Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning
Abstract We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucl...
Saved in:
| Published in | Nucleic acids research Vol. 47; no. 18; pp. 9511 - 9523 |
|---|---|
| Main Authors | , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
10.10.2019
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 0305-1048 1362-4962 1362-4962 |
| DOI | 10.1093/nar/gkz759 |
Cover
| Abstract | Abstract
We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models. |
|---|---|
| AbstractList | We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models. Abstract We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models. We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models. |
| Author | Flores, Oscar Orozco, Modesto Bayarri, Genis Hospital, Adam Heath, Isabelle Brun Buitrago, Diana Illa, Ricard Royo, Romina Gelpí, Josep Lluís Del Pino, Marc Heath, Simon Codó, Laia de Jorge, Pau Battistini, Federica |
| AuthorAffiliation | 4 Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain 2 Barcelona Supercomputing Center (BSC) , Jordi Girona 31, Barcelona 08028. Spain 3 Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology , Barcelona, Spain 1 Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10, Barcelona 08028, Spain |
| AuthorAffiliation_xml | – name: 1 Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac 10, Barcelona 08028, Spain – name: 2 Barcelona Supercomputing Center (BSC) , Jordi Girona 31, Barcelona 08028. Spain – name: 3 Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology , Barcelona, Spain – name: 4 Departament de Bioquímica i Biomedicina. Facultat de Biologia, Universitat de Barcelona , Avgda Diagonal 647, Barcelona 08028, Spain |
| Author_xml | – sequence: 1 givenname: Diana surname: Buitrago fullname: Buitrago, Diana organization: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain – sequence: 2 givenname: Laia orcidid: 0000-0002-6797-8746 surname: Codó fullname: Codó, Laia organization: Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain – sequence: 3 givenname: Ricard surname: Illa fullname: Illa, Ricard organization: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain – sequence: 4 givenname: Pau surname: de Jorge fullname: de Jorge, Pau organization: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain – sequence: 5 givenname: Federica surname: Battistini fullname: Battistini, Federica organization: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain – sequence: 6 givenname: Oscar surname: Flores fullname: Flores, Oscar organization: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain – sequence: 7 givenname: Genis surname: Bayarri fullname: Bayarri, Genis organization: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain – sequence: 8 givenname: Romina surname: Royo fullname: Royo, Romina organization: Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain – sequence: 9 givenname: Marc surname: Del Pino fullname: Del Pino, Marc organization: Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain – sequence: 10 givenname: Simon surname: Heath fullname: Heath, Simon organization: Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain – sequence: 11 givenname: Adam surname: Hospital fullname: Hospital, Adam organization: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain – sequence: 12 givenname: Josep Lluís orcidid: 0000-0002-0566-7723 