Spatio-temporal mRNA tracking in the early zebrafish embryo

Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA...

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Published inNature communications Vol. 12; no. 1; pp. 3358 - 13
Main Authors Holler, Karoline, Neuschulz, Anika, Drewe-Boß, Philipp, Mintcheva, Janita, Spanjaard, Bastiaan, Arsiè, Roberto, Ohler, Uwe, Landthaler, Markus, Junker, Jan Philipp
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 07.06.2021
Nature Publishing Group
Nature Portfolio
Subjects
38
38/91
631/136/756
631/1647/2217/2218
631/1647/334/1874/763
631/61/212/2019
631/80/85/2361
64/116
Animals
Cell Tracking - methods
Conserved sequence
Danio rerio
Embryo, Nonmammalian - cytology
Embryo, Nonmammalian - embryology
Embryo, Nonmammalian - metabolism
Embryogenesis
Embryonic growth stage
Embryos
Evolutionary conservation
Female
Gastrulation
Gene expression
Gene Expression Regulation, Developmental
Gene sequencing
Germ cells
Humanities and Social Sciences
Labeling
Localization
multidisciplinary
Oocytes - cytology
Oocytes - metabolism
Ribonucleic acid
RNA
RNA transport
RNA, Messenger - genetics
RNA, Messenger - metabolism
Science
Science (multidisciplinary)
Single-Cell Analysis - methods
Spatial analysis
Spatial discrimination
Spatio-Temporal Analysis
Species Specificity
Tracking
Transcriptome - genetics
Transcriptomes
Transcriptomics
Wildlife conservation
Xenopus - embryology
Xenopus - genetics
Xenopus laevis - embryology
Xenopus laevis - genetics
Zebrafish
Zebrafish - embryology
Zebrafish - genetics
Online AccessGet full text
ISSN2041-1723
2041-1723
DOI10.1038/s41467-021-23834-1

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Abstract Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs. Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a lack of methods for tracking of RNA. Here the authors combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development, revealing insights into this process.
AbstractList Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a lack of methods for tracking of RNA. Here the authors combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development, revealing insights into this process.
Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs. Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a lack of methods for tracking of RNA. Here the authors combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development, revealing insights into this process.
Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.
Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.
Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.
Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a lack of methods for tracking of RNA. Here the authors combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development, revealing insights into this process.
ArticleNumber 3358
Author Arsiè, Roberto
Ohler, Uwe
Mintcheva, Janita
Drewe-Boß, Philipp
Landthaler, Markus
Spanjaard, Bastiaan
Holler, Karoline
Junker, Jan Philipp
Neuschulz, Anika
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/34099733$$D View this record in MEDLINE/PubMed
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Cites_doi 10.1002/aja.1002030302
10.1242/dev.108.2.289
10.1038/s41467-020-15968-5
10.1016/j.ydbio.2017.06.029
10.1038/nmeth.2930
10.1007/978-3-319-46095-6_5
10.1038/328080a0
10.1016/S0960-9822(02)01220-4
10.1016/j.cell.2019.05.027
10.1016/j.cell.2015.04.044
10.1093/bioinformatics/btr261
10.1073/pnas.0803169105
10.1126/science.aan2399
10.1242/dev.119.4.1161
10.1242/dev.139220
10.1038/nrg1154
10.5281/zenodo.4738464
10.1126/science.aar4362
10.1038/s41586-018-0414-6
10.1091/mbc.E15-02-0115
10.1126/science.aaq1723
10.1093/nar/gky1270
10.1016/j.cell.2014.09.038
10.1101/sqb.2015.80.027201
10.1101/696724
10.1016/j.cell.2015.05.002
10.1242/dev.124.16.3157
10.1093/nar/gkz813
10.5281/zenodo.4738513
10.1038/s41586-019-1049-y
10.1038/s41586-019-0969-x
10.1242/dev.01283
10.1091/mbc.e04-03-0265
10.1016/j.molcel.2016.01.020
10.1146/annurev-genet-110410-132517
10.1016/j.molcel.2019.07.030
10.1038/nmeth.2772
10.1073/pnas.1912459116
10.1016/j.molcel.2017.11.014
10.1038/s41592-018-0175-z
10.1016/j.mod.2007.01.003
10.1038/s41592-020-0935-4
10.1038/s41467-017-00690-6
10.1016/j.celrep.2013.12.030
10.1038/nature17150
10.1126/science.aar3131
10.1126/science.aan6827
10.1038/nmeth.4435
10.1186/s13059-016-0938-8
10.1038/s41586-019-1369-y
10.1016/j.ymeth.2010.02.016
10.1007/978-1-4939-9009-2_9
10.1042/BC20040067
10.1038/s41467-019-11028-9
10.1126/science.aaw1219
10.1002/dvdy.21967
10.1080/19490992.2015.1080891
10.1016/j.cell.2009.01.044
10.1007/BF00337288
10.1261/rna.262607
10.1038/s41586-019-1773-3
10.1038/s41587-020-0480-9
10.1146/annurev.genet.37.110801.143752
10.1038/nmeth.4121
10.1038/s41596-020-0292-x
10.1016/j.copbio.2017.02.004
10.1038/nprot.2007.514
10.1038/s41467-021-21246-9
10.1016/S0960-9822(02)00723-6
10.1038/s41598-018-26592-1
10.1038/nbt.1621
10.1016/j.ydbio.2013.05.028
10.1126/science.aax3072
10.1016/j.cell.2007.08.003
10.7554/eLife.05003
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References KimmelCBBallardWWKimmelSRUllmannBSchillingTFStages of embryonic development of the zebrafishDev. Dyn.19952032533101:STN:280:DyaK287nt12qsw%3D%3D858942710.1002/aja.1002030302
Ciolli MattioliCAlternative 3′ UTRs direct localization of functionally diverse protein isoforms in neuronal compartmentsNucleic Acids Res.201947256025733059074510.1093/nar/gky12701:CAS:528:DC%2BC1MXhs1KrtL7O
WheelerGNBrändliAWSimple vertebrate models for chemical genetics and drug discovery screens: lessons from zebrafish and XenopusDev. Dyn.2009238128713081:CAS:528:DC%2BD1MXnsF2itr0%3D1944106010.1002/dvdy.21967
Holler, K. et al. Spatio-temporal mRNA tracking in the early zebrafish embryo. tomo-seq, https://doi.org/10.5281/zenodo.4738513 (2021).
