Open Access
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
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TLDR
In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.Abstract:
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.read more
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Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci.
Jarrett D. Morrow,Kimberly Glass,Michael H. Cho,Craig P. Hersh,Victor Pinto-Plata,Bartolome R. Celli,Nathaniel Marchetti,Gerard J. Criner,Raphael Bueno,George R. Washko,Augustine M.K. Choi,John Quackenbush,Edwin K. Silverman,Dawn L. DeMeo +13 more
TL;DR: Colocalization of mQTL and GWAS loci provides regulatory characterization of significant and subthreshold GWAS findings, supporting a role for genetic control of methylation in COPD pathogenesis.
Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure
Alessia Visconti,David L. Duffy,Fan Liu,Fan Liu,Fan Liu,Gu Zhu,Wenting Wu,Yan Chen,Yan Chen,Pirro G. Hysi,Changqing Zeng,Marianna Sanna,Mark M. Iles,Peter A. Kanetsky,Florence Demenais,Florence Demenais,Merel A. Hamer,André G. Uitterlinden,M. Arfan Ikram,Tamar Nijsten,Nicholas G. Martin,Manfred Kayser,Tim D. Spector,Jiali Han,Jiali Han,Veronique Bataille,Veronique Bataille,Mario Falchi +27 more
TL;DR: This paper reported a large genome-wide association study of ease of skin tanning in 176,678 subjects of European ancestry and identified significant association with tanning ability at 20 loci.
Journal ArticleDOI
Long term in vitro expansion of epithelial stem cells enabled by pharmacological inhibition of PAK1-ROCK-Myosin II and TGF-β signaling
Chengkang Zhang,Hyung Joo Lee,Anura Shrivastava,Ruipeng Wang,Travis J. McQuiston,Sharon S. Challberg,Brian A. Pollok,Ting Wang +7 more
TL;DR: The EpiX method, which utilizes small molecules that inhibit PAK1-ROCK-Myosin II and TGF-β signaling to achieve over one trillion-fold expansion of human epithelial stem and progenitor cells from skin, airway, mammary, and prostate glands in the absence of feeder cells, provides a solution to exploit the potential of tissue-resident epithelial cells for regenerative medicine.
Journal ArticleDOI
Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes
Hongbo Liu,Xiaojuan Liu,Shumei Zhang,Jie Lv,Song Li,Shipeng Shang,Shanshan Jia,Yanjun Wei,Fang Wang,Jianzhong Su,Qiong Wu,Yan Zhang +11 more
TL;DR: An entropy-based framework termed SMART is proposed to integrate the whole genome bisulfite sequencing methylomes across 42 human tissues/cells and helps to elucidate the critical features and functions of cell type-specific hypomethylation.
Journal ArticleDOI
Osteoarthritis year in review 2016: genetics, genomics and epigenetics
TL;DR: An overview of last year's publications in the field of genetics, genomics and epigenetics in the osteoarthritis (OA) field is provided and general developments in the fast evolving field of (epi)genetics are reviewed and relevance for the OA field is summarized.
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