Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing. Methods Mol Biol 2017;1468:91-109
Date
09/25/2016Pubmed ID
27662872Pubmed Central ID
PMC5111358DOI
10.1007/978-1-4939-4035-6_8Scopus ID
2-s2.0-84988726214 (requires institutional sign-in at Scopus site) 15 CitationsAbstract
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.
Author List
Blinka S, Reimer MH Jr, Pulakanti K, Pinello L, Yuan GC, Rao SAuthor
Sridhar Rao MD, PhD Associate Professor in the Pediatrics department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
AnimalsChromatin Immunoprecipitation
Computational Biology
Enhancer Elements, Genetic
Gene Expression Regulation
Mice
Mouse Embryonic Stem Cells
Promoter Regions, Genetic
RNA, Long Noncoding
Real-Time Polymerase Chain Reaction
Sequence Analysis, RNA
Transcription, Genetic