WagnerDESingle-cell mapping of gene expression landscapes and lineage in the zebrafish embryoScience20183609819872018Sci...360..981W1:CAS:528:DC%2BC1cXhtVags77J29700229608344510.1126/science.aar4362
FazalFMAtlas of subcellular RNA localization revealed by APEX-SeqCell2019178473490.e261:CAS:528:DC%2BC1MXht1Wqt7jJ31230715678677310.1016/j.cell.2019.05.027
KuMMeltonDAXwnt-11: a maternally expressed Xenopus wnt geneDevelopment1993119116111731:CAS:528:DyaK2cXmtVWhsLg%3D830688010.1242/dev.119.4.1161
SchierAFTalbotWSMolecular genetics of axis formation in zebrafishAnnu. Rev. Genet.2005395616131:CAS:528:DC%2BD28Xlt1WqsA%3D%3D1628587210.1146/annurev.genet.37.110801.143752
HashimshonyTCEL-Seq2: sensitive highly-multiplexed single-cell RNA-SeqGenome Biol.20161727121950484878210.1186/s13059-016-0938-81:CAS:528:DC%2BC28XhsVert7jN
LeinEBormLELinnarssonSThe promise of spatial transcriptomics for neuroscience in the era of molecular cell typingScience201735864692017Sci...358...64L1:CAS:528:DC%2BC2sXhsF2jtLrJ2898304410.1126/science.aan6827
ClaussenMPielerTIdentification of vegetal RNA-localization elements in Xenopus oocytesMethods2010511461511:CAS:528:DC%2BC3cXlvVaqt78%3D2017884510.1016/j.ymeth.2010.02.016
CaoJZhouWSteemersFTrapnellCShendureJSci-fate characterizes the dynamics of gene expression in single cellsNat. Biotechnol.2020389809881:CAS:528:DC%2BB3cXmvFylu7k%3D32284584741649010.1038/s41587-020-0480-9
RothschildSCCaMK-II activation is essential for zebrafish inner ear development and acts through Delta-Notch signalingDev. Biol.20133811791881:CAS:528:DC%2BC3sXhtVWgurrN2374759910.1016/j.ydbio.2013.05.028
Qiu, X. et al. Mapping vector field of single cells. Preprint at bioRxiv, https://doi.org/10.1101/696724 (2021).
KosakaKKawakamiKSakamotoHInoueKSpatiotemporal localization of germ plasm RNAs during zebrafish oogenesisMech. Dev.20071242792891:CAS:528:DC%2BD2sXjtVahu7k%3D1729309410.1016/j.mod.2007.01.003
BaileyTLDREME: motif discovery in transcription factor ChIP-seq dataBioinformatics201127165316591:CAS:528:DC%2BC3MXntFGkurg%3D21543442310619910.1093/bioinformatics/btr261
ZappuloARNA localization is a key determinant of neurite-enriched proteomeNat. Commun.201782017NatCo...8..583Z28928394560562710.1038/s41467-017-00690-61:CAS:528:DC%2BC1cXos1KqtLc%3D
TaliaferroJMDistal alternative last exons localize mRNAs to neural projectionsMol. Cell2016618218331:CAS:528:DC%2BC28XivFOqt70%3D26907613479890010.1016/j.molcel.2016.01.020
HollerKJunkerJPRNA tomography for spatially resolved transcriptomics (Tomo-Seq)Methods Mol. Biol.201919201291411:CAS:528:DC%2BC1MXitVyrsrnM3073769010.1007/978-1-4939-9009-2_9
NitzanMKaraiskosNFriedmanNRajewskyNGene expression cartographyNature20195761321372019Natur.576..132N1:CAS:528:DC%2BC1MXitF2qt7nF3174874810.1038/s41586-019-1773-3
ClaußenMGlobal analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus speciesMol. Biol. Cell2015263777378726337391462606310.1091/mbc.E15-02-01151:CAS:528:DC%2BC28XmsVOmsLs%3D
ElkoubyYMMullinsMCCoordination of cellular differentiation, polarity, mitosis and meiosis – new findings from early vertebrate oogenesisDev. Biol.20174302752871:CAS:528:DC%2BC2sXhtFChtL3L28666956562361710.1016/j.ydbio.2017.06.029
ErhardFscSLAM-seq reveals core features of transcription dynamics in single cellsNature20195714194231:CAS:528:DC%2BC1MXhtl2qsLjO3129254510.1038/s41586-019-1369-y
CangZNieQInferring spatial and signaling relationships between cells from single cell transcriptomic dataNat. Commun.2020112020NatCo..11.2084C1:CAS:528:DC%2BB3cXosVOmu7k%3D32350282719065910.1038/s41467-020-15968-5
ColemanRAImaging transcription: past, present, and futureCold Spring Harb. Symp. Quant. Biol.201580182676398410.1101/sqb.2015.80.027201
KnautHSteinbeisserHSchwarzHNüsslein-VolhardCAn evolutionary conserved region in the vasa 3’UTR targets RNA translation to the germ cells in the zebrafishCurr. Biol.2002124544661:CAS:528:DC%2BD38XitlGgur4%3D1190953010.1016/S0960-9822(02)00723-6
KohonenTSelf-organized formation of topologically correct feature mapsBiol. Cybern.19824359696678890466.9200210.1007/BF00337288
EngC-HLTranscriptome-scale super-resolved imaging in tissues by RNA seqFISHNature20195682352392019Natur.568..235E1:CAS:528:DC%2BC1MXmslKksrg%3D30911168654402310.1038/s41586-019-1049-y
BetleyJNFrithMCGraberJHChooSDeshlerJOA ubiquitous and conserved signal for RNA localization in chordatesCurr. Biol.200212175617611:CAS:528:DC%2BD38Xot1ags7g%3D1240117010.1016/S0960-9822(02)01220-4
HendriksG-JNASC-seq monitors RNA synthesis in single cellsNat. Commun.2019102019NatCo..10.3138H31316066663724010.1038/s41467-019-11028-91:CAS:528:DC%2BC1MXhsVWlt7zL
