GSE185990
Low RNA stability signifies increased post-transcriptional regulation of cell identity genes
Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g., by super-enhancers and Broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed that significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains, and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, likely due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-seq showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run and brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression. Overall design: For T cell RNA-seq, the T cells were collected from the patient's blood and separated using the apheresis method. The cells were cultured in the complete median and treated with transcription inhibition ActD at 4 different time points, 0-hour, 0.25-hour, 1 hour, and 2 hours. Total mRNA was extracted by the TRIzol reagent (Invitrogen), and the Poly(A) RNA-seq library was performed by using the TruSeq RNA Sample Prep kit, following the manufacturer's instructions. Two samples including shCTRL and shMETTL3 of  T cells were used to do nanopore direct RNA-seq to detect the m6A modifications. The RNA-seq reads were mapped to human hg19 and hg38 genome version.