|
| Status |
Public on Mar 27, 2023 |
| Title |
Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis |
| Organism |
Xenopus tropicalis |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Histone acetylation is a pivotal epigenetic modification that controls chromatin structures and regulates gene expression. It plays an essential role in modulating zygotic transcription and cell lineage specification of developing embryos. While the outcomes of many inductive signals have been described to require enzymatic activities of histone acetyltransferases and deacetylases (HDACs), the mechanisms by which HDACs confines the utilization of the zygotic genome are not well-characterized. Here, we show that histone deacetylase 1 (Hdac1) progressively binds to the zygotic genome from early blastula and onward. The recruitment of Hdac1 to the genome at the blastula stage is instructed maternally. Cis-regulatory modules (CRMs) bound by Hdac1 possess distinctive epigenetic signatures. We highlight a dual functional model of Hdac1 where Hdac1 not only sustains a histone hypoacetylation state on inactive chromatin but also participates in dynamic histone acetylation cycles on active chromatin. As a result, Hdac1 maintains differential histone acetylation states of bound CRMs between different germ layers and reinforces the transcriptional program underlying cell lineage identities both in time and space. Taken together, our study reveals a comprehensive role of Hdac1 during early vertebrate embryogenesis.
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| |
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| Overall design |
Examination of Hdac1, Hdac2, Sox3, H3K18ac, pan-H3Kac bindings in Xenopus tropicalis early embryos; Examination of gene expression changes due to HDAC inhibition by TSA, VPA in Xenopus tropicalis gastrulae
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| |
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| Contributor(s) |
Cho KW, Zhou JJ |
| Citation(s) |
36971347 |
| |
| Submission date |
Mar 10, 2022 |
| Last update date |
May 02, 2023 |
| Contact name |
Ken Cho |
| E-mail(s) |
kwcho@uci.edu
|
| Organization name |
University of California, Irvine
|
| Street address |
University of California, Irvine
|
| City |
Irvine |
| ZIP/Postal code |
92617 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL23182 |
Illumina HiSeq 4000 (Xenopus tropicalis) |
| GPL30018 |
Illumina NovaSeq 6000 (Xenopus tropicalis) |
|
| Samples (45)
|
|
| Relations |
| BioProject |
PRJNA814725 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE198378_RAW.tar |
16.0 Mb |
(http)(custom) |
TAR (of NARROWPEAK, RESULTS) |
| GSE198378_final.GSE198378_st105_hdac1_we_IDR0.05_in_merged_peaks.narrowPeak.gz |
580.5 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE198378_final.GSE198378_st9_hdac1_we_IDR0.05_in_merged_peaks.narrowPeak.gz |
119.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE198378_final.st8_hdac1_we_IDR0.05_in_merged_peaks.narrowPeak.gz |
27.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE198378_st105_panh3kac_ac_dmso_overlap2reps_peaks.narrowPeak.gz |
616.1 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE198378_st105_panh3kac_vg_dmso_overlap2reps_peaks.narrowPeak.gz |
590.6 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE198378_st105_panh3kac_we_overlap2reps_peaks.narrowPeak.gz |
697.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE198378_st9_sox3_we_idr_0.05_filtered_peaks.narrowPeak.gz |
630.5 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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