|
| Status |
Public on Jan 04, 2022 |
| Title |
Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [ChIP-seq] |
| Organism |
Danio rerio |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal how developmental gene poising is established de novo in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with ‘Placeholder’ nucleosomes (bearing H2A.Z, H3K4me1, and H3K27ac), and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 (PRC1), and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA, H2Aub1 enables Aebp2-containing PRC2 recruitment and H3K27me3 deposition. Notably, preventing H2Aub1 (via Rnf2 inhibition) eliminates recruitment of Aebp2-PRC2 and H3K27me3, and elicits transcriptional upregulation of certain developmental genes during ZGA. However, upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together, we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos.
|
| |
|
| Overall design |
ChIP-seq of histone marks/variant, Polycomb group proteins, and Jarid2 in early Zebrafish embryos.
|
| |
|
| Contributor(s) |
Hickey GJ, Cairns BR |
| Citation(s) |
34982026 |
| Submission date |
Mar 05, 2021 |
| Last update date |
Jan 28, 2022 |
| Contact name |
Graham James McGuire Hickey |
| E-mail(s) |
graham.hickey@hci.utah.edu
|
| Organization name |
University of Utah
|
| Department |
Oncological Sciences
|
| Lab |
Cairns Lab
|
| Street address |
2000 Circle of Hope Drive
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL18413 |
Illumina HiSeq 2500 (Danio rerio) |
| GPL24995 |
Illumina NovaSeq 6000 (Danio rerio) |
|
| Samples (58)
|
|
| This SubSeries is part of SuperSeries: |
| GSE168362 |
Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos |
|
| Relations |
| BioProject |
PRJNA707028 |
| SRA |
SRP309489 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE168360_Aebp2_4.3hpf_ChIP.bw |
756.9 Mb |
(ftp)(http) |
BW |
| GSE168360_Aebp2_4.3hpf_ChIP.narrowPeak.gz |
1.5 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_Aebp2_DMSO_4hpf_ChIP.bw |
718.9 Mb |
(ftp)(http) |
BW |
| GSE168360_Aebp2_DMSO_4hpf_ChIP.narrowPeak.gz |
1.4 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_Aebp2_PRT4165_4hpf_ChIP.bw |
52.4 Mb |
(ftp)(http) |
BW |
| GSE168360_Aebp2_PRT4165_4hpf_ChIP.narrowPeak.gz |
652.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_H2Aub1_4.3hpf_ChIP.narrowPeak.gz |
3.2 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_H2Aub1_ZGA_ChIP.narrowPeak.gz |
327.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_H2Aub1_preZGA_ChIP.narrowPeak.gz |
897.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_H2Aub_2.5hpf_ChIP.bw |
527.3 Mb |
(ftp)(http) |
BW |
| GSE168360_H2Aub_3.5_ChIP.bw |
247.3 Mb |
(ftp)(http) |
BW |
| GSE168360_H2Aub_4.3hpf_ChIP.bw |
1.0 Gb |
(ftp)(http) |
BW |
| GSE168360_H2Az_3.5hpf_ChIP.bw |
860.7 Mb |
(ftp)(http) |
BW |
| GSE168360_H2Az_3.5hpf_ChIP.narrowPeak.gz |
1.9 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_H3K27me3_4hpf_DMSO_ChIP.bw |
251.5 Mb |
(ftp)(http) |
BW |
| GSE168360_H3K27me3_4hpf_DMSO_ChIP.narrowPeak.gz |
490.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_H3K27me3_4hpf_PRT4165_ChIP.bw |
27.3 Mb |
(ftp)(http) |
BW |
| GSE168360_H3K27me3_4hpf_PRT4165_ChIP.narrowPeak.gz |
12.6 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_H3K4me1_3.5hpf_ChIP.bw |
534.1 Mb |
(ftp)(http) |
BW |
| GSE168360_H3K4me1_3.5hpf_ChIP.narrowPeak.gz |
2.2 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_Jarid2_4.3hpf_ChIP.bw |
906.7 Mb |
(ftp)(http) |
BW |
| GSE168360_Jarid2_4.3hpf_ChIP.narrowPeak.gz |
801.6 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_Rnf2_2.5hpf_ChIP.bw |
394.0 Mb |
(ftp)(http) |
BW |
| GSE168360_Rnf2_2.5hpf_ChIP.narrowPeak.gz |
376.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_Rnf2_3.5hpf_ChIP.bw |
333.4 Mb |
(ftp)(http) |
BW |
| GSE168360_Rnf2_3.5hpf_ChIP.narrowPeak.gz |
1.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE168360_Rnf2_4.3hpf_ChIP.bw |
789.1 Mb |
(ftp)(http) |
BW |
| GSE168360_Rnf2_4.3hpf_ChIP.narrowPeak.gz |
757.8 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...