Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

Summary

Transcription is a highly dynamic process. Consequently, we have developed native elongating transcript sequencing technology for mammalian chromatin (mNET-seq), which generates single-nucleotide resolution, nascent transcription profiles. Nascent RNA was detected in the active site of RNA polymerase II (Pol II) along with associated RNA processing intermediates. In particular, we detected 5′splice site cleavage by the spliceosome, showing that cleaved upstream exon transcripts are associated with Pol II CTD phosphorylated on the serine 5 position (S5P), which is accumulated over downstream exons. Also, depletion of termination factors substantially reduces Pol II pausing at gene ends, leading to termination defects. Notably, termination factors play an additional promoter role by restricting non-productive RNA synthesis in a Pol II CTD S2P-specific manner. Our results suggest that CTD phosphorylation patterns established for yeast transcription are significantly different in mammals. Taken together, mNET-seq provides dynamic and detailed snapshots of the complex events underlying transcription in mammals.

Graphical Abstract

Highlights

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  Development of mammalian native elongating transcript sequencing (mNET-seq)

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  Dynamic Pol II CTD phosphorylation during transcription cycle

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  Co-transcriptional splicing and microprocessing detected by mNET-seq

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  Termination factors are associated with Pol II pausing at both TES and TSS

Abstract

Sequencing nascent transcripts from the active site of mammalian RNA polymerase II by a technique called mNET-seq unravels dynamic insights into the transcription cycle, including co-transcriptional splicing and RNA microprocessing.