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GEO Series: GSE122551

Title: The Spatio-Temporal Control of Zygotic Genome Activation

Summary

One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the mid-blastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation, and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal and BMP signaling together generate most of the spatio-temporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.


Contributors: George Gentsch, George Gentsch, James Smith

Experiment Type: This study generated four 4sU-Seq samples and 48 RNA-Seq samples.

Experiment Reagents: 1062368-24-4, ctnnb1 MO2, eomes MO1,

Article: XB-ART-56693, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
Input WE - NF10.25 GSM3473723  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
   WE - NF10.25 DEG GSM3473721  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
Input WE - NF8 GSM3473722  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
   WE - NF8 DEG GSM3473720  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WT + hbg1 cMO - NF12 GSM3473768  GSM3473769  GSM3473770  GSM3473771  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection   hbg1 NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12  
   WE + eomes MO + vegt MO + tbxt MO + tbxt.2 MO - NF12 DEG GSM3473756  GSM3473757  GSM3473758  GSM3473759  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection vegt MO3 vegt NF stage 1 zygote
morpholino injection tbxt.2 MO4 tbxt.2 NF stage 1 zygote
morpholino injection tbxt.2 MO3 tbxt.2 NF stage 1 zygote
morpholino injection tbxt MO3 tbxt NF stage 1 zygote
morpholino injection tbxt MO2 tbxt NF stage 1 zygote
morpholino injection eomes MO1 eomes NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12  
WT + hbg1 cMO - NF11 GSM3473764  GSM3473765  GSM3473766  GSM3473767  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection   hbg1 NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
   WE + eomes MO + vegt MO + tbxt MO + tbxt.2 MO - NF11 DEG GSM3473752  GSM3473753  GSM3473754  GSM3473755  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection vegt MO3 vegt NF stage 1 zygote
morpholino injection tbxt.2 MO4 tbxt.2 NF stage 1 zygote
morpholino injection tbxt.2 MO3 tbxt.2 NF stage 1 zygote
morpholino injection tbxt MO3 tbxt NF stage 1 zygote
morpholino injection tbxt MO2 tbxt NF stage 1 zygote
morpholino injection eomes MO1 eomes NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
WT + hbg1 cMO - NF10.25 GSM3473760  GSM3473761  GSM3473762  GSM3473763  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection   hbg1 NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
   WE + eomes MO + vegt MO + tbxt MO + tbxt.2 MO - NF10.25 DEG GSM3473748  GSM3473749  GSM3473750  GSM3473751  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection vegt MO3 vegt NF stage 1 zygote
morpholino injection tbxt.2 MO4 tbxt.2 NF stage 1 zygote
morpholino injection tbxt.2 MO3 tbxt.2 NF stage 1 zygote
morpholino injection tbxt MO3 tbxt NF stage 1 zygote
morpholino injection tbxt MO2 tbxt NF stage 1 zygote
morpholino injection eomes MO1 eomes NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
WE - NF9 GSM3473736  GSM3473737  GSM3473738  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + LDN193189 - NF9 DEG GSM3473742  GSM3473743  GSM3473744  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical 1062368-24-4 NF stage 4 (8-cell) embryo
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + SB431542 + LDN193189 - NF9 DEG GSM3473745  GSM3473746  GSM3473747  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical SB431542 NF stage 4 (8-cell) embryo
chemical 1062368-24-4 NF stage 4 (8-cell) embryo
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + SB431542 - NF9 DEG GSM3473739  GSM3473740  GSM3473741  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical SB431542 NF stage 4 (8-cell) embryo
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + ctnnb1 MO + LDN193189 + SB431542 - NF9 DEG GSM3473733  GSM3473734  GSM3473735  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 1 zygote
chemical 1062368-24-4 NF stage 4 (8-cell) embryo
chemical SB431542 NF stage 4 (8-cell) embryo
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + ctnnb1 MO + LDN193189 - NF9 DEG GSM3473730  GSM3473731  GSM3473732  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 1 zygote
chemical 1062368-24-4 NF stage 4 (8-cell) embryo
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + ctnnb1 MO + SB431542 - NF9 DEG GSM3473727  GSM3473728  GSM3473729  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 1 zygote
chemical SB431542 NF stage 4 (8-cell) embryo
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + ctnnb1 MO - NF9 DEG GSM3473724  GSM3473725  GSM3473726  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
Select All DEG      Select All 
Xtr   
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