JambhekarADerisiJLCis-acting determinants of asymmetric, cytoplasmic RNA transportRNA2007136256421:CAS:528:DC%2BD2sXltVaktbY%3D17449729185281110.1261/rna.262607
CaoJThe single-cell transcriptional landscape of mammalian organogenesisNature20195664965022019Natur.566..496C1:CAS:528:DC%2BC1MXnslOmtr4%3D30787437643495210.1038/s41586-019-0969-x
XiaCFanJEmanuelGHaoJZhuangXSpatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expressionProc. Natl Acad. Sci. USA201911619490194991:CAS:528:DC%2BC1MXhvVGnsr3N3150133110.1073/pnas.19124591166765259
La MannoGRNA velocity of single cellsNature20185604944982018Natur.560..494L30089906613080110.1038/s41586-018-0414-61:CAS:528:DC%2BC1cXhsVynsrrL
ChangPLocalization of RNAs to the mitochondrial cloud in Xenopus oocytes through entrapment and association with endoplasmic reticulumMol. Biol. Cell200415466946811:CAS:528:DC%2BD2cXosVOitLc%3D1529245251915810.1091/mbc.e04-03-0265
RabaniMPieperLChewG-LSchierAFA massively parallel reporter assay of 3’ UTR sequences identifies in vivo rules for mRNA degradationMol. Cell20176810831094.e51:CAS:528:DC%2BC2sXhvFCisrvO29225039599490710.1016/j.molcel.2017.11.014
YartsevaVTakacsCMVejnarCELeeMTGiraldezAJRESA identifies mRNA-regulatory sequences at high resolutionNat. Methods2017142012071:CAS:528:DC%2BC28XitFGhs7bJ2802416010.1038/nmeth.4121
MoorAEGlobal mRNA polarization regulates translation efficiency in the intestinal epitheliumScience2017357129913032017Sci...357.1299M1:CAS:528:DC%2BC2sXhsFWhurfM28798045595521510.1126/science.aan2399
LangdonYGMullinsMCMaternal and zygotic control of zebrafish dorsoventral axial patterningAnnu. Rev. Genet.2011453573771:CAS:528:DC%2BC3MXhs1ahtrrL2194236710.1146/annurev-genet-110410-132517
Holler, K. et al. Spatio-temporal mRNA tracking in the early zebrafish embryo. scSLAM-seq, https://doi.org/10.5281/zenodo.4738464 (2021).
OwensDAHigh-throughput analysis reveals novel maternal germline RNAs crucial for primordial germ cell preservation and proper migrationDevelopment20171442923041:CAS:528:DC%2BC2sXhtF2gsr7E28096217539475510.1242/dev.139220
IslamSQuantitative single-cell RNA-seq with unique molecular identifiersNat. Methods2014111631661:CAS:528:DC%2BC3sXhvFOls7zK2436302310.1038/nmeth.2772
ClaussenMHorvayKPielerTEvidence for overlapping, but not identical, protein machineries operating in vegetal RNA localization along early and late pathways in Xenopus oocytesDevelopment2004131426342731:CAS:528:DC%2BD2cXotVyju7c%3D1529486310.1242/dev.01283
YoonCKawakamiKHopkinsNZebrafish vasa homologue RNA is localized to the cleavage planes of 2- and 4-cell-stage embryos and is expressed in the primordial germ cellsDevelopment1997124315731651:CAS:528:DyaK2sXlvVehs7Y%3D927295610.1242/dev.124.16.3157
HerzogVAThiol-linked alkylation of RNA to assess expression dynamicsNat. Methods201714119812041:CAS:528:DC%2BC2sXhsFGjs73L28945705571221810.1038/nmeth.4435
PadrónAIwasakiSIngoliaNTProximity RNA labeling by APEX-seq reveals the organization of translation initiation complexes and repressive RNA granulesMol. Cell201975875887.e531442426683436210.1016/j.molcel.2019.07.0301:CAS:528:DC%2BC1MXhs1emsr7O
YisraeliJKSokolSMeltonDAA two-step model for the localization of maternal mRNA in Xenopus oocytes: involvement of microtubules and microfilaments in the translocation and anchoring of Vg1 mRNADevelopment19901082892981:CAS:528:DyaK3cXhvFGntLc%3D235107110.1242/dev.108.2.289
KingMLMessittTJMowryKLPutting RNAs in the right place at the right time: RNA localization in the frog oocyteBiol. Cell20059719331:CAS:528:DC%2BD2MXhtlSrtL8%3D1560125510.1042/BC20040067
Plass, M. et al. Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics. Science360, eaaq1723 (2018).
MartinKCEphrussiAmRNA localization: gene expression in the spatial dimensionCell20091367197301:CAS:528:DC%2BD1MXkvFGksbY%3D19239891281992410.1016/j.cell.2009.01.044
ThisseCThisseBHigh-resolution in situ hybridization to whole-mount zebrafish embryosNat. Protoc.2008359691:CAS:528:DC%2BD1cXlsVOjtw%3D%3D1819302210.1038/nprot.2007.514
MeltonDATranslocation of a localized maternal mRNA to the vegetal pole of Xenopus oocytesNature198732880821987Natur.328...80M1:CAS:528:DyaL2sXkslCksbs%3D360077710.1038/328080a0
JinSInference and analysis of cell-cell communication using CellChatNat. Commun.2021122021NatCo..12.1088J1:CAS:528:DC%2BB3MXksFSms7c%3D33597522788987110.1038/s41467-021-21246-9
Farrell, J. A. et al. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science360, eaar3131 (2018).