surname: Gelpí fullname: Gelpí, Josep Lluís organization: Barcelona Supercomputing Center (BSC), Jordi Girona 31, Barcelona 08028. Spain – sequence: 13 givenname: Isabelle Brun surname: Heath fullname: Heath, Isabelle Brun organization: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain – sequence: 14 givenname: Modesto surname: Orozco fullname: Orozco, Modesto email: modesto.orozco@irbbarcelona.org organization: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, Barcelona 08028, Spain |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31504766$$D View this record in MEDLINE/PubMed |
| BookMark | eNp9kUtLxTAQhYMoen1s_AGSjSBCNa-mrQtBfIMoiK5Dmju5Rtvk2rTK9ddbqW_E1SzmO-cMc5bRvA8eEFqnZIeSgu963exOHl6ytJhDI8olS0Qh2TwaEU7ShBKRL6HlGO8JoYKmYhEtcZoSkUk5QteXnakgxFADPpp5XTsT97DGHp5xG0KFbWhwewd4PCyx9rqaRRdxsNh_aachutYF7_xkFS1YXUVYe58r6Pbk-ObwLLm4Oj0_PLhIjCB5mwgGor-1AFZyK4AIw21prQHGJR3bjJhcC9AlT1luMiqBlj1pLM8IZCAJX0H7g--0K2sYG_Btoys1bVytm5kK2qmfG-_u1CQ8KZnJlBHeG2y9GzThsYPYqtpFA1WlPYQuKsbyPKNFXuQ9uvE96zPk45E9QAbANCHGBqwyrtVvH-mjXaUoUW9dqb4rNXTVS7Z_ST5c_4Q3Bzh00_-4V3AWpYg |
| CitedBy_id | crossref_primary_10_1111_cpr_12898 crossref_primary_10_1016_j_csbj_2022_12_009 crossref_primary_10_1093_nar_gkae689 crossref_primary_10_1038_s41598_024_60236_x crossref_primary_10_1186_s13059_021_02465_1 crossref_primary_10_1038_s41467_021_23142_8 crossref_primary_10_1038_s41467_024_52425_z crossref_primary_10_1126_sciadv_adn5175 crossref_primary_10_1101_gr_279326_124 crossref_primary_10_1016_j_csbj_2022_07_037 crossref_primary_10_1038_s41586_025_08595_x crossref_primary_10_1038_s41564_023_01483_y crossref_primary_10_1038_s41594_024_01239_0 crossref_primary_10_1038_s41594_022_00839_y crossref_primary_10_1038_s41598_022_19471_3 |
| Cites_doi | 10.1093/bioinformatics/btr345 10.1186/1471-2164-12-489 10.1038/nature11142 10.1038/nmeth.2688 10.1016/j.tig.2010.08.003 10.1101/gr.142067.112 10.1016/j.molp.2017.05.001 10.1093/nar/gky379 10.1016/j.bbaexp.2003.10.014 10.1186/s13072-017-0165-x 10.1042/bj3550625 10.1126/science.1112178 10.1038/nrg2522 10.1111/j.1365-2672.2009.04657.x 10.1038/nature07667 10.1038/nrm.2017.47 10.1534/genetics.115.179788 10.1038/nature06929 10.1186/s13072-017-0125-5 10.1101/gr.229102 10.1038/nsmb.2419 10.1016/j.molcel.2018.05.030 10.1038/23506 10.1093/nar/gkv978 10.1016/j.cell.2007.05.009 10.1101/gad.274910.115 10.1016/j.ceb.2007.04.006 10.1093/bib/bbv086 10.1093/nar/gku1057 10.1016/j.molcel.2016.12.009 10.1038/ng.2305 10.1038/srep19729 10.1073/pnas.1315809110 10.1126/science.1120499 10.1101/gr.208173.116 10.1016/j.cell.2016.10.049 10.7554/eLife.01861 10.1093/bioinformatics/btl567 10.1038/ncomms5909 10.1128/MCB.23.6.1935-1945.2003 10.1186/s13059-016-0924-1 10.1093/nar/gku165 10.1101/gad.244434.114 10.1186/s12864-017-3541-9 10.1186/s13059-018-1398-0 |
| ContentType | Journal Article |
| Copyright | The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| Copyright_xml | – notice: The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 – notice: The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| DBID | TOX AAYXX CITATION NPM 7X8 5PM |
| DOI | 10.1093/nar/gkz759 |
| DatabaseName | Oxford Journals Open Access Collection CrossRef PubMed MEDLINE - Academic PubMed Central (Full Participant titles) |
| DatabaseTitle | CrossRef PubMed MEDLINE - Academic |
| DatabaseTitleList | PubMed CrossRef MEDLINE - Academic |
