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| Status |
Public on Jul 27, 2023 |
| Title |
Accessibility and activity of transcriptional regulatory elements during sea urchin embryogenesis and differentiation [ATAC-seq] |
| Organism |
Strongylocentrotus purpuratus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
Transcriptional regulatory elements (TREs) are the primary nodes of the gene regulatory networks that control development. TREs are identified by PRO-seq and their accessibility by ATAC-seq during sea urchin embryonic development and differentiation. Our analysis identifies surprisingly early accessibility in 4-cell cleavage embryo TREs that is not necessarily followed by subsequent transcription, and an excess of ATAC-seq peaks transcriptionally disengaged during the stages analyzed. Embryonic accessibility shifts are driven by transcriptionally engaged TREs, and PRO-seq transcriptional differences at TREs provide more contrast among embryonic stages than ATAC-seq accessibility differences. TRE accessibility reaches a maximum around the 20-hour late blastula, which coincides with major embryo regionalizations. At the same time, a large number of distal TREs become transcriptionally disengaged, in support of an early Pol II primed model for developmental gene regulation that eventually resolves in transcriptional activation or silencing. A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during early embryogenesis.
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| Overall design |
Chromatin accesibility during early embryogenesis is characterized by ATAC-seq or OmniATAC and transcriptional engagement by PRO-seq or qPROseq. All reads are mapped to the Sp5.0 version of the Strongylocentrotus purpuratus genome.
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| Contributor(s) |
Arenas-Mena C |
| Citation missing |
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| |
| Submission date |
Jun 05, 2023 |
| Last update date |
Jul 28, 2023 |
| Contact name |
Cesar Arenas-Mena |
| E-mail(s) |
cesar.arenasmena@csi.cuny.edu
|
| Organization name |
CSI CUNY
|
| Department |
Biology
|
| Street address |
2800 Victory Boulevard
|
| City |
Staten Island |
| State/province |
New York |
| ZIP/Postal code |
10314 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL20965 |
Illumina HiSeq 2500 (Strongylocentrotus purpuratus) |
| GPL23218 |
Illumina NextSeq 500 (Strongylocentrotus purpuratus) |
|
| Samples (15)
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| This SubSeries is part of SuperSeries: |
| GSE234143 |
Widespread priming of transcriptional regulatory elements by incipient accessibility or Pol II pause in early embryos of the sea urchin Strongylocentrotus purpuratus |
|
| Relations |
| BioProject |
PRJNA980192 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE234139_12h_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
| GSE234139_20h_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
| GSE234139_72h19_72h_72hM_2022_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
| GSE234139_8C_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
| GSE234139_8h_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed.gz |
1.5 Mb |
(ftp)(http) |
BED |
| GSE234139_ATAC_12h6_ATAC12h7_RPM.bw |
289.2 Mb |
(ftp)(http) |
BW |
| GSE234139_ATAC_20h1_1_20h2_1.merged.sort_RPM.bw |
210.6 Mb |
(ftp)(http) |
BW |
| GSE234139_ATAC_72h19_72h_72M__merged_RPM.bw |
295.2 Mb |
(ftp)(http) |
BW |
| GSE234139_ATAC_8C5h7_4CD227A8_merged_sort_RPM.bw |
361.0 Mb |
(ftp)(http) |
BW |
| GSE234139_ATAC_8h521_ATAC8h529_RPM.bw |
167.2 Mb |
(ftp)(http) |
BW |
| GSE234139_ATAC_RSCnB1_1_RSCnB2_1_merged_sort_RPM.bw |
222.5 Mb |
(ftp)(http) |
BW |
| GSE234139_A_72h_22_1_72h_22_2_merged_sort_RPM.bw |
265.4 Mb |
(ftp)(http) |
BW |
| GSE234139_RAW.tar |
408.4 Mb |
(http)(custom) |
TAR (of BW, NARROWPEAK) |
| GSE234139_RSCn_B1_B2_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak_merge_sort.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
| GSE234139_RSCo_T1_T2_2022_5.0_rep.pooled.pval0.01.300K.narrowPeak.gz |
4.6 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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