossil snake with limbs publication-title: Science doi: 10.1126/science.287.5460.2010 – volume: 132 start-page: 797 year: 2005 ident: 10.1016/j.cell.2016.09.028_bib67 article-title: Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb publication-title: Development doi: 10.1242/dev.01613 – volume: 49 start-page: 116 year: 2016 ident: 10.1016/j.cell.2016.09.028_bib50 article-title: The many lives of SHH in limb development and evolution publication-title: Semin. Cell Dev. Biol. doi: 10.1016/j.semcdb.2015.12.018 – volume: 48 start-page: 336 year: 2016 ident: 10.1016/j.cell.2016.09.028_bib1 article-title: A single three-dimensional chromatin compartment in amphioxus indicates a stepwise evolution of vertebrate Hox bimodal regulation publication-title: Nat. Genet. doi: 10.1038/ng.3497 – volume: 35 start-page: 107 year: 2015 ident: 10.1016/j.cell.2016.09.028_bib38 article-title: Shared enhancer activity in the limbs and phallus and functional divergence of a limb-genital cis-regulatory element in snakes publication-title: Dev. Cell doi: 10.1016/j.devcel.2015.09.003 – volume: 342 start-page: 1241006 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib5 article-title: Fine tuning of craniofacial morphology by distant-acting enhancers publication-title: Science doi: 10.1126/science.1241006 – volume: 30 start-page: 772 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib41 article-title: MAFFT multiple sequence alignment software version 7: Improvements in performance and usability publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/mst010 – volume: 445 start-page: 311 year: 2007 ident: 10.1016/j.cell.2016.09.028_bib18 article-title: Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning publication-title: Nature doi: 10.1038/nature05436 – volume: 368 start-page: 20120357 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib34 article-title: Alterations to the remote control of Shh gene expression cause congenital abnormalities publication-title: Philos. Trans. R. Soc. Lond. B Biol. Sci. doi: 10.1098/rstb.2012.0357 – volume: 27 start-page: 1017 year: 2011 ident: 10.1016/j.cell.2016.09.028_bib26 article-title: FIMO: Scanning for occurrences of a given motif publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr064 – volume: 165 start-page: 349 year: 1969 ident: 10.1016/j.cell.2016.09.028_bib7 article-title: Gene regulation for higher cells: A theory publication-title: Science doi: 10.1126/science.165.3891.349 – year: 1892 ident: 10.1016/j.cell.2016.09.028_bib65 – volume: 17 start-page: 540 year: 2000 ident: 10.1016/j.cell.2016.09.028_bib12 article-title: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis publication-title: Mol. Biol. Evol. doi: 10.1093/oxfordjournals.molbev.a026334 – volume: 149 start-page: 1381 year: 2012 ident: 10.1016/j.cell.2016.09.028_bib82 article-title: Comparative epigenomic annotation of regulatory DNA publication-title: Cell doi: 10.1016/j.cell.2012.04.029 – volume: 511 start-page: 41 year: 2014 ident: 10.1016/j.cell.2016.09.028_bib15 article-title: Patterning and post-patterning modes of evolutionary digit loss in mammals publication-title: Nature doi: 10.1038/nature13496 – volume: 484 start-page: 46 year: 2012 ident: 10.1016/j.cell.2016.09.028_bib35 