Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation

Joo Hyung Lee, Ruoyu Wang, Feng Xiong, Joanna Krakowiak, Zian Liao, Phuoc T. Nguyen, Elena V. Moroz-Omori, Jiaofang Shao, Xiaoyu Zhu, Michael J. Bolt, Haoyi Wu, Pankaj K. Singh, Mingjun Bi, Caleb J. Shi, Naadir Jamal, Guojie Li, Ragini Mistry, Sung Yun Jung, Kuang Lei Tsai, Josephine C. FerreonFabio Stossi, Amedeo Caflisch, Zhijie Liu, Michael A. Mancini, Wenbo Li

Research output: Contribution to journalArticlepeer-review

Abstract

The mechanistic understanding of nascent RNAs in transcriptional control remains limited. Here, by a high sensitivity method methylation-inscribed nascent transcripts sequencing (MINT-seq), we characterized the landscapes of N6-methyladenosine (m6A) on nascent RNAs. We uncover heavy but selective m6A deposition on nascent RNAs produced by transcription regulatory elements, including promoter upstream antisense RNAs and enhancer RNAs (eRNAs), which positively correlates with their length, inclusion of m6A motif, and RNA abundances. m6A-eRNAs mark highly active enhancers, where they recruit nuclear m6A reader YTHDC1 to phase separate into liquid-like condensates, in a manner dependent on its C terminus intrinsically disordered region and arginine residues. The m6A-eRNA/YTHDC1 condensate co-mixes with and facilitates the formation of BRD4 coactivator condensate. Consequently, YTHDC1 depletion diminished BRD4 condensate and its recruitment to enhancers, resulting in inhibited enhancer and gene activation. We propose that chemical modifications of eRNAs together with reader proteins play broad roles in enhancer activation and gene transcriptional control.

Original languageEnglish (US)
Pages (from-to)3368-3385.e9
JournalMolecular Cell
Volume81
Issue number16
DOIs
StatePublished - Aug 19 2021
Externally publishedYes

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