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Series GSE69738 Query DataSets for GSE69738
Status Public on Jun 10, 2018
Title Gene body H2B1ub regulates RNA Polymerase II pause release and is not needed for transcription elongation
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Histone H2B monoubiquitylation (H2Bub1) is localized to transcribed regions of genes and spread in parallel with the progress of RNA polymerase II (Pol II). H2Bub1 levels are highly correlated both with transcription and elongation rates of mammalian genes. Although H2Bub1 correlate with elongation rates, it is not clear whether the correlation is due to causative role of H2Bub1 in regulating elongation rate or the vice versa.
By utilizing our recently developed method to measure genomewide elongation rate – 4sUDRB-seq, we tested genomewide elongation rates in H2Bub1 depleted cells. Our results show that H2Bub1, although widely appreciate as an elongation factor, is not needed for proper transcription elongation. Although H2Bub1 depletion does not affect transcription elongation, its depletion results in the upregulation of more than 1000 genes. Our findings show that H2Bub1 regulates the pause release of Pol II at these genes. This specificity might be mediated through the relatively high proximity of H2Bub1 to paused Pol II at these genes. Overall, our data shed light on the regulation of transcription by H2Bub1 and suggest that the role of H2Bub1 in transcription elongation should be reconsidered.
see also: Fuchs G, Voichek Y, Benjamin S, Gilad S et al. 4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells. Genome Biol 2014 May 9;15(5):R69. PMID: 24887486
see also Dataset GSE57116, Samples GSM1375518 – GSM1375525
Overall design Pol II ChIP-seq, mRNA and 4sUDRB-seq were derived for different replicates of RNF20 siRNA and control siLacZ
Contributor(s) Fuchs G, Rosenthal E
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Submission date Jun 10, 2015
Last update date May 15, 2019
Contact name Eran Rosenthal
Organization name Hebrew University
Department Computer Science
Lab Tommy Kaplan
Street address Givat Ram
City Jerusalem
ZIP/Postal code 91904
Country Israel
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (18)
GSM1708026 siLacZ-384-mRNA
GSM1708027 siLacZ-385-mRNA
GSM1708028 siRNF20-384-mRNA
BioProject PRJNA286307
SRA SRP059327

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Supplementary file Size Download File type/resource
GSE69738_RAW.tar 1.6 Gb (http)(custom) TAR (of BIGWIG, BW, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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