article-title: Genomics: Stickleback is the catch of the day publication-title: Nature doi: 10.1038/484046a – volume: 110 start-page: 10682 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib28 article-title: Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1300592110 – volume: 110 start-page: 20645 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib11 article-title: The Burmese python genome reveals the molecular basis for extreme adaptation in snakes publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1314475110 – volume: 5 start-page: 347 year: 2016 ident: 10.1016/j.cell.2016.09.028_bib29 article-title: Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan publication-title: eLife doi: 10.7554/eLife.16087 – volume: 160 start-page: 554 year: 2015 ident: 10.1016/j.cell.2016.09.028_bib74 article-title: Enhancer evolution across 20 mammalian species publication-title: Cell doi: 10.1016/j.cell.2015.01.006 – volume: 440 start-page: 1037 year: 2006 ident: 10.1016/j.cell.2016.09.028_bib3 article-title: A Cretaceous terrestrial snake with robust hindlimbs and a sacrum publication-title: Nature doi: 10.1038/nature04413 – volume: 110 start-page: 20651 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib77 article-title: The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1314702110 – volume: 188 start-page: 107 year: 1975 ident: 10.1016/j.cell.2016.09.028_bib42 article-title: Evolution at two levels in humans and chimpanzees publication-title: Science doi: 10.1126/science.1090005 – volume: 321 start-page: 1346 year: 2008 ident: 10.1016/j.cell.2016.09.028_bib60 article-title: Human-specific gain of function in a developmental enhancer publication-title: Science doi: 10.1126/science.1159974 – volume: 154 start-page: 185 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib16 article-title: The evolution of lineage-specific regulatory activities in the human embryonic limb publication-title: Cell doi: 10.1016/j.cell.2013.05.056 – volume: 6 start-page: 343 year: 2009 ident: 10.1016/j.cell.2016.09.028_bib25 article-title: Enzymatic assembly of DNA molecules up to several hundred kilobases publication-title: Nat. Methods doi: 10.1038/nmeth.1318 – volume: 93 start-page: 9067 year: 1996 ident: 10.1016/j.cell.2016.09.028_bib8 article-title: Single-copy transgenic mice with chosen-site integration publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.93.17.9067 – volume: 112 start-page: 803 year: 2015 ident: 10.1016/j.cell.2016.09.028_bib24 article-title: Deep conservation of wrist and digit enhancers in fish publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.1420208112 – volume: 9 start-page: 772 year: 2012 ident: 10.1016/j.cell.2016.09.028_bib19 article-title: jModelTest 2: More models, new heuristics and parallel computing publication-title: Nat. Methods doi: 10.1038/nmeth.2109 – volume: 17 start-page: 978 year: 2008 ident: 10.1016/j.cell.2016.09.028_bib47 article-title: Point mutations in a distant sonic hedgehog cis-regulator generate a variable regulatory output responsible for preaxial polydactyly publication-title: Hum. Mol. Genet. doi: 10.1093/hmg/ddm370 – volume: 457 start-page: 854 year: 2009 ident: 10.1016/j.cell.2016.09.028_bib76 article-title: ChIP-seq accurately