Lee et al. 2013 (PRJNA206070)

General Details

Title Nanog, SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal-to-zygotic transition
Organism
Number of Samples 60
Release Date 2013/05/31 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP023492
ENA SRP023492
GEO GSE47558
BioProject PRJNA206070

Publication

Title
Authors Lee MT,Bonneau AR,Takacs CM,Bazzini AA,DiVito KR,Fleming ES,Giraldez AJ
Journal Nature
Publication Date 2013 Nov 21
Abstract After fertilization, maternal factors direct development and trigger zygotic genome activation (ZGA) at the maternal-to-zygotic transition (MZT). In zebrafish, ZGA is required for gastrulation and clearance of maternal messenger RNAs, which is in part regulated by the conserved microRNA miR-430. However, the factors that activate the zygotic program in vertebrates are unknown. Here we show that Nanog, Pou5f1 (also called Oct4) and SoxB1 regulate zygotic gene activation in zebrafish. We identified several hundred genes directly activated by maternal factors, constituting the first wave of zygotic transcription. Ribosome profiling revealed that nanog, sox19b and pou5f1 are the most highly translated transcription factors pre-MZT. Combined loss of these factors resulted in developmental arrest before gastrulation and a failure to activate >75% of zygotic genes, including miR-430. Our results demonstrate that maternal Nanog, Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and induce clearance of the maternal program by activating miR-430 expression.
PMC PMC3925760
PMID 24056933
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR870722 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870723 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870724 PRJNA206070 Danio rerio RNA-Seq
SRR870725 PRJNA206070 Danio rerio RNA-Seq
SRR870726 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870727 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870728 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870729 PRJNA206070 Danio rerio RNA-Seq alpha-amanitin
SRR870730 PRJNA206070 Danio rerio U2OS RNA-Seq
SRR870731 PRJNA206070 Danio rerio RNA-Seq
SRR870732 PRJNA206070 Danio rerio RNA-Seq
SRR870733 PRJNA206070 Danio rerio RNA-Seq
SRR870734 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870735 PRJNA206070 Danio rerio RNA-Seq
SRR870736 PRJNA206070 Danio rerio RNA-Seq
SRR870737 PRJNA206070 Danio rerio RNA-Seq
SRR870738 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870739 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870740 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870741 PRJNA206070 Danio rerio RNA-Seq alpha-amanitin
SRR870742 PRJNA206070 Danio rerio RNA-Seq Cycloheximide
SRR870743 PRJNA206070 Danio rerio RNA-Seq
SRR870744 PRJNA206070 Danio rerio RNA-Seq
SRR870745 PRJNA206070 Danio rerio RNA-Seq
SRR870746 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870758 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870759 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870760 PRJNA206070 Danio rerio RNA-Seq
SRR870761 PRJNA206070 Danio rerio RNA-Seq
SRR870794 PRJNA206070 Danio rerio U2OS RNA-Seq untreated
SRR870795 PRJNA206070 Danio rerio U2OS RNA-Seq untreated
SRR870796 PRJNA206070 Danio rerio U2OS RNA-Seq
SRR870797 PRJNA206070 Danio rerio U2OS RNA-Seq
SRR870830 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870831 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870832 PRJNA206070 Danio rerio RNA-Seq
SRR870833 PRJNA206070 Danio rerio RNA-Seq
SRR870866 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870867 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870868 PRJNA206070 Danio rerio RNA-Seq
SRR870869 PRJNA206070 Danio rerio RNA-Seq
SRR870902 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870903 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870904 PRJNA206070 Danio rerio RNA-Seq
SRR870905 PRJNA206070 Danio rerio RNA-Seq
SRR870938 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870939 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870940 PRJNA206070 Danio rerio RNA-Seq
SRR870941 PRJNA206070 Danio rerio RNA-Seq
SRR870974 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870975 PRJNA206070 Danio rerio RNA-Seq untreated
SRR870976 PRJNA206070 Danio rerio RNA-Seq
SRR870977 PRJNA206070 Danio rerio RNA-Seq
SRR959336 PRJNA206070 Danio rerio RNA-Seq untreated
SRR959337 PRJNA206070 Danio rerio RNA-Seq untreated
SRR959338 PRJNA206070 Danio rerio RNA-Seq
SRR959339 PRJNA206070 Danio rerio RNA-Seq
SRR959372 PRJNA206070 Danio rerio RNA-Seq untreated
SRR959373 PRJNA206070 Danio rerio RNA-Seq untreated
SRR10295266 PRJNA206070 Danio rerio RNA-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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