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Series GSE140053 Query DataSets for GSE140053
Status Public on Feb 05, 2021
Title Stress-induced nuclear condensation of NELF drives global transcriptional downregulation
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary In response to stress, human cells actively downregulate ongoing gene expression programs. Translational downregulation is accompanied by the assembly of stress granules which are cytosolic condensates containing ribosomes and mRNA. Transcriptional downregulation is caused by an increased recruitment of Negative Elongation Factors (NELF) to promoters, inhibiting RNA Pol II elongation. We report here that NELF forms nuclear condensates upon stress which can be recapitulated by liquid-liquid phase separation of recombinant NELF in vitro. Stress leads to rapid dephosphorylation and SUMOylation of NELF in cells facilitating condensate formation driven by intrinsically disordered domains of NELFA and NELFE subunits. Using NELF mutants that do not form condensates we provide evidence that condensation is required for increased recruitment of NELF to downregulated promoters and cellular survival in stress. Thus, our study has uncovered a novel nuclear condensate that is conceptually similar to cytosolic stress granule in downregulating gene expression during stressful conditions.
Overall design Effect of SUMOylation to chromatin binding of RNA polymerase II was studied in UBE2I silenced (siRNA for UBE2I) and control (non-targeting siRNA transfected, siNON) VCaP cells (non-stressed or heat shocked (30 min at 43C)). All samples were done as biological replicates.

Slam-seq analysis pf HeLa cells to identify the effect of NELF condensates on transcription.
Contributor(s) Rawat P, Sawarkar R
Citation(s) 33548202
Submission date Nov 06, 2019
Last update date Mar 19, 2021
Contact name Barbara Hummel
Organization name Max Planck Institute of Immunobiology and Epigenetics
Street address Stübeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (32)
GSM4152127 VCaP: Pol2_siCtrl_Ctrl1
GSM4152128 VCaP: Pol2_siCtrl_Ctrl2
GSM4152129 VCaP: Pol2_siCtrl_HS1
BioProject PRJNA588093
SRA SRP228821

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Supplementary file Size Download File type/resource
GSE140053_RAW.tar 2.3 Gb (http)(custom) TAR (of BW, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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