predicts tissue-specific activity of enhancers publication-title: Nature doi: 10.1038/nature07730 – volume: 42 start-page: 806 year: 2010 ident: 10.1016/j.cell.2016.09.028_bib6 article-title: ChIP-Seq identification of weakly conserved heart enhancers publication-title: Nat. Genet. doi: 10.1038/ng.650 – volume: 75 start-page: 1417 year: 1993 ident: 10.1016/j.cell.2016.09.028_bib21 article-title: Sonic hedgehog, a member of a family of putative signaling molecules, is implicated in the regulation of CNS polarity publication-title: Cell doi: 10.1016/0092-8674(93)90627-3 – volume: 324 start-page: 504 year: 2015 ident: 10.1016/j.cell.2016.09.028_bib81 article-title: Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states. J. Exp. Zool. B Mol publication-title: Dev. Evol. – volume: 444 start-page: 499 year: 2006 ident: 10.1016/j.cell.2016.09.028_bib59 article-title: In vivo enhancer analysis of human conserved non-coding sequences publication-title: Nature doi: 10.1038/nature05295 – volume: 15 start-page: 23 year: 2004 ident: 10.1016/j.cell.2016.09.028_bib66 article-title: Phylogenetic conservation of a limb-specific, cis-acting regulator of Sonic hedgehog ( Shh) publication-title: Mamm. Genome doi: 10.1007/s00335-033-2317-5 – volume: 154 start-page: 1370 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib83 article-title: One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering publication-title: Cell doi: 10.1016/j.cell.2013.08.022 – volume: 520 start-page: 86 year: 2015 ident: 10.1016/j.cell.2016.09.028_bib32 article-title: Evolution of the snake body form reveals homoplasy in amniote Hox gene function publication-title: Nature doi: 10.1038/nature14042 – volume: 12 start-page: 1725 year: 2003 ident: 10.1016/j.cell.2016.09.028_bib46 article-title: A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly publication-title: Hum. Mol. Genet. doi: 10.1093/hmg/ddg180 – volume: 105 start-page: 707 year: 1989 ident: 10.1016/j.cell.2016.09.028_bib44 article-title: Inducible expression of an hsp68-lacZ hybrid gene in transgenic mice publication-title: Development doi: 10.1242/dev.105.4.707 – volume: 347 start-page: 1155 year: 2015 ident: 10.1016/j.cell.2016.09.028_bib64 article-title: Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis publication-title: Science doi: 10.1126/science.1260943 – volume: 13 start-page: 59 year: 2011 ident: 10.1016/j.cell.2016.09.028_bib79 article-title: Cis-regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence publication-title: Nat. Rev. Genet. doi: 10.1038/nrg3095 – volume: 37 start-page: 581 year: 2005 ident: 10.1016/j.cell.2016.09.028_bib45 article-title: Phylogeny of the Colubroidea (Serpentes): New evidence from mitochondrial and nuclear genes publication-title: Mol. Phylogenet. Evol. doi: 10.1016/j.ympev.2005.07.016 – volume: 21 start-page: 138 year: 1999 ident: 10.1016/j.cell.2016.09.028_bib68 article-title: Fgf10 is essential for limb and lung formation publication-title: Nat. Genet. doi: 10.1038/5096 – volume: 130 start-page: 2741 year: 2003 ident: 10.1016/j.cell.2016.09.028_bib63 article-title: Tbx5 is required for forelimb bud formation and continued outgrowth publication-title: Development doi: 10.1242/dev.00473 – volume: 59 start-page: 307 