| 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: TOX name: Oxford Journals Open Access Collection url: https://academic.oup.com/journals/ sourceTypes: Publisher |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Anatomy & Physiology Chemistry |
| EISSN | 1362-4962 |
| EndPage | 9523 |
| ExternalDocumentID | PMC6765203 31504766 10_1093_nar_gkz759 10.1093/nar/gkz759 |
| Genre | Journal Article |
| GrantInformation_xml | – fundername: Catalan Government grantid: 2017-SGR-134 – fundername: Spanish Ministry of Science grantid: RTI2018-096704-B-100 – fundername: ; grantid: 2017-SGR-134 – fundername: ; grantid: RTI2018-096704-B-100 |
| GroupedDBID | --- -DZ -~X .I3 0R~ 123 18M 1TH 29N 2WC 4.4 482 53G 5VS 5WA 70E 85S A8Z AAFWJ AAHBH AAMVS AAOGV AAPXW AAUQX AAVAP ABEJV ABGNP ABPTD ABQLI ABXVV ACGFO ACGFS ACIWK ACNCT ACPRK ACUTJ ADBBV ADHZD AEGXH AENEX AENZO AFFNX AFPKN AFRAH AFYAG AHMBA AIAGR ALMA_UNASSIGNED_HOLDINGS ALUQC AMNDL AOIJS BAWUL BAYMD BCNDV CAG CIDKT CS3 CZ4 DIK DU5 D~K E3Z EBD EBS EMOBN F5P GROUPED_DOAJ GX1 H13 HH5 HYE HZ~ IH2 KAQDR KQ8 KSI M49 OAWHX OBC OBS OEB OES OJQWA P2P PEELM PQQKQ R44 RD5 RNS ROL ROZ RPM RXO SV3 TN5 TOX TR2 WG7 WOQ X7H XSB YSK ZKX ~91 ~D7 ~KM AAYXX CITATION OVT AAPPN ADIXU AFULF BTTYL M~E NPM ROX 7X8 5PM |
| ID | FETCH-LOGICAL-c408t-42e43629e2b3f4e04c3fbffce2361df70c8a4eab3528c716e1b2b3cf370e7e603 |
| IEDL.DBID | TOX |
| ISSN | 0305-1048 1362-4962 |
| IngestDate | Thu Aug 21 14:32:54 EDT 2025 Thu Jul 10 22:07:26 EDT 2025 Wed Feb 19 02:33:23 EST 2025 Thu Apr 24 23:07:36 EDT 2025 Tue Jul 01 02:07:23 EDT 2025 Wed Apr 02 07:01:59 EDT 2025 |
| IsDoiOpenAccess | true |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 18 |
| Language | English |
| License | This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com http://creativecommons.org/licenses/by-nc/4.0 The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. |
| LinkModel | DirectLink |
| MergedId | FETCHMERGED-LOGICAL-c408t-42e43629e2b3f4e04c3fbffce2361df70c8a4eab3528c716e1b2b3cf370e7e603 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors. |
| ORCID | 0000-0002-6797-8746 0000-0002-0566-7723 |
| OpenAccessLink | https://dx.doi.org/10.1093/nar/gkz759 |
| PMID | 31504766 |
| PQID | 2288719898 |
| PQPubID | 23479 |
| PageCount | 13 |
| ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_6765203 proquest_miscellaneous_2288719898 pubmed_primary_31504766 crossref_citationtrail_10_1093_nar_gkz759 crossref_primary_10_1093_nar_gkz759 oup_primary_10_1093_nar_gkz759 |
| ProviderPackageCode | CITATION AAYXX |
| PublicationCentury | 2000 |
| PublicationDate | 2019-10-10 |
| PublicationDateYYYYMMDD | 2019-10-10 |
| PublicationDate_xml | – month: 10 year: 2019 text: 2019-10-10 day: 10 |
| PublicationDecade | 2010 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England |
| PublicationTitle | Nucleic acids research |
| PublicationTitleAlternate | Nucleic Acids Res |
| PublicationYear | 2019 |
| Publisher | Oxford University Press |
| Publisher_xml | – name: Oxford University Press |