SindelkaRAsymmetric distribution of biomol
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E Lécuyer (23834_CR59) 2007; 131
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M Claussen (23834_CR40) 2004; 131
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The Alliance of Genome Resources Consortium. (23834_CR72) 2019; 48
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AE Moor (23834_CR12) 2017; 46
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References_xml – reference: YartsevaVTakacsCMVejnarCELeeMTGiraldezAJRESA identifies mRNA-regulatory sequences at high resolutionNat. Methods2017142012071:CAS:528:DC%2BC28XitFGhs7bJ2802416010.1038/nmeth.4121
– reference: QiuQMassively parallel and time-resolved RNA sequencing in single cells with scNT-seqNat. Methods20201799110011:CAS:528:DC%2BB3cXhslWgtLvE32868927810379710.1038/s41592-020-0935-4
– reference: ClaussenMPielerTIdentification of vegetal RNA-localization elements in Xenopus oocytesMethods2010511461511:CAS:528:DC%2BC3cXlvVaqt78%3D2017884510.1016/j.ymeth.2010.02.016
– reference: SindelkaRAsymmetric distribution of biomolecules of maternal origin in the Xenopuslaevis egg and their impact on the developmental planSci. Rep.201882018NatSR...8.8315S29844480597432010.1038/s41598-018-26592-11:CAS:528:DC%2BC1cXhslOgtLvF
– reference: RabaniMKerteszMSegalEComputational prediction of RNA structural motifs involved in posttranscriptional regulatory processesProc. Natl Acad. Sci. USA200810514885148902008PNAS..10514885R1:CAS:528:DC%2BD1cXht1aqur7K1881537610.1073/pnas.08031691052567462
– reference: HashimshonyTCEL-Seq2: sensitive highly-multiplexed single-cell RNA-SeqGenome Biol.20161727121950484878210.1186/s13059-016-0938-81:CAS:528:DC%2BC28XhsVert7jN
– reference: LeinEBormLELinnarssonSThe promise of spatial transcriptomics for neuroscience in the era of molecular cell typingScience201735864692017Sci...358...64L1:CAS:528:DC%2BC2sXhsF2jtLrJ2898304410.1126/science.aan6827
– reference: Jambor, H. et al. Systematic imaging reveals features and changing localization of mRNAs in Drosophila development. Elife4, e05003 (2015).
– reference: TaliaferroJMDistal alternative last exons localize mRNAs to neural projectionsMol. Cell2016618218331:CAS:528:DC%2BC28XivFOqt70%3D26907613479890010.1016/j.molcel.2016.01.020
– reference: MartinKCEphrussiAmRNA localization: gene expression in the spatial dimensionCell20091367197301:CAS:528:DC%2BD1MXkvFGksbY%3D19239891281992410.1016/j.cell.2009.01.044
– reference: RazEPrimordial germ-cell development: the zebrafish perspectiveNat. Rev. Genet.200346907001:CAS:528:DC%2BD3sXmvVWlsrk%3D1295157010.1038/nrg1154
– reference: TrapnellCTranscript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiationNat. Biotechnol.2010285115151:CAS:528:DC%2BC3cXlsVyitLY%3D20436464314604310.1038/nbt.1621
– reference: LangdonYGMullinsMCMaternal and zygotic control of zebrafish dorsoventral axial patterningAnnu. Rev. Genet.2011453573771:CAS:528:DC%2BC3MXhs1ahtrrL2194236710.1146/annurev-genet-110410-132517
– reference: ThisseCThisseBHigh-resolution in situ hybridization to whole-mount zebrafish embryosNat. Protoc.2008359691:CAS:528:DC%2BD1cXlsVOjtw%3D%3D1819302210.1038/nprot.2007.514
– reference: ElkoubyYMMullinsMCCoordination of cellular differentiation, polarity, mitosis and meiosis – new findings from early vertebrate oogenesisDev. Biol.20174302752871:CAS:528:DC%2BC2sXhtFChtL3L28666956562361710.1016/j.ydbio.2017.06.029
– reference: CaoJThe single-cell transcriptional landscape of mammalian organogenesisNature20195664965022019Natur.566..496C1:CAS:528:DC%2BC1MXnslOmtr4%3D30787437643495210.1038/s41586-019-0969-x
– reference: WelchEPelegriFCortical depth and differential transport of vegetally localized dorsal and germ line determinants in the zebrafish embryoBioarchitecture2014513262652872910.1080/19490992.2015.1080891
– reference: OwensDAHigh-throughput analysis reveals novel maternal germline RNAs crucial for primordial germ cell preservation and proper migrationDevelopment20171442923041:CAS:528:DC%2BC2sXhtF2gsr7E28096217539475510.1242/dev.139220
– reference: ErhardFscSLAM-seq reveals core features of transcription dynamics in single cellsNature20195714194231:CAS:528:DC%2BC1MXhtl2qsLjO3129254510.1038/s41586-019-1369-y
– reference: LécuyerEGlobal analysis of mRNA localization reveals a prominent role in organizing cellular architecture and functionCell20071311741871792309610.1016/j.cell.2007.08.0031:CAS:528:DC%2BD2sXht1CntLbM
– reference: JunkerJPGenome-wide RNA tomography in the zebrafish embryoCell20141596626751:CAS:528:DC%2BC2cXhvVanur7E2541711310.1016/j.cell.2014.09.038
– reference: Plass, M. et al. Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics. Science360, eaaq1723 (2018).
– reference: XiaCFanJEmanuelGHaoJZhuangXSpatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expressionProc. Natl Acad. Sci. USA201911619490194991:CAS:528:DC%2BC1MXhvVGnsr3N3150133110.1073/pnas.19124591166765259
– reference: BattichNSequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategiesScience2020367115111562020Sci...367.1151B1:CAS:528:DC%2BB3cXktlOisLg%3D3213954710.1126/science.aax3072
– reference: YisraeliJKSokolSMeltonDAA two-step model for the localization of maternal mRNA in Xenopus oocytes: involvement of microtubules and microfilaments in the translocation and anchoring of Vg1 mRNADevelopment19901082892981:CAS:528:DyaK3cXhvFGntLc%3D235107110.1242/dev.108.2.289
– reference: KuMMeltonDAXwnt-11: a maternally expressed Xenopus wnt geneDevelopment1993119116111731:CAS:528:DyaK2cXmtVWhsLg%3D830688010.1242/dev.119.4.1161
– reference: HerzogVAThiol-linked alkylation of RNA to assess expression dynamicsNat. Methods201714119812041:CAS:528:DC%2BC2sXhsFGjs73L28945705571221810.1038/nmeth.4435
– reference: Holler, K. et al. Spatio-temporal mRNA tracking in the early zebrafish embryo. tomo-seq, https://doi.org/10.5281/zenodo.4738513 (2021).
