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

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.