| References | R Core Team. (2020071623530084000_B29) 2016 Deniz (2020071623530084000_B39) 2016; 6 Moyle-Heyrman (2020071623530084000_B26) 2013; 110 Stanley (2020071623530084000_B46) 2010; 109 Chereji (2020071623530084000_B36) 2017; 65 Collings (2020071623530084000_B8) 2017; 10 Brogaard (2020071623530084000_B22) 2012; 486 Henikoff (2020071623530084000_B27) 2014; 3 Yuan (2020071623530084000_B3) 2005; 309 Bai (2020071623530084000_B48) 2010; 26 Buenrostro (2020071623530084000_B14) 2013; 10 Kolesnikov (2020071623530084000_B33) 2015; 43 Chen (2020071623530084000_B42) 2017; 10 Thakur (2020071623530084000_B25) 2015; 201 Tu (2020071623530084000_B44) 2005; 310 Flores (2020071623530084000_B17) 2011; 27 Voong (2020071623530084000_B24) 2016; 167 Gutiérrez (2020071623530084000_B21) 2017; 10 Teif (2020071623530084000_B18) 2016; 17 Jeffers (2020071623530084000_B38) 2017; 27 Deniz (2020071623530084000_B20) 2011; 12 Kent (2020071623530084000_B35) 2002; 12 Nocetti (2020071623530084000_B43) 2016; 30 Flores (2020071623530084000_B19) 2014; 42 Whitehouse (2020071623530084000_B13) 2003; 23 Buels (2020071623530084000_B34) 2016; 17 Barski (2020071623530084000_B1) 2007; 129 Rodríguez (2020071623530084000_B47) 2001; 355 Mavrich (2020071623530084000_B2) 2008; 453 Kubik (2020071623530084000_B9) 2018; 71 Chen (2020071623530084000_B15) 2013; 23 Afgan (2020071623530084000_B31) 2018; 46 Rando (2020071623530084000_B5) 2007; 19 Chen (2020071623530084000_B16) 2014; 5 Falcon (2020071623530084000_B40) 2007; 23 Jiang (2020071623530084000_B6) 2009; 10 Teif (2020071623530084000_B41) 2012; 19 Kaplan (2020071623530084000_B45) 2009; 458 Chereji (2020071623530084000_B23) 2018; 19 Chereji (2020071623530084000_B37) 2016; 44 Whitehouse (2020071623530084000_B12) 1999; 400 Knight (2020071623530084000_B11) 2014; 28 Codó (2020071623530084000_B30) 2019 Mellor (2020071623530084000_B10) 2004; 1677 Lai (2020071623530084000_B4) 2017; 18 Liu (2020071623530084000_B28) 2017; 18 Raveh-Sadka (2020071623530084000_B7) 2012; 44 Giancoli (2020071623530084000_B32) 2000 |
| References_xml | – year: 2019 ident: 2020071623530084000_B30 article-title: MuGVRE. A virtual research environment for 3D/4D genomics Bioinformatics – volume: 27 start-page: 2149 year: 2011 ident: 2020071623530084000_B17 article-title: nucleR: a package for non-parametric nucleosome positioning publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr345 – volume: 12 start-page: 489 year: 2011 ident: 2020071623530084000_B20 article-title: Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast publication-title: BMC Genomics doi: 10.1186/1471-2164-12-489 – volume: 486 start-page: 496 year: 2012 ident: 2020071623530084000_B22 article-title: A map of nucleosome positions in yeast at base-pair resolution publication-title: Nature doi: 10.1038/nature11142 – volume: 10 start-page: 1213 year: 2013 ident: 2020071623530084000_B14 article-title: Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position publication-title: Nat. Methods doi: 10.1038/nmeth.2688 – volume-title: R-A Language and Environment for Statistical Computing year: 2016 ident: 2020071623530084000_B29 – volume: 26 start-page: 476 year: 2010 ident: 2020071623530084000_B48 article-title: Gene regulation by nucleosome positioning publication-title: Trends Genet. doi: 10.1016/j.tig.2010.08.003 – volume: 23 start-page: 341 year: 2013 ident: 2020071623530084000_B15 article-title: DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing publication-title: Genome Res. doi: 10.1101/gr.142067.112 – volume: 10 start-page: 962 year: 2017 ident: 2020071623530084000_B42 article-title: Genome-wide nucleosome occupancy and organization modulates the plasticity of gene transcriptional status in maize publication-title: Mol. Plant doi: 10.1016/j.molp.2017.05.001 – volume: 46 start-page: W537 year: 2018 ident: 