– reference: KnautHSteinbeisserHSchwarzHNüsslein-VolhardCAn evolutionary conserved region in the vasa 3’UTR targets RNA translation to the germ cells in the zebrafishCurr. Biol.2002124544661:CAS:528:DC%2BD38XitlGgur4%3D1190953010.1016/S0960-9822(02)00723-6
– reference: The Alliance of Genome Resources Consortium.Alliance of Genome Resources Portal: unified model organism research platformNucleic Acids Res.201948D650D65810.1093/nar/gkz8131:CAS:528:DC%2BB3cXhslWltrjO
– reference: ColemanRAImaging transcription: past, present, and futureCold Spring Harb. Symp. Quant. Biol.201580182676398410.1101/sqb.2015.80.027201
– reference: MacoskoEZHighly parallel genome-wide expression profiling of individual cells using nanoliter dropletsCell2015161120212141:CAS:528:DC%2BC2MXpt1Sgt7o%3D26000488448113910.1016/j.cell.2015.05.002
– reference: La MannoGRNA velocity of single cellsNature20185604944982018Natur.560..494L30089906613080110.1038/s41586-018-0414-61:CAS:528:DC%2BC1cXhsVynsrrL
– reference: BaileyTLDREME: motif discovery in transcription factor ChIP-seq dataBioinformatics201127165316591:CAS:528:DC%2BC3MXntFGkurg%3D21543442310619910.1093/bioinformatics/btr261
– reference: MeltonDATranslocation of a localized maternal mRNA to the vegetal pole of Xenopus oocytesNature198732880821987Natur.328...80M1:CAS:528:DyaL2sXkslCksbs%3D360077710.1038/328080a0
– reference: PadrónAIwasakiSIngoliaNTProximity RNA labeling by APEX-seq reveals the organization of translation initiation complexes and repressive RNA granulesMol. Cell201975875887.e531442426683436210.1016/j.molcel.2019.07.0301:CAS:528:DC%2BC1MXhs1emsr7O
– reference: KingMLMessittTJMowryKLPutting RNAs in the right place at the right time: RNA localization in the frog oocyteBiol. Cell20059719331:CAS:528:DC%2BD2MXhtlSrtL8%3D1560125510.1042/BC20040067
– reference: Farrell, J. A. et al. Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science360, eaar3131 (2018).
– reference: SchierAFTalbotWSMolecular genetics of axis formation in zebrafishAnnu. Rev. Genet.2005395616131:CAS:528:DC%2BD28Xlt1WqsA%3D%3D1628587210.1146/annurev.genet.37.110801.143752
– reference: RodriquesSGSlide-seq: a scalable technology for measuring genome-wide expression at high spatial resolutionScience2019363146314672019Sci...363.1463R1:CAS:528:DC%2BC1MXlvVSmsLw%3D30923225692720910.1126/science.aaw1219
– reference: RothschildSCCaMK-II activation is essential for zebrafish inner ear development and acts through Delta-Notch signalingDev. Biol.20133811791881:CAS:528:DC%2BC3sXhtVWgurrN2374759910.1016/j.ydbio.2013.05.028
– reference: EfremovaMVento-TormoMTeichmannSAVento-TormoRCellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexesNat. Protoc.202015148415061:CAS:528:DC%2BB3cXjvFynsL0%3D3210320410.1038/s41596-020-0292-x
– reference: GrünDKesterLvan OudenaardenAValidation of noise models for single-cell transcriptomicsNat. Methods2014116376402474781410.1038/nmeth.29301:CAS:528:DC%2BC2cXmsVKlsLc%3D
– reference: Qiu, X. et al. Mapping vector field of single cells. Preprint at bioRxiv, https://doi.org/10.1101/696724 (2021).
– reference: CaoJZhouWSteemersFTrapnellCShendureJSci-fate characterizes the dynamics of gene expression in single cellsNat. Biotechnol.2020389809881:CAS:528:DC%2BB3cXmvFylu7k%3D32284584741649010.1038/s41587-020-0480-9
– reference: KimmelCBBallardWWKimmelSRUllmannBSchillingTFStages of embryonic development of the zebrafishDev. Dyn.19952032533101:STN:280:DyaK287nt12qsw%3D%3D858942710.1002/aja.1002030302
– reference: ClaußenMGlobal analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus speciesMol. Biol. Cell2015263777378726337391462606310.1091/mbc.E15-02-01151:CAS:528:DC%2BC28XmsVOmsLs%3D
– reference: Escobar-Aguirre, M., Elkouby, Y. M. & Mullins, M. C. Localization in oogenesis of maternal regulators of embryonic development. Adv. Exp. Med. Biolo.953, 173–207 (2017).
