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Series GSE199801 Query DataSets for GSE199801
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.
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.
Contributor(s) Hughes A, Klose RJ
Citation(s) 36759609
Submission date Mar 30, 2022
Last update date Mar 02, 2023
Contact name Emilia Dimitrova
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
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)
GSM5986722 T7SET1AChIP_Rep1_0hr
GSM5986723 T7SET1AChIP_Rep1_2hr
GSM5986724 T7SET1AChIP_Rep2_0hr
This SubSeries is part of SuperSeries:
GSE199805 A CpG island-encoded mechanism protects genes from premature transcription termination
BioProject PRJNA821514

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource 138.6 Mb (ftp)(http) BW 133.4 Mb (ftp)(http) BW 125.9 Mb (ftp)(http) BW 100.0 Mb (ftp)(http) BW 480.8 Mb (ftp)(http) BW 484.3 Mb (ftp)(http) BW 554.9 Mb (ftp)(http) BW 559.5 Mb (ftp)(http) BW 366.9 Mb (ftp)(http) 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
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