2020071623530084000_B31 article-title: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update publication-title: Nucleic Acids Res. doi: 10.1093/nar/gky379 – volume: 1677 start-page: 100 year: 2004 ident: 2020071623530084000_B10 article-title: ISWI complexes in Saccharomyces cerevisiae publication-title: Biochim. Biophys. Acta (BBA) - Gene Struct. Expression doi: 10.1016/j.bbaexp.2003.10.014 – volume: 10 start-page: 58 year: 2017 ident: 2020071623530084000_B21 article-title: Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning publication-title: Epigenet. Chromatin doi: 10.1186/s13072-017-0165-x – volume: 355 start-page: 625 year: 2001 ident: 2020071623530084000_B47 article-title: The hexokinase 2 protein regulates the expression of the GLK1, HXK1 and HXK2 genes of Saccharomyces cerevisiae publication-title: Biochem. J. doi: 10.1042/bj3550625 – volume: 309 start-page: 626 year: 2005 ident: 2020071623530084000_B3 article-title: Genome-Scale Identification of Nucleosome Positions in S. cerevisiae publication-title: Science doi: 10.1126/science.1112178 – volume: 10 start-page: 161 year: 2009 ident: 2020071623530084000_B6 article-title: Nucleosome positioning and gene regulation: advances through genomics publication-title: Nat. Rev. Genet. doi: 10.1038/nrg2522 – volume: 109 start-page: 13 year: 2010 ident: 2020071623530084000_B46 article-title: The ethanol stress response and ethanol tolerance of Saccharomycescerevisiae publication-title: J. Appl. Microbiol. doi: 10.1111/j.1365-2672.2009.04657.x – volume: 458 start-page: 362 year: 2009 ident: 2020071623530084000_B45 article-title: The DNA-encoded nucleosome organization of a eukaryotic genome publication-title: Nature doi: 10.1038/nature07667 – volume: 18 start-page: 548 year: 2017 ident: 2020071623530084000_B4 article-title: Understanding nucleosome dynamics and their links to gene expression and DNA replication publication-title: Nat. Rev. Mol. Cell Biol. doi: 10.1038/nrm.2017.47 – volume: 201 start-page: 543 year: 2015 ident: 2020071623530084000_B25 article-title: Inner kinetochore protein interactions with regional centromeres of fission yeast publication-title: Genetics doi: 10.1534/genetics.115.179788 – volume: 453 start-page: 358 year: 2008 ident: 2020071623530084000_B2 article-title: Nucleosome organization in the Drosophila genome publication-title: Nature doi: 10.1038/nature06929 – volume: 10 start-page: 18 year: 2017 ident: 2020071623530084000_B8 article-title: Links between DNA methylation and nucleosome occupancy in the human genome publication-title: Epigenet. Chromatin doi: 10.1186/s13072-017-0125-5 – volume: 12 start-page: 996 year: 2002 ident: 2020071623530084000_B35 article-title: The human genome browser at UCSC publication-title: Genome Res. doi: 10.1101/gr.229102 – volume: 19 start-page: 1185 year: 2012 ident: 2020071623530084000_B41 article-title: Genome-wide nucleosome positioning during embryonic stem cell development publication-title: Nat. Struct. Mol. Biol. doi: 10.1038/nsmb.2419 – volume: 71 start-page: 89 year: 2018 ident: 2020071623530084000_B9 article-title: Sequence-directed action of RSC remodeler and general regulatory factors modulates +1 nucleosome position to facilitate transcription publication-title: Mol. Cell doi: 10.1016/j.molcel.2018.05.030 – volume: 400 start-page: 784 year: 1999 ident: 2020071623530084000_B12 article-title: Nucleosome mobilization catalysed by the