title: Identifying transcription start sites and active enhancer elements using BruUV-seq.
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.
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Magnuson
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.|Bioinformatics Program and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Artur
authors.initials: A
authors.lastname: Veloso
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.|Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Killeen S
authors.initials: KS
authors.lastname: Kirkconnell
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.|Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo, Brazil.
authors.forename: Leonardo Carmo
authors.initials: LC
authors.lastname: de Andrade Lima
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Michelle T
authors.initials: MT
authors.lastname: Paulsen
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Emily A
authors.initials: EA
authors.lastname: Ljungman
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Karan
authors.initials: K
authors.lastname: Bedi
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Jayendra
authors.initials: J
authors.lastname: Prasad
authors.affiliation: Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA.|Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Wilson
authors.affiliation: Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center and Translational Oncology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA.|Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA.
authors.forename: Mats
authors.initials: M
authors.lastname: Ljungman
mesh_terms: D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D004742:Enhancer Elements, Genetic; D005786:Gene Expression Regulation / Q000528:radiation effects*; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D058977:Molecular Sequence Annotation; D061805:Transcription Elongation, Genetic / Q000528:radiation effects; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000528:radiation effects; D014466:Ultraviolet Rays