A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids

Autor: Ramdas, Shweta, Judd, Jonathan, Graham, Sarah E, Kanoni, Stavroula, Wang, Yuxuan, Surakka, Ida, Wenz, Brandon, Clarke, Shoa L, Chesi, Alessandra, Wells, Andrew, Bhatti, Konain Fatima, Vedantam, Sailaja, Winkler, Thomas W, Locke, Adam E, Marouli, Eirini, Zajac, Greg J M, Wu, Kuan-Han H, Ntalla, Ioanna, Hui, Qin, Klarin, Derek, Hilliard, Austin T, Wang, Zeyuan, Xue, Chao, Thorleifsson, Gudmar, Helgadottir, Anna, Gudbjartsson, Daniel F, Holm, Hilma, Olafsson, Isleifur, Hwang, Mi Yeong, Han, Sohee, Akiyama, Masato, Sakaue, Saori, Terao, Chikashi, Kanai, Masahiro, Zhou, Wei, Brumpton, Ben M, Rasheed, Humaira, Havulinna, Aki S, Veturi, Yogasudha, Pacheco, Jennifer Allen, Rosenthal, Elisabeth A, Lingren, Todd, Feng, QiPing, Kullo, Iftikhar J, Narita, Akira, Takayama, Jun, Martin, Hilary C, Hunt, Karen A, Trivedi, Bhavi, Haessler, Jeffrey, Giulianini, Franco, Bradford, Yuki, Miller, Jason E, Campbell, Archie, Lin, Kuang, Millwood, Iona Y, Rasheed, Asif, Hindy, George, Faul, Jessica D, Zhao, Wei, Weir, David R, Turman, Constance, Huang, Hongyan, Graff, Mariaelisa, Choudhury, Ananyo, Sengupta, Dhriti, Mahajan, Anubha, Brown, Michael R, Zhang, Weihua, Yu, Ketian, Schmidt, Ellen M, Pandit, Anita, Gustafsson, Stefan, Yin, Xianyong, Luan, Jian'an, Zhao, Jing-Hua, Matsuda, Fumihiko, Jang, Hye-Mi, Yoon, Kyungheon, Medina-Gomez, Carolina, Pitsillides, Achilleas, Hottenga, Jouke Jan, Wood, Andrew R, Ji, Yingji, Gao, Zishan, Haworth, Simon, Mitchell, Ruth E, Chai, Jin Fang, Aadahl, Mette, Bjerregaard, Anne A, Yao, Jie, Manichaikul, Ani, Lee, Wen-Jane, Hsiung, Chao Agnes, Warren, Helen R, Ramirez, Julia, Bork-Jensen, Jette, Kårhus, Line L, Goel, Anuj, Sabater-Lleal, Maria, Noordam, Raymond, Mauro, Pala, Matteo, Floris, McDaid, Aaron F, Marques-Vidal, Pedro, Wielscher, Matthias, Trompet, Stella, Sattar, Naveed, Møllehave, Line T, Munz, Matthias, Zeng, Lingyao, Huang, Jianfeng, Yang, Bin, Poveda, Alaitz, Kurbasic, Azra, Schönherr, Sebastian, Forer, Lukas, Scholz, Markus, Galesloot, Tessel E, Bradfield, Jonathan P, Ruotsalainen, Sanni E, Daw, E Warwick, Zmuda, Joseph M, Mitchell, Jonathan S, Fuchsberger, Christian, Christensen, Henry, Brody, Jennifer A, Le, Phuong, Feitosa, Mary F, Wojczynski, Mary K, Hemerich, Daiane, Preuss, Michael, Mangino, Massimo, Christofidou, Paraskevi, Verweij, Niek, Benjamins, Jan W, Engmann, Jorgen, Noah, Tsao L, Verma, Anurag, Slieker, Roderick C, Lo, Ken Sin, Zilhao, Nuno R, Kleber, Marcus E, Delgado, Graciela E, Huo, Shaofeng, Ikeda, Daisuke D, Iha, Hiroyuki, Yang, Jian, Liu, Jun, Demirkan, Ayşe, Leonard, Hampton L, Marten, Jonathan, Emmel, Carina, Schmidt, Börge, Smyth, Laura J, Cañadas-Garre, Marisa, Wang, Chaolong, Nakatochi, Masahiro, Wong, Andrew, Hutri-Kähönen, Nina, Sim, Xueling, Xia, Rui, Huerta-Chagoya, Alicia, Fernandez-Lopez, Juan Carlos, Lyssenko, Valeriya, Nongmaithem, Suraj S, Sankareswaran, Alagu, Irvin, Marguerite R, Oldmeadow, Christopher, Kim, Han-Na, Ryu, Seungho, Timmers, Paul R H J, Arbeeva, Liubov, Dorajoo, Rajkumar, Lange, Leslie A, Prasad, Gauri, Lorés-Motta, Laura, Pauper, Marc, Long, Jirong, Li, Xiaohui, Theusch, Elizabeth, Takeuchi, Fumihiko, Spracklen, Cassandra N, Loukola, Anu, Bollepalli, Sailalitha, Warner, Sophie C, Wang, Ya Xing, Wei, Wen B, Nutile, Teresa, Ruggiero, Daniela, Sung, Yun