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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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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. [5, 7] ; Ljungman, Mats [8, 1, 2]
Total Authors: 10
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
Total Affiliations: 8
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)