– reference: ClaussenMHorvayKPielerTEvidence for overlapping, but not identical, protein machineries operating in vegetal RNA localization along early and late pathways in Xenopus oocytesDevelopment2004131426342731:CAS:528:DC%2BD2cXotVyju7c%3D1529486310.1242/dev.01283
– reference: EngC-HLTranscriptome-scale super-resolved imaging in tissues by RNA seqFISHNature20195682352392019Natur.568..235E1:CAS:528:DC%2BC1MXmslKksrg%3D30911168654402310.1038/s41586-019-1049-y
– reference: ZappuloARNA localization is a key determinant of neurite-enriched proteomeNat. Commun.201782017NatCo...8..583Z28928394560562710.1038/s41467-017-00690-61:CAS:528:DC%2BC1cXos1KqtLc%3D
– reference: YoonCKawakamiKHopkinsNZebrafish vasa homologue RNA is localized to the cleavage planes of 2- and 4-cell-stage embryos and is expressed in the primordial germ cellsDevelopment1997124315731651:CAS:528:DyaK2sXlvVehs7Y%3D927295610.1242/dev.124.16.3157
– reference: MoorAEGlobal mRNA polarization regulates translation efficiency in the intestinal epitheliumScience2017357129913032017Sci...357.1299M1:CAS:528:DC%2BC2sXhsFWhurfM28798045595521510.1126/science.aan2399
– reference: FazalFMAtlas of subcellular RNA localization revealed by APEX-SeqCell2019178473490.e261:CAS:528:DC%2BC1MXht1Wqt7jJ31230715678677310.1016/j.cell.2019.05.027
– reference: RabaniMPieperLChewG-LSchierAFA massively parallel reporter assay of 3’ UTR sequences identifies in vivo rules for mRNA degradationMol. Cell20176810831094.e51:CAS:528:DC%2BC2sXhvFCisrvO29225039599490710.1016/j.molcel.2017.11.014
– reference: NitzanMKaraiskosNFriedmanNRajewskyNGene expression cartographyNature20195761321372019Natur.576..132N1:CAS:528:DC%2BC1MXitF2qt7nF3174874810.1038/s41586-019-1773-3
– reference: CodeluppiSSpatial organization of the somatosensory cortex revealed by osmFISHNat. Methods2018159329351:CAS:528:DC%2BC1cXitVCks7nK3037736410.1038/s41592-018-0175-z
– reference: KohonenTSelf-organized formation of topologically correct feature mapsBiol. Cybern.19824359696678890466.9200210.1007/BF00337288
– reference: VourekasAAlexiouPVrettosNMaragkakisMMourelatosZSequence-dependent but not sequence-specific piRNA adhesion traps mRNAs to the germ plasmNature20165313903942016Natur.531..390V1:CAS:528:DC%2BC28XjvVGnur0%3D26950602479596310.1038/nature17150
– reference: KosakaKKawakamiKSakamotoHInoueKSpatiotemporal localization of germ plasm RNAs during zebrafish oogenesisMech. Dev.20071242792891:CAS:528:DC%2BD2sXjtVahu7k%3D1729309410.1016/j.mod.2007.01.003
– reference: CangZNieQInferring spatial and signaling relationships between cells from single cell transcriptomic dataNat. Commun.2020112020NatCo..11.2084C1:CAS:528:DC%2BB3cXosVOmu7k%3D32350282719065910.1038/s41467-020-15968-5
– reference: Ciolli MattioliCAlternative 3′ UTRs direct localization of functionally diverse protein isoforms in neuronal compartmentsNucleic Acids Res.201947256025733059074510.1093/nar/gky12701:CAS:528:DC%2BC1MXhs1KrtL7O
– reference: IslamSQuantitative single-cell RNA-seq with unique molecular identifiersNat. Methods2014111631661:CAS:528:DC%2BC3sXhvFOls7zK2436302310.1038/nmeth.2772
– reference: JinSInference and analysis of cell-cell communication using CellChatNat. Commun.2021122021NatCo..12.1088J1:CAS:528:DC%2BB3MXksFSms7c%3D33597522788987110.1038/s41467-021-21246-9
– reference: HeynPThe earliest transcribed zygotic genes are short, newly evolved, and different across speciesCell Rep.201462852921:CAS:528:DC%2BC2cXhs1Khsbo%3D2444071910.1016/j.celrep.2013.12.030
– reference: Holler, K. et al. Spatio-temporal mRNA tracking in the early zebrafish embryo. scSLAM-seq, https://doi.org/10.5281/zenodo.4738464 (2021).
– reference: JambhekarADerisiJLCis-acting determinants of asymmetric, cytoplasmic RNA transportRNA2007136256421:CAS:528:DC%2BD2sXltVaktbY%3D17449729185281110.1261/rna.262607
– reference: HendriksG-JNASC-seq monitors RNA synthesis in single cellsNat. Commun.2019102019NatCo..10.3138H31316066663724010.1038/s41467-019-11028-91:CAS:528:DC%2BC1MXhsVWlt7zL
– reference: ChangPLocalization of RNAs to the mitochondrial cloud in Xenopus oocytes through entrapment and association with endoplasmic reticulumMol. Biol. Cell200415466946811:CAS:528:DC%2BD2cXosVOitLc%3D1529245251915810.1091/mbc.e04-03-0265
– reference: WheelerGNBrändliAWSimple vertebrate models for chemical genetics and drug discovery screens: lessons from zebrafish and XenopusDev. Dyn.2009238128713081:CAS:528:DC%2BD1MXnsF2itr0%3D1944106010.1002/dvdy.21967
– reference: WagnerDESingle-cell mapping of gene expression landscapes and lineage in the zebrafish embryoScience20183609819872018Sci...360..981W1:CAS:528:DC%2BC1cXhtVags77J29700229608344510.1126/science.aar4362
– reference: MoorAEItzkovitzSSpatial transcriptomics: paving the way for tissue-level systems biologyCurr. Opin. Biotechnol.2017461261331:CAS:528:DC%2BC2sXktlyqt7s%3D2834689110.1016/j.copbio.2017.02.004
– reference: BetleyJNFrithMCGraberJHChooSDeshlerJOA ubiquitous and conserved signal for RNA localization in chordatesCurr. Biol.200212175617611:CAS:528:DC%2BD38Xot1ags7g%3D1240117010.1016/S0960-9822(02)01220-4
– reference: KleinAMDroplet barcoding for single-cell transcriptomics applied to embryonic stem cellsCell2015161118712011:CAS:528:DC%2BC2MXpt1SgtL0%3D26000487444176810.1016/j.cell.2015.04.044
– reference: HollerKJunkerJPRNA tomography for spatially resolved transcriptomics (Tomo-Seq)Methods Mol. Biol.201919201291411:CAS:528:DC%2BC1MXitVyrsrnM3073769010.1007/978-1-4939-9009-2_9
– volume: 203
  start-page: 253
  year: 1995
  ident: 23834_CR30
  publication-title: Dev. Dyn.
  doi: 10.1002/aja.1002030302
– volume: 108
  start-page: 289
  year: 1990
  ident: 23834_CR31
  publication-title: Development
  doi: 10.1242/dev.108.2.289
– volume: 11
  year: 2020
  ident: 23834_CR56
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-020-15968-5
– volume: 430
  start-page: 275
  year: 2017
  ident: 23834_CR2
  publication-title: Dev. Biol.
