Defective RNA processing and ELOA-mediated transcriptional elongation in reversible cellular senescence suggest aging by transcription

Negative elongation factor (NELF) is a transcriptional regulator that is primarily known for its role in the promoter-proximal pausing of RNA polymerase II (RNAPII) [1-2]. We have previously demonstrated that acute depletion of the NELF subunit NELF-C causes genome-wide RNAPII pausing at a second site associated with the +1 nucleosome [3]. Here, we show that acute depletion of the NELF subunit NELF-C results in a reversible cellular senescence phenotype that includes impaired growth, robustly detectable ß-galactosidase activity, and upregulated expression of senescence-associated genes. We also identify a small set of genes at which NELF-C depletion induces RNAPII release rather than second site pausing. We identify Elongin A (ELOA) as a transcription factor mediating the impacts of NELF depletion, and we demonstrate that the primate-specific ELOA homolog ELOA3 can also play this role. Mechanistically, ELOA mediates the impacts of NELF depletion at least in part by altering the kinetic coupling between the elongation and splicing of nascent transcripts, which results in intron retention and other splicing defects. Despite reports implicating splicing defects in aging-related phenomena [4-6] [7-9], mechanisms have remained elusive. The findings presented here indicate that the crosstalk between splicing factors, ELOA, and NELF may be critical to understanding cellular senescence and aging Overall design: TT-seq in NELFC-AID and ELOA-KO DLD1 cells