Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.

Autor:	Blinka S; Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.; BloodCenter of Wisconsin, Blood Research Institute, 8733 West Watertown Plank Road, Milwaukee, WI, 53226, USA., Reimer MH Jr; Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA.; BloodCenter of Wisconsin, Blood Research Institute, 8733 West Watertown Plank Road, Milwaukee, WI, 53226, USA., Pulakanti K; BloodCenter of Wisconsin, Blood Research Institute, 8733 West Watertown Plank Road, Milwaukee, WI, 53226, USA., Pinello L; Department of Biostatistics and Computational Biology, Harvard TH Chan School of Public Health, Dana-Farber Cancer Institute, Boston, MA, USA., Yuan GC; Department of Biostatistics and Computational Biology, Harvard TH Chan School of Public Health, Dana-Farber Cancer Institute, Boston, MA, USA., Rao S; Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA. sridhar.rao@bcw.edu.; BloodCenter of Wisconsin, Blood Research Institute, 8733 West Watertown Plank Road, Milwaukee, WI, 53226, USA. sridhar.rao@bcw.edu.; Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, USA. sridhar.rao@bcw.edu.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2017; Vol. 1468, pp. 91-109.
DOI:	10.1007/978-1-4939-4035-6_8
Abstrakt:	Recent work has shown that RNA polymerase II-mediated transcription at distal cis-regulatory elements serves as a mark of highly active enhancers. Production of noncoding RNAs at enhancers, termed eRNAs, correlates with higher expression of genes that the enhancer interacts with; hence, eRNAs provide a new tool to model gene activity in normal and disease tissues. Moreover, this unique class of noncoding RNA has diverse roles in transcriptional regulation. Transcribed enhancers can be identified by a common signature of epigenetic marks by overlaying a series of genome-wide chromatin immunoprecipitation and RNA sequencing datasets. A computational approach to filter non-enhancer elements and other classes of noncoding RNAs is essential to not cloud downstream analysis. Here we present a protocol that combines wet and dry bench methods to accurately identify transcribed enhancers genome-wide as well as an experimental procedure to validate these datasets.
Databáze:	MEDLINE
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