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

Author(s)

Magnuson, Brian ^{[1, 2]} ; Veloso, Artur ^{[3, 1, 2, 4]} ; Kirkconnell, Killeen S. ^{[1, 2, 5]} ; de Andrade Lima, Leonardo Carmo ^{[6, 1, 2]} ; Paulsen, Michelle T. ^{[1, 2]} ; Ljungman, Emily A. ^{[1, 2]} ; Bedi, Karan ^{[1, 2]} ; Prasad, Jayendra ^{[1, 2]} ; Wilson, Thomas E. ^{[7, 5]} ; Ljungman, Mats ^{[8, 1, 2]}

Affiliation

^[1] Univ Michigan, Dept Radiat Oncol, Ctr Comprehens Canc, Ann Arbor, MI 48109 - USA

^[2] Univ Michigan, Sch Med, Translat Oncol Program, Ann Arbor, MI - USA

^[3] Univ Michigan, Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 - USA

^[4] Univ Michigan, Bioinformat Program, Ann Arbor, MI 48109 - USA

^[5] Univ Michigan, Sch Med, Dept Human Genet, Ann Arbor, MI - USA

^[6] Univ Sao Paulo, Dept Microbiol, Inst Biomed Sci, BR-05508 Sao Paulo - Brazil

^[7] Univ Michigan, Sch Med, Dept Pathol, Ann Arbor, MI - USA

^[8] Univ Michigan, Sch Publ Hlth, Dept Environm Hlth Sci, Ann Arbor, MI 48109 - USA

• Document type: Journal article
• Source: SCIENTIFIC REPORTS; v. 5, DEC 11 2015.
• Web of Science Citations: 8

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. (AU)