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Series GSE205504 Query DataSets for GSE205504
Status Public on Jun 30, 2023
Title Essential Signaling Function of Cytoplasmic NELFB Independent of RNA Polymerase II Pausing [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Biochemical studies have established that the four-subunit negative elongation factor (NELF) complex mediates RNA polymerase II (Pol II) pausing at promoter proximal regions. Genetic ablation of individual NELF subunits destabilizes the entire NELF complex and causes lethality of cultured cells, leading to the prevailing concept that NELF-mediated Pol II pausing is essential for cell survival. Using separation-of-function mutations, we show here that NELFB’s effects on cell proliferation can be uncoupled from its function in Pol II pausing. NELFB mutants localized in the cytoplasm and incapacitated in the NELF complex assembly still retain their ability to support cell proliferation and at least part of NELFB-dependent transcriptome. Furthermore, we demonstrate that cytoplasmic NELFB physically and functionally interacts with multiple pro-survival signaling kinases, most notably PI3K/AKT. Enforced activation of PI3K/AKT-related kinases largely rescues deficiency of NELFB-depleted cells in proliferation, but not Pol II pausing. Together, these data revise the current understanding of the growth impact of Pol II pausing and underscore multiplicity of the biological function of individual NELF subunits.
 
Overall design Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for RNA Polymerase II or flag (to detect WT and NELFB mutants)
 
Contributor(s) Pan H, Li R, Cheng X
Citation(s) 37717699
Submission date Jun 06, 2022
Last update date Nov 09, 2023
Contact name Haihui Pan
E-mail(s) panh@email.gwu.edu
Organization name George Washington University
Department Biochemistry and Molecular Medicine
Street address 2121 I St NW
City Washington
State/province DC
ZIP/Postal code 20052
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (47)
GSM6213909 MEFs, MT144, Pol II ChIP-seq, biol rep 1
GSM6213910 MEFs, MT144, Pol II ChIP-seq, biol rep 2
GSM6213911 MEFs, WT, Pol II ChIP-seq, biol rep 1
Relations
BioProject PRJNA846157

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Supplementary file Size Download File type/resource
GSE205504_RAW.tar 8.6 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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