yeast SWI/SNF complex publication-title: Nature doi: 10.1038/23506 – volume: 44 start-page: 1036 year: 2016 ident: 2020071623530084000_B37 article-title: Genome-wide profiling of nucleosome sensitivity and chromatin accessibility in Drosophila melanogaster publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkv978 – volume: 129 start-page: 823 year: 2007 ident: 2020071623530084000_B1 article-title: High-Resolution profiling of histone methylations in the human genome publication-title: Cell doi: 10.1016/j.cell.2007.05.009 – volume: 30 start-page: 660 year: 2016 ident: 2020071623530084000_B43 article-title: Nucleosome repositioning underlies dynamic gene expression publication-title: Genes Dev. doi: 10.1101/gad.274910.115 – volume: 19 start-page: 250 year: 2007 ident: 2020071623530084000_B5 article-title: Rules and regulation in the primary structure of chromatin publication-title: Curr. Opin. Cell Biol. doi: 10.1016/j.ceb.2007.04.006 – volume: 17 start-page: 745 year: 2016 ident: 2020071623530084000_B18 article-title: Nucleosome positioning: resources and tools online publication-title: Brief. Bioinform. doi: 10.1093/bib/bbv086 – volume: 43 start-page: D1113 year: 2015 ident: 2020071623530084000_B33 article-title: ArrayExpress update—simplifying data submissions publication-title: Nucleic Acids Res. doi: 10.1093/nar/gku1057 – volume: 65 start-page: 565 year: 2017 ident: 2020071623530084000_B36 article-title: MNase-sensitive complexes in yeast: nucleosomes and non-histone barriers publication-title: Mol. Cell doi: 10.1016/j.molcel.2016.12.009 – volume: 44 start-page: 743 year: 2012 ident: 2020071623530084000_B7 article-title: Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast publication-title: Nat. Genet. doi: 10.1038/ng.2305 – volume: 6 start-page: 19729 year: 2016 ident: 2020071623530084000_B39 article-title: Nucleosome architecture throughout the cell cycle publication-title: Sci. Rep. doi: 10.1038/srep19729 – volume: 110 start-page: 20158 year: 2013 ident: 2020071623530084000_B26 article-title: Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning publication-title: Proc. Natl. Acad. Sci. U.S.A. doi: 10.1073/pnas.1315809110 – volume: 310 start-page: 1152 year: 2005 ident: 2020071623530084000_B44 article-title: Logic of the yeast metabolic Cycle: Temporal compartmentalization of cellular processes publication-title: Science doi: 10.1126/science.1120499 – volume: 27 start-page: 75 year: 2017 ident: 2020071623530084000_B38 article-title: Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C.elegans publication-title: Genome Res. doi: 10.1101/gr.208173.116 – volume: 167 start-page: 1555 year: 2016 ident: 2020071623530084000_B24 article-title: Insights into nucleosome organization in mouse embryonic stem cells through chemical mapping publication-title: Cell doi: 10.1016/j.cell.2016.10.049 – volume-title: Physics for Scientists & Engineers with Modern Physics year: 2000 ident: 2020071623530084000_B32 – volume: 3 start-page: e01861 year: 2014 ident: 2020071623530084000_B27 article-title: The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo publication-title: eLife doi: 10.7554/eLife.01861 – volume: 23 start-page: 257 year: 2007 ident: 2020071623530084000_B40 article-title: Using GOstats to test gene lists for GO term association publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl567 – volume: 5 start-page: 4909 year: 2014 ident: 