Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

By Stephen C. J. Parker, M. Stitzel, D. L. Taylor, Jose M. Orozco, M. Erdos, J. Akiyama, Kelly Lammerts van Bueren, P. Chines, Narisu Narisu, Nisc Comparative Sequencing Program and 36 more. Proceedings of the National Academy of Sciences of the United States of America, 2013

661 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3552a24b98e05e130c6babd5acdb2f53ee340d90

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Citations in the corpus

Mutation severity spectrum of rare alleles in the human genome is predictive of disease type (2019, neutral): “2 function, and genetic instability [7-11].”
Chromatin-state discovery and genome annotation with ChromHMM (2017, positive): “ChromHMM has had applications to studying diseases such as Alzheimer’s disease 28,29 , neurodegeneration 30 , type 2 diabetes 31 , and cancer 32–35 , among many other diseases.”
The mechanisms behind the therapeutic activity of BET bromodomain inhibition (2014, background): “…studies describe a similar phenomenon in which a specific subset of regulatory DNA elements exhibits high levels of occupancy for TFs, histone modifications, and/or coregulators (e.g., stretch enhancers and HOT regions) (modENCODE Consortium et al., 2010; Parker et al., 2013; Yan et al., 2013).”
Partitioning heritability by functional annotation using genome-wide association summary statistics (2015, result): “These results are concordant with the medical literature [39, 40] and with previous analysis of these GWAS datasets [9, 18, 27, 31, 41, 42].”
An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans (2017, neutral): “The development of T2D involves dysfunction of multiple mechanisms across several distinct tissues (9,29,31,47,48).”
dbSUPER: a database of super-enhancers in mouse and human genome (2015, methodology): “Downstream computational and in vivo analysis revealed that these stretch enhancer regions are key chromatin features for cell-type-specific gene expression programs, and a sequence variant in these stretch enhancer regions promotes the risk of common human diseases (18).”
Cohesin loss eliminates all loop domains (2017, background): “…we found was in the presence of superenhancers (also called stretch enhancers, or SEs), which are regions of the mammalian genome containing a very high density of enhancer elements, and which are marked by extremely high levels of H3K27 acetylation (Hnisz et al., 2013; Parker et al., 2013).”