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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.

Original publication

DOI

10.1016/j.cell.2015.03.027

Type

Journal article

Journal

Cell

Publication Date

23/04/2015

Volume

161

Pages

526 - 540

Keywords

Genome, Human, HeLa Cells, Humans, MicroRNAs, Phosphorylation, Protein Structure, Tertiary, RNA Polymerase II, RNA Processing, Post-Transcriptional, Sequence Analysis, RNA, Transcription, Genetic