Journal
SCIENTIFIC REPORTS
Volume 5, Issue -, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/srep17978
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Funding
- University of Michigan Bioinformatics Program
- University of Michigan Biomedical Research Council
- Will and Jeanne Caldwell Endowed Research Fund of the University of Michigan Comprehensive Cancer Center
- University of Michigan School of Public Health [NIEHS P30]
- Department of Defense
- Uniting Against Lung Cancer
- National Institute of Environmental Health Sciences [1R21ES020946, T32ES007062]
- National Human Genome Research Institute [1R01HG006786]
- National Institute of Health [P50CA130810]
- University of Michigan School of Public Health Environmental Toxicology and Epidemiology Program
- CAPES Foundation, Brazil [0138-12-6]
- FAPESP, Brazil [2009/50036-6]
- NIH training grant [T32GM07544]
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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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