E-GEOD-51522 - Transcriptional super-enhancers connected to cell identity and disease

Released on 23 October 2013, last updated on 3 May 2014
Homo sapiens, Mus musculus
Samples (5)
Protocols (9)
Super-enhancers are large clusters of transcriptional enhancers that drive expression of genes that control and define cell identity. Improved understanding of the roles super-enhancers play in biology would be afforded by knowing the constellation of factors that constitute these domains and by identifying super-enhancers across the spectrum of human cell types. We describe here the population of transcription factors, cofactors, chromatin regulators and core transcription apparatus that occupy super-enhancers in embryonic stem cells (ESCs) and evidence that super-enhancers are highly transcribed. We then use epigenomic data to produce a catalogue of super-enhancers in a broad range of human cell types. These super-enhancer domains are associated with genes encoding master transcription factors and other components that play important roles in the biology of these cells. Interestingly, sequence variation associated with a broad spectrum of diseases is especially enriched in the super-enhancers of disease-relevant cell types. Furthermore, we find that cancer cells generate super-enhancers at oncogenes and other genes that play important roles in tumor pathogenesis. We discuss these insights and their implications for future study of human health and disease. ChIP-Seq for transcription factors in mouse embryonic stem cells and H3K27ac in Jurkat T-ALL cell line RNA-Seq for mouse embryonic stem cells
Experiment types
ChIP-seq, RNA-seq of coding RNA 
Richard A Young <young_computation@wi.mit.edu>, Alla Sigova, Ashley Lau, Brian J Abraham, Denes Hnisz, Heather Hoke, Jamie J Newman, Lee N Lawton, Peter Rahl, Violaine Saint-Andre, Warren Whyte
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-51522.idf.txt
Sample and data relationshipE-GEOD-51522.sdrf.txt
Processed data (2)E-GEOD-51522.processed.1.zip, E-GEOD-51522.processed.2.zip