Stress-induced nuclear condensation of NELF drives global transcriptional downregulation

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.