year: 2010 ident: 10.1016/j.cell.2016.09.028_bib30 article-title: New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0 publication-title: Syst. Biol. doi: 10.1093/sysbio/syq010 – volume: 496 start-page: 311 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib2 article-title: The African coelacanth genome provides insights into tetrapod evolution publication-title: Nature doi: 10.1038/nature12027 – volume: 471 start-page: 216 year: 2011 ident: 10.1016/j.cell.2016.09.028_bib54 article-title: Human-specific loss of regulatory DNA and the evolution of human-specific traits publication-title: Nature doi: 10.1038/nature09774 – volume: 17 start-page: 1246 year: 2001 ident: 10.1016/j.cell.2016.09.028_bib69 article-title: CONSEL: For assessing the confidence of phylogenetic tree selection publication-title: Bioinformatics doi: 10.1093/bioinformatics/17.12.1246 – volume: 22 start-page: 459 year: 2012 ident: 10.1016/j.cell.2016.09.028_bib48 article-title: Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly publication-title: Dev. Cell doi: 10.1016/j.devcel.2011.12.010 – volume: 44 start-page: 89 year: 2011 ident: 10.1016/j.cell.2016.09.028_bib53 article-title: Large-scale discovery of enhancers from human heart tissue publication-title: Nat. Genet. doi: 10.1038/ng.1006 – volume: 46 start-page: 685 year: 2014 ident: 10.1016/j.cell.2016.09.028_bib4 article-title: Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution publication-title: Nat. Genet. doi: 10.1038/ng.3009 – volume: 349 start-page: 416 year: 2015 ident: 10.1016/j.cell.2016.09.028_bib52 article-title: EVOLUTION. A four-legged snake from the Early Cretaceous of Gondwana publication-title: Science doi: 10.1126/science.aaa9208 – volume: 42 start-page: W401 year: 2014 ident: 10.1016/j.cell.2016.09.028_bib56 article-title: CHOPCHOP: A CRISPR/Cas9 and TALEN web tool for genome editing publication-title: Nucleic Acids Res. doi: 10.1093/nar/gku410 – volume: 58 start-page: 881 year: 2014 ident: 10.1016/j.cell.2016.09.028_bib72 article-title: The genome sequence of the corn snake (Pantherophis guttatus), a valuable resource for EvoDevo studies in squamates publication-title: Int. J. Dev. Biol. doi: 10.1387/ijdb.150060at – volume: 17 start-page: 428 year: 2007 ident: 10.1016/j.cell.2016.09.028_bib85 article-title: Shh and Gremlin1 chromosomal landscapes in development and disease publication-title: Curr. Opin. Genet. Dev. doi: 10.1016/j.gde.2007.07.006 – volume: 399 start-page: 474 year: 1999 ident: 10.1016/j.cell.2016.09.028_bib14 article-title: Developmental basis of limblessness and axial patterning in snakes publication-title: Nature doi: 10.1038/20944 – volume: 22 start-page: 141 year: 2008 ident: 10.1016/j.cell.2016.09.028_bib17 article-title: Regulatory divergence modifies limb length between mammals publication-title: Genes Dev. doi: 10.1101/gad.1620408 – volume: 12 start-page: 3156 year: 1998 ident: 10.1016/j.cell.2016.09.028_bib55 article-title: Fgf-10 is required for both limb and lung development and exhibits striking functional similarity to Drosophila branchless publication-title: Genes Dev. doi: 10.1101/gad.12.20.3156 – volume: 15 start-page: 87 year: 2015 ident: 10.1016/j.cell.2016.09.028_bib36 article-title: The origin of