Identifying Transcription Start Sites and Active Enhancer Elements Using BruUV-seq

Overview

Journal Sci Rep

Specialty Science

Date 2015 Dec 15

PMID 26656874

Citations 16

Authors

Brian Magnuson

Artur Veloso

Killeen S Kirkconnell

Leonardo Carmo de Andrade Lima

Michelle T Paulsen

Emily A Ljungman

Karan Bedi

Jayendra Prasad

Thomas E Wilson

Mats Ljungman

Affiliations

Soon will be listed here.

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.

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