Identification of Transcribed Enhancers by Genome-Wide Chromatin Immunoprecipitation Sequencing.
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.
['Blinka|Steven|S|', 'Reimer|Michael H|MH|', 'Pulakanti|Kirthi|K|', 'Pinello|Luca|L|', 'Yuan|Guo-Cheng|GC|', 'Rao|Sridhar|S|']
D000818:Animals D047369:Chromatin Immunoprecipitation D019295:Computational Biology D004742:Enhancer Elements, Genetic D005786:Gene Expression Regulation D051379:Mice D000066450:Mouse Embryonic Stem Cells D011401:Promoter Regions, Genetic D062085:RNA, Long Noncoding D060888:Real-Time Polymerase Chain Reaction D017423:Sequence Analysis, RNA D014158:Transcription, Genetic
Transcribed enhancer Chromatin immunoprecipitation sequencing Noncoding RNA eRNA ENCODE Global run on sequencing