N6-methyladenosine in 7SK small nuclear RNA underlies RNA polymerase II transcription regulation

Mol Cell. 2023 Nov 2;83(21):3818-3834.e7. doi: 10.1016/j.molcel.2023.09.020. Epub 2023 Oct 10.

Abstract

N6-methyladenosine (m6A) modifications play crucial roles in RNA metabolism. How m6A regulates RNA polymerase II (RNA Pol II) transcription remains unclear. We find that 7SK small nuclear RNA (snRNA), a regulator of RNA Pol II promoter-proximal pausing, is highly m6A-modified in non-small cell lung cancer (NSCLC) cells. In A549 cells, we identified eight m6A sites on 7SK and discovered methyltransferase-like 3 (METTL3) and alkB homolog 5 (ALKBH5) as the responsible writer and eraser. When the m6A-7SK is specifically erased by a dCasRx-ALKBH5 fusion protein, A549 cell growth is attenuated due to reduction of RNA Pol II transcription. Mechanistically, removal of m6A leads to 7SK structural rearrangements that facilitate sequestration of the positive transcription elongation factor b (P-TEFb) complex, which results in reduction of serine 2 phosphorylation (Ser2P) in the RNA Pol II C-terminal domain and accumulation of RNA Pol II in the promoter-proximal region. Taken together, we uncover that m6A modifications of a non-coding RNA regulate RNA Pol II transcription and NSCLC tumorigenesis.

Keywords: 7SK snRNA; NSCLC; Pol II transcription; RNA Pol II transcription; m(6)A modification.

MeSH terms

  • Carcinoma, Non-Small-Cell Lung* / genetics
  • HeLa Cells
  • Humans
  • Lung Neoplasms* / genetics
  • Methyltransferases / genetics
  • Methyltransferases / metabolism
  • Positive Transcriptional Elongation Factor B / genetics
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • RNA, Small Nuclear / genetics
  • Transcription, Genetic

Substances

  • RNA Polymerase II
  • N-methyladenosine
  • Positive Transcriptional Elongation Factor B
  • RNA, Small Nuclear
  • METTL3 protein, human
  • Methyltransferases