Nuclear retention coupled with sequential polyadenylation dictates post-transcriptional m6A modification in the nucleus

Abstract

N⁶-methyladenosine (m⁶A) modification is deemed to be co-transcriptionally installed on pre-mRNAs, thereby influencing various downstream RNA metabolism events. However, the causal relationship between m⁶A modification and RNA processing is often unclear, resulting in premature or even misleading generalizations on the function of m⁶A modification. Here, we develop 4sU-coupled m⁶A-level and isoform-characterization sequencing (4sU-m⁶A-LAIC-seq) and 4sU-GLORI to quantify the m⁶A levels for both newly synthesized and steady-state RNAs at transcript and single-base-resolution levels, respectively, which enable dissecting the relationship between m⁶A modification and alternative RNA polyadenylation. Unexpectedly, our results show that many m⁶A addition events occur post-transcriptionally, especially on transcripts with high m⁶A levels. Importantly, we find higher m⁶A levels on shorter 3′ UTR isoforms, which likely result from sequential polyadenylation of longer 3′ UTR isoforms with prolonged nuclear dwelling time. Therefore, m⁶A modification can also take place post-transcriptionally to intimately couple with other key RNA metabolism processes to establish and dynamically regulate epi-transcriptomics in mammalian cells.