Volume 50 of Issue 8 | Nature genetics
Authors: Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, De Jager PL, Chang HY, Aiden EL, Benoist C, Beer MA, Ye CJ, Regev A
Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4 T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression.
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Journal of medical Internet research
Authors: Cleret de Langavant L, Bayen E, Yaffe K
Neuropsychology
Authors: Kaup AR, Xia F, Launer LJ, Sidney S, Nasrallah I, Erus G, Allen N, Yaffe K
Brain injury
Authors: Bertenthal D, Yaffe K, Barnes DE, Byers AL, Gibson CJ, Seal KH
Journal of clinical oncology : official journal of the American Society of Clinical Oncology
Authors: Aggarwal R, Huang J, Alumkal JJ, Zhang L, Feng FY, Thomas GV, Weinstein AS, Friedl V, Zhang C, Witte ON, Lloyd P, Gleave M, Evans CP, Youngren J, Beer TM, Rettig M, Wong CK, True L, Foye A, Playdle D, Ryan CJ, Lara P, Chi KN, Uzunangelov V, Sokolov A, Newton Y, Beltran H, Demichelis F, Rubin MA, Stuart JM, Small EJ
International journal of geriatric psychiatry
Authors: Tranah GJ, Maglione JE, Yaffe K, Katzman SM, Manini TM, Kritchevsky S, Newman AB, Harris TB, Cummings SR
Volume 33 | EBioMedicine
Authors: Kumar R, Graham B
Patient education and counseling
Authors: Pecanac KE, Brown RL, Steingrub J, Anderson W, Matthay MA, White DB
AIDS research and human retroviruses
Authors: Nance R, Crane H, Ritchings C, Rosenblatt LC, Budoff M, Heckbert SR, Drozd D, Matthews WC, Geng E, Hunt PW, Feinstein MJ, Moore R, Hseu P, Eron JJ, Burkholder GA, Rodriguez B, Mugavero MJ, Saag M, Kitahata MM, Delaney JA
BMC public health
Authors: Fell AKM, Svendsen MV, Kim JL, Abrahamsen R, Henneberger PK, Torén K, Blanc PD, Kongerud J