  doi: 10.1016/j.ydbio.2017.06.029
– volume: 11
  start-page: 637
  year: 2014
  ident: 23834_CR73
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.2930
– ident: 23834_CR1
  doi: 10.1007/978-3-319-46095-6_5
– volume: 328
  start-page: 80
  year: 1987
  ident: 23834_CR42
  publication-title: Nature
  doi: 10.1038/328080a0
– volume: 12
  start-page: 1756
  year: 2002
  ident: 23834_CR46
  publication-title: Curr. Biol.
  doi: 10.1016/S0960-9822(02)01220-4
– volume: 178
  start-page: 473
  year: 2019
  ident: 23834_CR20
  publication-title: Cell
  doi: 10.1016/j.cell.2019.05.027
– volume: 161
  start-page: 1187
  year: 2015
  ident: 23834_CR5
  publication-title: Cell
  doi: 10.1016/j.cell.2015.04.044
– volume: 27
  start-page: 1653
  year: 2011
  ident: 23834_CR52
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btr261
– volume: 105
  start-page: 14885
  year: 2008
  ident: 23834_CR63
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.0803169105
– volume: 357
  start-page: 1299
  year: 2017
  ident: 23834_CR60
  publication-title: Science
  doi: 10.1126/science.aan2399
– volume: 119
  start-page: 1161
  year: 1993
  ident: 23834_CR41
  publication-title: Development
  doi: 10.1242/dev.119.4.1161
– volume: 144
  start-page: 292
  year: 2017
  ident: 23834_CR44
  publication-title: Development
  doi: 10.1242/dev.139220
– volume: 4
  start-page: 690
  year: 2003
  ident: 23834_CR38
  publication-title: Nat. Rev. Genet.
  doi: 10.1038/nrg1154
– ident: 23834_CR69
  doi: 10.5281/zenodo.4738464
– volume: 360
  start-page: 981
  year: 2018
  ident: 23834_CR7
  publication-title: Science
  doi: 10.1126/science.aar4362
– volume: 560
  start-page: 494
  year: 2018
  ident: 23834_CR22
  publication-title: Nature
  doi: 10.1038/s41586-018-0414-6
– volume: 26
  start-page: 3777
  year: 2015
  ident: 23834_CR43
  publication-title: Mol. Biol. Cell
  doi: 10.1091/mbc.E15-02-0115
– ident: 23834_CR10
  doi: 10.1126/science.aaq1723
– volume: 47
  start-page: 2560
  year: 2019
  ident: 23834_CR61
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gky1270
– volume: 159
  start-page: 662
  year: 2014
  ident: 23834_CR14
  publication-title: Cell
  doi: 10.1016/j.cell.2014.09.038
– volume: 80
  start-page: 1
  year: 2015
  ident: 23834_CR21
  publication-title: Cold Spring Harb. Symp. Quant. Biol.
  doi: 10.1101/sqb.2015.80.027201
– ident: 23834_CR26
  doi: 10.1101/696724
– volume: 161
  start-page: 1202
  year: 2015
  ident: 23834_CR6
  publication-title: Cell
  doi: 10.1016/j.cell.2015.05.002
– volume: 124
  start-page: 3157
  year: 1997
  ident: 23834_CR37
  publication-title: Development
  doi: 10.1242/dev.124.16.3157
– volume: 48
  start-page: D650
  year: 2019
  ident: 23834_CR72
  publication-title: Nucleic Acids Res.
  doi: 10.1093/nar/gkz813
– ident: 23834_CR68
  doi: 10.5281/zenodo.4738513
– volume: 568
  start-page: 235
  year: 2019
  ident: 23834_CR16
  publication-title: Nature
  doi: 10.1038/s41586-019-1049-y
– volume: 566
  start-page: 496
  year: 2019
  ident: 23834_CR9
  publication-title: Nature
  doi: 10.1038/s41586-019-0969-x
– volume: 131
  start-page: 4263
  year: 2004
  ident: 23834_CR40
  publication-title: Development
  doi: 10.1242/dev.01283
– volume: 15
  start-page: 4669
  year: 2004
  ident: 23834_CR54
  publication-title: Mol. Biol. Cell
  doi: 10.1091/mbc.e04-03-0265
– volume: 61
  start-page: 821
  year: 2016
  ident: 23834_CR49
  publication-title: Mol. Cell
  doi: 10.1016/j.molcel.2016.01.020
– volume: 45
  start-page: 357
  year: 2011
  ident: 23834_CR32
  publication-title: Annu. Rev. Genet.
  doi: 10.1146/annurev-genet-110410-132517
– volume: 75
  start-page: 875
  year: 2019
  ident: 23834_CR19
  publication-title: Mol. Cell
  doi: 10.1016/j.molcel.2019.07.030
– volume: 11
  start-page: 163
  year: 2014
  ident: 23834_CR4
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.2772
– volume: 116
  start-page: 19490
  year: 2019
  ident: 23834_CR17
  publication-title: Proc. Natl Acad. Sci. USA
  doi: 10.1073/pnas.1912459116
– volume: 68
  start-page: 1083
  year: 2017
  ident: 23834_CR53
  publication-title: Mol. Cell
  doi: 10.1016/j.molcel.2017.11.014
– volume: 15
  start-page: 932
  year: 2018
  ident: 23834_CR18
  publication-title: Nat. Methods
  doi: 10.1038/s41592-018-0175-z
– volume: 124
  start-page: 279
  year: 2007
  ident: 23834_CR48
  publication-title: Mech. Dev.
  doi: 10.1016/j.mod.2007.01.003
– volume: 17
  start-page: 991
  year: 2020
  ident: 23834_CR27
  publication-title: Nat. Methods
  doi: 10.1038/s41592-020-0935-4
– volume: 8
  year: 2017
  ident: 23834_CR62
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-017-00690-6
– volume: 6
  start-page: 285
  year: 2014
  ident: 23834_CR36
  publication-title: Cell Rep.
