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

ABSTRACT

We previously established distinct roles for the transcriptional elongation factors PAF1, negative elongation factor (NELF), SPT4/5, and SPT6 using auxin-inducible degron systems in human cell lines. Here, we integrate long- and short-read RNA-seq data from these degron lines to quantify transcript isoform usage at single-molecule resolution, identifying elongation factor-specific RNA processing regulons, including a cellular senescence-enriched regulon impacted by NELF and SPT6. Long-term NELF or SPT6 depletion causes reversible growth arrest following early upregulation of senescence-associated genes. Our genetic suppressor screens implicate the elongation factor Elongin A (ELOA) in these effects. ELOA knockout suppresses the progression of RNA polymerase II (RNAPII) past transcription end sites (TESs) at NELF depletion-induced genes. Acute depletion of TES-proximal ELOA causes a loss of RNAPII processivity at the 3' end of genes. ELOA loss also confers a growth advantage to aging primary human fibroblasts. These findings establish NELF/ELOA-dependent mechanisms regulating transcriptional elongation and RNA processing and link them to senescence and aging.