snakes: Revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record publication-title: BMC Evol. Biol. doi: 10.1186/s12862-015-0358-5 – volume: 435 start-page: 1113 year: 2005 ident: 10.1016/j.cell.2016.09.028_bib43 article-title: Early developmental arrest of mammalian limbs lacking HoxA/HoxD gene function publication-title: Nature doi: 10.1038/nature03648 – volume: 164 start-page: 45 year: 2016 ident: 10.1016/j.cell.2016.09.028_bib37 article-title: Evolving new skeletal traits by cis-regulatory changes in bone morphogenetic proteins publication-title: Cell doi: 10.1016/j.cell.2015.12.007 – volume: 153 start-page: 910 year: 2013 ident: 10.1016/j.cell.2016.09.028_bib78 article-title: One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering publication-title: Cell doi: 10.1016/j.cell.2013.04.025 – volume: 9 start-page: 1956 year: 2014 ident: 10.1016/j.cell.2016.09.028_bib84 article-title: Generating genetically modified mice using CRISPR/Cas-mediated genome engineering publication-title: Nat. Protoc. doi: 10.1038/nprot.2014.134 – reference: 1090005 - Science. 1975 Apr 11;188(4184):107-16 – reference: 22481355 - Nature. 2012 Apr 04;484(7392):46-7 – reference: 23650631 - Philos Trans R Soc Lond B Biol Sci. 2013 May 06;368(1620):20120357 – reference: 25058643 - Nat Protoc. 2014 Aug;9(8):1956-68 – reference: 20147105 - Cold Spring Harb Protoc. 2009 Mar;2009(3):pdb.prot5170 – reference: 24908250 - Nat Genet. 2014 Jul;46(7):685-92 – reference: 21390129 - Nature. 2011 Mar 10;471(7337):216-9 – reference: 26829752 - Nat Genet. 2016 Mar;48(3):336-41 – reference: 12736217 - Development. 2003 Jun;130(12):2741-51 – reference: 22682255 - Cell. 2012 Jun 8;149(6):1381-92 – reference: 24715461 - Development. 2014 Apr;141(8):1715-25 – reference: 18772437 - Science. 2008 Sep 5;321(5894):1346-50 – reference: 23332764 - Cell. 2013 Jan 17;152(1-2):327-39 – reference: 22340503 - Dev Cell. 2012 Feb 14;22(2):459-67 – reference: 17130149 - Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92 – reference: 24990743 - Nature. 2014 Jul 3;511(7507):46-51 – reference: 23598338 - Nature. 2013 Apr 18;496(7445):311-6 – reference: 10742046 - Mol Biol Evol. 2000 Apr;17(4):540-52 – reference: 11751242 - Bioinformatics. 2001 Dec;17(12):1246-7 – reference: 20525638 - Syst Biol. 2010 May;59(3):307-21 – reference: 20203609 - Nature. 2010 Mar 4;464(7285):99-103 – reference: 15677727 - Development. 2005 Feb;132(4):797-803 – reference: 25745175 - Science. 2015 Mar 6;347(6226):1155-9 – reference: 23627680 - BMC Evol Biol. 2013 Apr 29;13:93 – reference: 16908629 - Development. 2006 Sep;133(17 ):3419-28 – reference: 8799155 - Proc Natl Acad Sci U S A. 1996 Aug 20;93(17):9067-72 – reference: 26774823 - Cell. 2016 Jan 14;164(1-2):45-56 – reference: 10365960 - Nature. 1999 Jun 3;399(6735):474-9 – reference: 9784490 - Genes Dev. 1998 Oct 15;12(20):3156-61 – reference: 24297902 - Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20645-50 – reference: 18198333 - Genes Dev. 2008 Jan 15;22(2):141-51 – reference: 22143240 - Nat Rev Genet. 2011 Dec 06;13(1):59-69 – reference: 24297900 - Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20651-6 – reference: 27019111 - Nat Genet. 2016 May;48(5):528-36 – reference: 9916808 - Nat Genet. 