N6-adenosine Methylation of Enhancer RNAs and YTHDC1 Facilitate Transcriptional Condensate Formation and 3D Chromatin Organization

Eukaryotic chromatin is pervasively transcribed into nascent RNAs. However, a mechanistic understanding of their general roles remains lacking. Here, we characterized the landscapes of N6-adenosine methylation (i.e. m6A) on nascent RNAs using a new method that we referred to as MINT-Seq. We found widespread m6A deposition on nascent RNAs produced from regulatory elements including enhancer RNAs (eRNAs) and promoter upstream antisense RNAs (uaRNAs). The lanscape of m6A methylation on enhancer RNAs in human cells using MINT-Seq. We also examined the roles of m6A-eRNAs and YTHDC1 in transcriptional regulation and 3D genome structure with GRO-Seq, TT-Seq, ChIP-Seq and, Hi-C.