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| Status |
Public on Dec 22, 2022 |
| Title |
A CpG island-encoded mechanism protects genes from premature transcription termination [SET1_ChIPseq] |
| Organisms |
Drosophila melanogaster; Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Transcription must be highly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, we reveal that actively transcribed CpG island-associated gene promoters recruit SET1 chromatin modifying complexes to enable gene expression. Counterintuitively, this effect is independent of SET1 complex histone modifying activity, and instead relies on the capacity of these complexes to interact with the RNA Polymerase II-binding protein, WDR82. Unexpectedly, we discover that SET1 complexes sustain gene transcription by counteracting the activity of the ZC3H4/WDR82 protein complex, which we show can pervasively terminate both genic and extragenic transcription. Therefore, we discover a new gene regulatory mechanism whereby CpG island elements nucleate a protein complex that protects genic transcription from premature termination, effectively distinguishing genic from non-genic transcription to enable gene expression.
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| Overall design |
The genomic distribution of SET1A was profiled in dTAG-SET1A ESCs, in which SET1A can be conditionally depleted. The genomic distribution of H3K4me3 and RNA Pol II was profiled in dTAG-SET1A/B ESCs, in which both SET1A and SET1B can be conditionally depleted. The genomic distribution of ZC3H4 was profiled in untreated ESCs.
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| Contributor(s) |
Hughes A, Klose RJ |
| Citation(s) |
36759609 |
| |
| Submission date |
Mar 30, 2022 |
| Last update date |
Mar 02, 2023 |
| Contact name |
Emilia Dimitrova |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Oxford
|
| Department |
Biochemistry
|
| Lab |
Rob Klose
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3QU |
| Country |
United Kingdom |
| |
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| Platforms (3) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
| GPL25537 |
Illumina NextSeq 500 (Drosophila melanogaster; Mus musculus) |
|
| Samples (60)
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| This SubSeries is part of SuperSeries: |
| GSE199805 |
A CpG island-encoded mechanism protects genes from premature transcription termination |
|
| Relations |
| BioProject |
PRJNA821514 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE199801_SET1ABH3K4me30hrdownsampledMERGE.bw |
138.6 Mb |
(ftp)(http) |
BW |
| GSE199801_SET1ABH3K4me324hrdownsampledMERGE.bw |
133.4 Mb |
(ftp)(http) |
BW |
| GSE199801_SET1ABH3K4me32hrdownsampledMERGE.bw |
125.9 Mb |
(ftp)(http) |
BW |
| GSE199801_SET1ABH3K4me34hrdownsampledMERGE.bw |
100.0 Mb |
(ftp)(http) |
BW |
| GSE199801_SET1ABRNAPIINTD0hr.bw |
480.8 Mb |
(ftp)(http) |
BW |
| GSE199801_SET1ABRNAPIINTD2hr.bw |
484.3 Mb |
(ftp)(http) |
BW |
| GSE199801_SET1AB_ZC3H4ChIP_0hr.bw |
554.9 Mb |
(ftp)(http) |
BW |
| GSE199801_SET1AB_ZC3H4ChIP_2hr.bw |
559.5 Mb |
(ftp)(http) |
BW |
| GSE199801_T7SET1AChIP_0hrMERGE.bw |
366.9 Mb |
(ftp)(http) |
BW |
| GSE199801_T7SET1AChIP_2hrMERGE.bw |
437.2 Mb |
(ftp)(http) |
BW |
| GSE199801_dTAGSET1AB_H3K4me3_TSSPeaks.bed.gz |
198.1 Kb |
(ftp)(http) |
BED |
| GSE199801_dTAGSET1AB_H3K4me3_deseq2.csv.gz |
4.1 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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