1999 Jan;21(1):138-41 – reference: 26365491 - Cell. 2015 Sep 24;163(1):68-83 – reference: 26439399 - Dev Cell. 2015 Oct 12;35(1):107-19 – reference: 27264195 - Ecol Lett. 2016 Jul;19(7):800-9 – reference: 25635462 - Cell. 2015 Jan 29;160(3):554-66 – reference: 12837695 - Hum Mol Genet. 2003 Jul 15;12 (14 ):1725-35 – reference: 24880339 - Nat Genet. 2014 Jul;46(7):748-52 – reference: 20007865 - Science. 2010 Jan 15;327(5963):302-5 – reference: 18156157 - Hum Mol Genet. 2008 Apr 1;17(7):978-85 – reference: 26762695 - Semin Cell Dev Biol. 2016 Jan;49:116-24 – reference: 27476854 - Elife. 2016 Aug 01;5:null – reference: 25535365 - Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):803-8 – reference: 17304246 - Nat Rev Genet. 2007 Mar;8(3):206-16 – reference: 2557196 - Development. 1989 Apr;105(4):707-14 – reference: 27768881 - Cell. 2016 Oct 20;167(3):598-600 – reference: 19212405 - Nature. 2009 Feb 12;457(7231):854-8 – reference: 17187056 - Nature. 2007 Jan 18;445(7125):311-4 – reference: 20729851 - Nat Genet. 2010 Sep;42(9):806-10 – reference: 5789433 - Science. 1969 Jul 25;165(3891):349-57 – reference: 24990742 - Nature. 2014 Jul 3;511(7507):41-5 – reference: 18614008 - Cell. 2008 Jul 11;134(1):25-36 – reference: 16172004 - Mol Phylogenet Evol. 2005 Nov;37(2):581-601 – reference: 16672333 - Development. 2006 Jun;133(11):2263-73 – reference: 15973411 - Nature. 2005 Jun 23;435(7045):1113-6 – reference: 24159046 - Science. 2013 Oct 25;342(6157):1241006 – reference: 20513432 - Mol Cell. 2010 May 28;38(4):576-89 – reference: 10720326 - Science. 2000 Mar 17;287(5460):2010-2 – reference: 16625194 - Nature. 2006 Apr 20;440(7087):1037-40 – reference: 11932743 - Nature. 2002 Apr 4;416(6880):527-31 – reference: 21478888 - Nat Genet. 2011 May;43(5):414-20 – reference: 23674686 - Proc Natl Acad Sci U S A. 2013 Jun 25;110(26):10682-6 – reference: 22847109 - Nat Methods. 2012 Jul 30;9(8):772 – reference: 21509892 - Dev Dyn. 2011 May;240(5):920-30 – reference: 26206932 - Science. 2015 Jul 24;349(6246):416-9 – reference: 26154328 - Int J Dev Biol. 2014;58(10-12):881-8 – reference: 17086198 - Nature. 2006 Nov 23;444(7118):499-502 – reference: 25539083 - Nature. 2015 Apr 2;520(7545):86-9 – reference: 23643243 - Cell. 2013 May 9;153(4):910-8 – reference: 17714931 - Curr Opin Genet Dev. 2007 Oct;17(5):428-34 – reference: 21330290 - Bioinformatics. 2011 Apr 1;27(7):1017-8 – reference: 23827682 - Cell. 2013 Jul 3;154(1):185-96 – reference: 7916661 - Cell. 1993 Dec 31;75(7):1417-30 – reference: 22138689 - Nat Genet. 2011 Dec 04;44(1):89-93 – reference: 19920852 - Nat Rev Genet. 2009 Dec;10(12):845-58 – reference: 27923134 - Curr Biol. 2016 Dec 5;26(23):R1237-R1240 – reference: 24861617 - Nucleic Acids Res. 2014 Jul;42(Web Server issue):W401-7 – reference: 26227660 - J Exp Zool B Mol Dev Evol. 2015 Sep;324(6):504-16 – reference: 23992847 - Cell. 2013 Sep 12;154(6):1370-9 – reference: 22481358 - Nature. 2012 Apr 04;484(7392):55-61 – reference: 19363495 - Nat Methods. 2009 May;6(5):343-5 – reference: 14727139 - Mamm Genome. 2004 Jan;15(1):23-34 – reference: 23329690 - Mol Biol Evol. 2013 Apr;30(4):772-80 – reference: 25989795 - BMC Evol Biol. 2015 May 20;15:87 |
| SSID | ssj0008555 |
| Score | 2.6132224 |
