Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks.
Helen He Zhu,Helen He Zhu,Liis Uusküla-Reimand,Keren Isaev,Keren Isaev,Lina Wadi,Azad Alizada,Shimin Shuai,Shimin Shuai,Vincent Huang,Dike Aduluso-Nwaobasi,Marta Paczkowska,Diala Abd-Rabbo,Oliver Ocsenas,Oliver Ocsenas,Minggao Liang,J. Drew Thompson,Yao Li,Luyao Ruan,Michal Krassowski,Irakli Dzneladze,Jared T. Simpson,Jared T. Simpson,Mathieu Lupien,Mathieu Lupien,Lincoln D. Stein,Lincoln D. Stein,Paul C. Boutros,Michael D. Wilson,Jüri Reimand,Jüri Reimand +30 more
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TLDR
A driver discovery method is developed and analyzed 120,788 cis-regulatory modules (CRMs) across 1,844 whole tumor genomes from the ICGC-TCGA PCAWG project, finding 30 CRMs with enriched SNVs and indels (FDR < 0.05).About:
This article is published in Molecular Cell.The article was published on 2020-03-19 and is currently open access. It has received 57 citations till now. The article focuses on the topics: Carcinogenesis & Genome.read more
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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
TL;DR: 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.
Activation of proto-oncogenes by disruption of chromosome neighborhoods
Denes Hnisz,Daniel S. Day,Anne-Laure Valton,Rasmus O. Bak,Johanna Goldmann,Bryan R. Lajoie,Alla A. Sigova,Tong Ihn Lee,Matthew H. Porteus,Job Dekker,Abraham S. Weintraub,Charles H. Li,Jessica Reddy,Diego Borges-Rivera,Rudolf Jaenisch,Zi Peng Fan,Richard A. Young +16 more
TL;DR: Wala et al. as discussed by the authors investigated whether proto-oncogenes occur within these structures and whether oncogene activation can occur via disruption of insulated neighborhood boundaries in cancer cells.
YY1 Is a Structural Regulator of Enhancer-Promoter Loops
Alla A. Sigova,Nancy M. Hannett,Daniel S. Day,Brian J. Abraham,Malkiel A. Cohen,Behnam Nabet,Dennis L. Buckley,Yang Eric Guo,Denes Hnisz,James E. Bradner,Nathanael S. Gray,Abraham S. Weintraub,Charles H. Li,Alicia Zamudio Montes de Oca,Rudolf Jaenisch,Richard A. Young +15 more
TL;DR: In this paper, the ubiquitously expressed transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF.
Journal ArticleDOI
A genomic and epigenomic atlas of prostate cancer in Asian populations.
Jing Li,Chuanliang Xu,Hyung Joo Lee,Shancheng Ren,Xiaoyuan Zi,Zhiming Zhang,Haifeng Wang,Yongwei Yu,Chenghua Yang,Chenghua Yang,Xiaofeng Gao,Jianguo Hou,Linhui Wang,Bo Yang,Qing Yang,Huamao Ye,Tie Zhou,Xin Lu,Yan Wang,Min Qu,Qingsong Yang,Wenhui Zhang,Nakul M. Shah,Erica C. Pehrsson,Shuo Wang,Zengjun Wang,Jun Jiang,Yan Zhu,Rui Chen,Huan Chen,Feng Zhu,Bijun Lian,Xiaoyun Li,Yun Zhang,Chao Wang,Yue Wang,Guangan Xiao,Junfeng Jiang,Yue Yang,Chaozhao Liang,Jian-quan Hou,Conghui Han,Ming Chen,Ning Jiang,Dahong Zhang,Song Wu,Jinjian Yang,Tao Wang,Yongliang Chen,Jiantong Cai,Wenzeng Yang,Jun Xu,Shaogang Wang,Xu Gao,Ting Wang,Yinghao Sun +55 more
TL;DR: Genomic, transcriptomic and DNA methylation data from tissue samples from 208 Chinese patients with prostate cancer define the landscape of alterations in this population, and comparison with data from Western cohorts suggests that the disease may stratify into different molecular subtypes.
An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element
Marc R. Mansour,Brian J. Abraham,Lars Anders,Alla Berezovskaya,Alejandro Gutierrez,Adam D. Durbin,Julia Etchin,Lee N. Lawton,Stephen E. Sallan,Lewis B. Silverman,Mignon L. Loh,Stephen P. Hunger,Takaomi Sanda,A T Look,Richard A. Young +14 more
TL;DR: In a subset of T-cell acute lymphoblastic leukemia (T-ALL) cases, it is found that heterozygous somatic mutations are acquired that introduce binding motifs for the MYB transcription factor in a precise noncoding site, which creates a super-enhancer upstream of the TAL1 oncogene.
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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S.P. Rao,Miriam H. Huntley,Neva C. Durand,Elena K. Stamenova,Ivan D. Bochkov,James T. Robinson,James T. Robinson,Adrian L. Sanborn,Ido Machol,Ido Machol,Arina D. Omer,Arina D. Omer,Eric S. Lander,Eric S. Lander,Eric S. Lander,Erez Lieberman Aiden +15 more
TL;DR: In situ Hi-C is used to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types, identifying ∼10,000 loops that frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species.
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