2020071623530084000_B16 article-title: Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data publication-title: Nat. Commun. doi: 10.1038/ncomms5909 – volume: 23 start-page: 1935 year: 2003 ident: 2020071623530084000_B13 article-title: Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme publication-title: Mol. Cell Biol. doi: 10.1128/MCB.23.6.1935-1945.2003 – volume: 17 start-page: 66 year: 2016 ident: 2020071623530084000_B34 article-title: JBrowse: a dynamic web platform for genome visualization and analysis publication-title: Genome Biol. doi: 10.1186/s13059-016-0924-1 – volume: 42 start-page: 4934 year: 2014 ident: 2020071623530084000_B19 article-title: Fuzziness and noise in nucleosomal architecture publication-title: Nucleic Acids Res. doi: 10.1093/nar/gku165 – volume: 28 start-page: 1695 year: 2014 ident: 2020071623530084000_B11 article-title: Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription publication-title: Genes Dev. doi: 10.1101/gad.244434.114 – volume: 18 start-page: 135 year: 2017 ident: 2020071623530084000_B28 article-title: An approach of identifying differential nucleosome regions in multiple samples publication-title: BMC Genomics doi: 10.1186/s12864-017-3541-9 – volume: 19 start-page: 19 year: 2018 ident: 2020071623530084000_B23 article-title: Precise genome-wide mapping of single nucleosomes and linkers in vivo publication-title: Genome Biol. doi: 10.1186/s13059-018-1398-0 |
| SSID | ssj0014154 |
| Score | 2.4050062 |
| Snippet | Abstract
We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and... We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics... |
| SourceID | pubmedcentral proquest pubmed crossref oup |
| SourceType | Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
| StartPage | 9511 |
| SubjectTerms | Computational Biology |
| Title | Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/31504766 https://www.proquest.com/docview/2288719898 https://pubmed.ncbi.nlm.nih.gov/PMC6765203 |
| Volume | 47 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwhV1LS8QwEA7iRS-iuz7WxxJRBA_FbJJNWm_LqojgCqKwt5JkExV3W9nHQX-9k760InrupJSZtN83nck3CB17gZHQdUSgDNA3bkbwzhFNAk21poobgHV_UPh2IK4f-c2wOyyaaGa_lPAjdpao6dnT64fs-mN6gL5-Nz_cDataAUBQLhKVaWrysBQhrS2twU7tKNs3RvmzMfIb0lyto7WCIuJeHtMNtGSTBmr2EkiPJ-_4BGdNm9nf8AZa6ZcD25rofuC1idNZOrH4Ih80PzvHCgNxxvM0HWPgpxj4Hh7lF7EqBElw6nDytbbs4wJQ20SPV5cP_eugGJkQGE7CecCp5QBJkaWaOW4JN8xp54z1GisjJ4kJFbdKe00XA6mS7UBQmHFMEiutIGwLLSdpYncQFjwaWSkN9cPTtVWKUelCoR1kIMyEnRY6LT0am0JP3I-1GMd5XZvF4P04934LHVW2b7mKxq9WbQjMnwaHZcxi8K0vbajEpotZTCl8LH37V9hC23kMq_sw4LxcCtFCshbdysArbNevJC_PmdK2kKJLCdv978H20CoQqchjWofso-X5dGEPgKzMdTtL8tvZjv0E2ynr-w |
| linkProvider | Oxford University Press |
| 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=Nucleosome+Dynamics%3A+a+new+tool+for+the+dynamic+analysis+of+nucleosome+positioning&rft.jtitle=Nucleic+acids+research&rft.au=Buitrago%2C+Diana&rft.au=Cod%C3%B3%2C+Laia&rft.au=Illa%2C+Ricard&rft.au=de%C2%A0Jorge%2C+Pau&rft.date=2019-10-10&rft.pub=Oxford+University+Press&rft.issn=0305-1048&rft.eissn=1362-4962&rft.volume=47&rft.issue=18&rft.spage=9511&rft.epage=9523&rft_id=info:doi/10.1093%2Fnar%2Fgkz759&rft_id=info%3Apmid%2F31504766&rft.externalDocID=PMC6765203 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0305-1048&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0305-1048&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0305-1048&client=summon |