| Snippet | The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major... |
| SourceID | pubmedcentral osti proquest pubmed crossref elsevier |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 633 |
| SubjectTerms | Animals Base Sequence BASIC BIOLOGICAL SCIENCES binding sites Biological Evolution cis-regulatory element CRISPR/Cas9 enhancer Enhancer Elements, Genetic evo-devo evolution Evolution, Molecular Extremities - growth & development fish Gene Knock-In Techniques genome editing Hedgehog Proteins - genetics humans limb development Mice Mice, Transgenic morphological evolution Mutation Phylogeny regulatory sequences snakes Snakes - classification Snakes - genetics Sonic hedgehog (Shh) transcription factors transgenic animals ZRS |
| Title | Progressive Loss of Function in a Limb Enhancer during Snake Evolution |
| URI | https://dx.doi.org/10.1016/j.cell.2016.09.028 https://www.ncbi.nlm.nih.gov/pubmed/27768887 https://www.proquest.com/docview/1834995831 https://www.proquest.com/docview/2000234166 https://www.osti.gov/biblio/1398431 https://pubmed.ncbi.nlm.nih.gov/PMC5484524 |
| Volume | 167 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3dS9xAEB_kQPCl1Na2qa1swbcSTDbZze5jlTtsqyK0wr0tu3u7mKo5safgf-9MPg6vyD308ZIdcpnvCTO_AdhXngdtC5s6Lm1aYqGcuoIabAj9q4oiFpYGnE_P5PFF-WMqphtwNMzCUFtl7_s7n9566_7KQc_Ng9u6phlfzZVsM4ockxQqgWiqlIb4podLb6yE6LYYaLR8PN0PznQ9XvRxnNq7ZIt1ShvZXw5Oozna20s56L-tlM9i0-Q1vOqTSvat-9_bsBGaN7DZrZl8fAuTc2rCon7Xh8BO8MFsHtkEAxoJhdUNs-ykvnFs3FySDtyxbnaR_WrsVWDjh147d-BiMv59dJz2-xNSL1S-SEMp1Uz6oPLo8xA8z0Kk0VNd5VZwq4pZVTgpXOm8lqWrvEMDDtxrn_sgnS7ewaiZN-EDsCzifYzks4zQZ7LoXLBY_KCcY9RoxwnkA-OM78HFacfFtRm6yP4YYrYhZptMG2R2Al-XNLcdtMba02KQh1lREIO-fy3dLgmPaAgV11P7EBJh4qswd0rgyyBTg3ZFxLYJ8_u_Bl0dFoNCrTvDW7ggVECZwPtOD5Zvwiss5NCDJ1CtaMjyAOF6r95p6ssW3xuLyFLw8uN_vvEubNEvCrA8-wSjxd19-IyZ08LtYc3w_edeayBPH78XDg |
| linkProvider | Elsevier |
| linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3db9MwED9NRQheEOMzDIaReEPREid27EeYWnXQTUhsUt8s27W1DEin0U3iv-cuHxWdpj7sNfapyX1f9bs7gI_K86BtYVPHpU1LLJRTVxDAhqZ_VVHEwlKD8_GJnJ6VX-divgOHQy8MwSp739_59NZb908Oem4eXNY19fhqrmSbUeSYpGAJ9ACzgYxU-2j-Ze2OlRDdGgONpo_X-86ZDuRF_44Tvku2w05pJfvd0Wm0RIO7Kwm9jaX8LzhNnsKTPqtkn7sX34Wd0DyDh92eyb_PYfKdUFgEeL0JbIY_zJaRTTCikVRY3TDLZvVvx8bNOSnBFeuaF9mPxv4MbHzTq-cLOJuMTw-nab9AIfVC5as0lFItpA8qjz4PwfMsROo91VVuBbeqWFSFk8KVzmtZuso7tODAvfa5D9Lp4iWMmmUTXgPLIp5jKF9kNH4mi84Fi9UPCjpGjYacQD4wzvh-ujgtufhlBhjZhSFmG2K2ybRBZifwaU1z2c3W2HpbDPIwGxpi0Plvpdsj4RENjcX1hB9CIsx8FSZPCXwYZGrQsIjYNmF5_cegr8NqUKhtd3g7Lwg1UCbwqtOD9ZfwCis5dOEJVBsasr5Ag703T5r6vB3wjVVkKXj55p5f_B4eTU-PZ2Z2dPJtDx7TCUVbnr2F0erqOrzDNGrl9lsz-Qeb3Rk4 |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Progressive+Loss+of+Function+in+a+Limb+Enhancer+during+Snake+Evolution&rft.jtitle=Cell&rft.au=Kvon%2C+Evgeny+Z.&rft.au=Kamneva%2C+Olga+K.&rft.au=Melo%2C+Uir%C3%A1+S.&rft.au=Barozzi%2C+Iros&rft.date=2016-10-20&rft.issn=0092-8674&rft.volume=167&rft.issue=3&rft.spage=633&rft.epage=642.e11&rft_id=info:doi/10.1016%2Fj.cell.2016.09.028&rft.externalDBID=n%2Fa&rft.externalDocID=10_1016_j_cell_2016_09_028 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0092-8674&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0092-8674&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0092-8674&client=summon |