Title: Identifying transcription start sites and active enhancer elements using BruUV-seq.

Authors: Magnuson, Brian; Veloso, Artur; Kirkconnell, Killeen S; de Andrade Lima, Leonardo Carmo; Paulsen, Michelle T; Ljungman, Emily A; Bedi, Karan; Prasad, Jayendra; Wilson, Thomas E; Ljungman, Mats

Published In Sci Rep, (2015 Dec 11)

Abstract: BruUV-seq utilizes UV light to introduce transcription-blocking DNA lesions randomly in the genome prior to bromouridine-labeling and deep sequencing of nascent RNA. By inhibiting transcription elongation, but not initiation, pre-treatment with UV light leads to a redistribution of transcription reads resulting in the enhancement of nascent RNA signal towards the 5'-end of genes promoting the identification of transcription start sites (TSSs). Furthermore, transcripts associated with arrested RNA polymerases are protected from 3'-5' degradation and thus, unstable transcripts such as putative enhancer RNA (eRNA) are dramatically increased. Validation of BruUV-seq against GRO-cap that identifies capped run-on transcripts showed that most BruUV-seq peaks overlapped with GRO-cap signal over both TSSs and enhancer elements. Finally, BruUV-seq identified putative enhancer elements induced by tumor necrosis factor (TNF) treatment concomitant with expression of nearby TNF-induced genes. Taken together, BruUV-seq is a powerful new approach for identifying TSSs and active enhancer elements genome-wide in intact cells.

PubMed ID: 26656874

MeSH Terms: No MeSH terms associated with this publication