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Nuclear retention coupled with sequential polyadenylation dictates post-transcriptional m 6 A modification in the nucleus.

Molecular Cell 2024 August 1
N6 -methyladenosine (m6 A) modification is deemed to be co-transcriptionally installed on pre-mRNAs, thereby influencing various downstream RNA metabolism events. However, the causal relationship between m6 A modification and RNA processing is often unclear, resulting in premature or even misleading generalizations on the function of m6 A modification. Here, we develop 4sU-coupled m6 A-level and isoform-characterization sequencing (4sU-m6 A-LAIC-seq) and 4sU-GLORI to quantify the m6 A levels for both newly synthesized and steady-state RNAs at transcript and single-base-resolution levels, respectively, which enable dissecting the relationship between m6 A modification and alternative RNA polyadenylation. Unexpectedly, our results show that many m6 A addition events occur post-transcriptionally, especially on transcripts with high m6 A levels. Importantly, we find higher m6 A levels on shorter 3' UTR isoforms, which likely result from sequential polyadenylation of longer 3' UTR isoforms with prolonged nuclear dwelling time. Therefore, m6 A 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.

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