  doi: 10.1016/j.celrep.2013.12.030
– volume: 531
  start-page: 390
  year: 2016
  ident: 23834_CR65
  publication-title: Nature
  doi: 10.1038/nature17150
– ident: 23834_CR8
  doi: 10.1126/science.aar3131
– volume: 358
  start-page: 64
  year: 2017
  ident: 23834_CR11
  publication-title: Science
  doi: 10.1126/science.aan6827
– volume: 14
  start-page: 1198
  year: 2017
  ident: 23834_CR35
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.4435
– volume: 17
  year: 2016
  ident: 23834_CR3
  publication-title: Genome Biol.
  doi: 10.1186/s13059-016-0938-8
– volume: 571
  start-page: 419
  year: 2019
  ident: 23834_CR23
  publication-title: Nature
  doi: 10.1038/s41586-019-1369-y
– volume: 51
  start-page: 146
  year: 2010
  ident: 23834_CR66
  publication-title: Methods
  doi: 10.1016/j.ymeth.2010.02.016
– volume: 1920
  start-page: 129
  year: 2019
  ident: 23834_CR15
  publication-title: Methods Mol. Biol.
  doi: 10.1007/978-1-4939-9009-2_9
– volume: 97
  start-page: 19
  year: 2005
  ident: 23834_CR55
  publication-title: Biol. Cell
  doi: 10.1042/BC20040067
– volume: 10
  year: 2019
  ident: 23834_CR24
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-019-11028-9
– volume: 363
  start-page: 1463
  year: 2019
  ident: 23834_CR13
  publication-title: Science
  doi: 10.1126/science.aaw1219
– volume: 238
  start-page: 1287
  year: 2009
  ident: 23834_CR74
  publication-title: Dev. Dyn.
  doi: 10.1002/dvdy.21967
– volume: 5
  start-page: 13
  year: 2014
  ident: 23834_CR33
  publication-title: Bioarchitecture
  doi: 10.1080/19490992.2015.1080891
– volume: 136
  start-page: 719
  year: 2009
  ident: 23834_CR64
  publication-title: Cell
  doi: 10.1016/j.cell.2009.01.044
– volume: 43
  start-page: 59
  year: 1982
  ident: 23834_CR29
  publication-title: Biol. Cybern.
  doi: 10.1007/BF00337288
– volume: 13
  start-page: 625
  year: 2007
  ident: 23834_CR47
  publication-title: RNA
  doi: 10.1261/rna.262607
– volume: 576
  start-page: 132
  year: 2019
  ident: 23834_CR57
  publication-title: Nature
  doi: 10.1038/s41586-019-1773-3
– volume: 38
  start-page: 980
  year: 2020
  ident: 23834_CR28
  publication-title: Nat. Biotechnol.
  doi: 10.1038/s41587-020-0480-9
– volume: 39
  start-page: 561
  year: 2005
  ident: 23834_CR34
  publication-title: Annu. Rev. Genet.
  doi: 10.1146/annurev.genet.37.110801.143752
– volume: 14
  start-page: 201
  year: 2017
  ident: 23834_CR51
  publication-title: Nat. Methods
  doi: 10.1038/nmeth.4121
– volume: 15
  start-page: 1484
  year: 2020
  ident: 23834_CR70
  publication-title: Nat. Protoc.
  doi: 10.1038/s41596-020-0292-x
– volume: 46
  start-page: 126
  year: 2017
  ident: 23834_CR12
  publication-title: Curr. Opin. Biotechnol.
  doi: 10.1016/j.copbio.2017.02.004
– volume: 3
  start-page: 59
  year: 2008
  ident: 23834_CR67
  publication-title: Nat. Protoc.
  doi: 10.1038/nprot.2007.514
– volume: 12
  year: 2021
  ident: 23834_CR71
  publication-title: Nat. Commun.
  doi: 10.1038/s41467-021-21246-9
– volume: 12
  start-page: 454
  year: 2002
  ident: 23834_CR39
  publication-title: Curr. Biol.
  doi: 10.1016/S0960-9822(02)00723-6
– volume: 8
  year: 2018
  ident: 23834_CR45
  publication-title: Sci. Rep.
  doi: 10.1038/s41598-018-26592-1
– volume: 28
  start-page: 511
  year: 2010
  ident: 23834_CR50
  publication-title: Nat. Biotechnol.
  doi: 10.1038/nbt.1621
– volume: 381
  start-page: 179
  year: 2013
  ident: 23834_CR75
  publication-title: Dev. Biol.
  doi: 10.1016/j.ydbio.2013.05.028
– volume: 367
  start-page: 1151
  year: 2020
  ident: 23834_CR25
  publication-title: Science
  doi: 10.1126/science.aax3072
– volume: 131
  start-page: 174
  year: 2007
  ident: 23834_CR59
  publication-title: Cell
  doi: 10.1016/j.cell.2007.08.003
– ident: 23834_CR58
  doi: 10.7554/eLife.05003
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Snippet Early stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by...
Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a...
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Animals
Cell Tracking - methods
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Embryo, Nonmammalian - embryology
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Embryos
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Gastrulation
Gene expression
Gene Expression Regulation, Developmental
Gene sequencing
Germ cells
Humanities and Social Sciences
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Oocytes - metabolism
Ribonucleic acid
RNA
RNA transport
RNA, Messenger - genetics
RNA, Messenger - metabolism
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Science (multidisciplinary)
Single-Cell Analysis - methods
Spatial analysis
Spatial discrimination
Spatio-Temporal Analysis
Species Specificity
Tracking
Transcriptome - genetics
Transcriptomes
Transcriptomics
Wildlife conservation
Xenopus - embryology
Xenopus - genetics
Xenopus laevis - embryology
Xenopus laevis - genetics
Zebrafish
Zebrafish - embryology
Zebrafish - genetics
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Title Spatio-temporal mRNA tracking in the early zebrafish embryo
URI https://link.springer.com/article/10.1038/s41467-021-23834-1
https://www.ncbi.nlm.nih.gov/pubmed/34099733
https://www.proquest.com/docview/2537860789
https://www.proquest.com/docview/2539212619
https://pubmed.ncbi.nlm.nih.gov/PMC8184788
https://doaj.org/article/ccde7f9fb6194c37951752ef36e5cf99
Volume 12
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