Ju, Chen, Shufeng, Liu, Fangchao, Yang, Jingyun, Kentistou, Katherine A, Banas, Bernhard, Morgan, Anna, Meidtner, Karina, Bielak, Lawrence F, Smith, Jennifer A, Hebbar, Prashantha, Farmaki, Aliki-Eleni, Hofer, Edith, Lin, Maoxuan, Concas, Maria Pina, Vaccargiu, Simona, van der Most, Peter J, Pitkänen, Niina, Cade, Brian E, van der Laan, Sander W, Chitrala, Kumaraswamy Naidu, Weiss, Stefan, Bentley, Amy R, Doumatey, Ayo P, Adeyemo, Adebowale A, Lee, Jong Young, Petersen, Eva R B, Nielsen, Aneta A, Choi, Hyeok Sun, Nethander, Maria, Freitag-Wolf, Sandra, Southam, Lorraine, Rayner, Nigel W, Wang, Carol A, Lin, Shih-Yi, Wang, Jun-Sing, Couture, Christian, Lyytikäinen, Leo-Pekka, Nikus, Kjell, Cuellar-Partida, Gabriel, Vestergaard, Henrik, Hidalgo, Bertha, Giannakopoulou, Olga, Cai, Qiuyin, Obura, Morgan O, van Setten, Jessica, He, Karen Y, Tang, Hua, Terzikhan, Natalie, Shin, Jae Hun, Jackson, Rebecca D, Reiner, Alexander P, Martin, Lisa Warsinger, Chen, Zhengming, Li, Liming, Kawaguchi, Takahisa, Thiery, Joachim, Bis, Joshua C, Launer, Lenore J, Li, Huaixing, Nalls, Mike A, Raitakari, Olli T, Ichihara, Sahoko, Wild, Sarah H, Nelson, Christopher P, Campbell, Harry, Jäger, Susanne, Nabika, Toru, Al-Mulla, Fahd, Niinikoski, Harri, Braund, Peter S, Kolcic, Ivana, Kovacs, Peter, Giardoglou, Tota, Katsuya, Tomohiro, de Kleijn, Dominique, de Borst, Gert J, Kim, Eung Kweon, Adams, Hieab H H, Ikram, M Arfan, Zhu, Xiaofeng, Asselbergs, Folkert W, Kraaijeveld, Adriaan O, Beulens, Joline W J, Shu, Xiao-Ou, Rallidis, Loukianos S, Pedersen, Oluf, Hansen, Torben, Mitchell, Paul, Hewitt, Alex W, Kähönen, Mika, Pérusse, Louis, Bouchard, Claude, Tönjes, Anke, Ida Chen, Yii-Der, Pennell, Craig E, Mori, Trevor A, Lieb, Wolfgang, Franke, Andre, Ohlsson, Claes, Mellström, Dan, Cho, Yoon Shin, Lee, Hyejin, Yuan, Jian-Min, Koh, Woon-Puay, Rhee, Sang Youl, Woo, Jeong-Taek, Heid, Iris M, Stark, Klaus J, Zimmermann, Martina E, Völzke, Henry, Homuth, Georg, Evans, Michele K, Zonderman, Alan B, Polasek, Ozren, Pasterkamp, Gerard, Hoefer, Imo E, Redline, Susan, Pahkala, Katja, Oldehinkel, Albertine J, Snieder, Harold, Biino, Ginevra, Schmidt, Reinhold, Schmidt, Helena, Bandinelli, Stefania, Dedoussis, George, Thanaraj, Thangavel Alphonse, Peyser, Patricia A, Kato, Norihiro, Schulze, Matthias B, Girotto, Giorgia, Böger, Carsten A, Jung, Bettina, Joshi, Peter K, Bennett, David A, De Jager, Philip L, Lu, Xiangfeng, Mamakou, Vasiliki, Brown, Morris, Caulfield, Mark J, Munroe, Patricia B, Guo, Xiuqing, Ciullo, Marina, Jonas, Jost B, Samani, Nilesh J, Kaprio, Jaakko, Pajukanta, Päivi, Tusié-Luna, Teresa, Aguilar-Salinas, Carlos A, Adair, Linda S, Bechayda, Sonny Augustin, de Silva, H Janaka, Wickremasinghe, Ananda R, Krauss, Ronald M, Wu, Jer-Yuarn, Zheng, Wei, den Hollander, Anneke I, Bharadwaj, Dwaipayan, Correa, Adolfo, Wilson, James G, Lind, Lars, Heng, Chew-Kiat, Nelson, Amanda E, Golightly, Yvonne M, Wilson, James F, Penninx, Brenda, Kim, Hyung-Lae, Attia, John, Scott, Rodney J, Rao, D C, Arnett, Donna K, Walker, Mark, Scott, Laura J, Koistinen, Heikki A, Chandak, Giriraj R, Mercader, Josep M, Villalpando, Clicerio Gonzalez, Orozco, Lorena, Fornage, Myriam, Tai, E Shyong, van Dam, Rob M, Lehtimäki, Terho, Chaturvedi, Nish, Yokota, Mitsuhiro, Liu, Jianjun, Reilly, Dermot F, McKnight, Amy Jayne, Kee, Frank, Jöckel, Karl-Heinz, McCarthy, Mark I, Palmer, Colin N A, Vitart, Veronique, Hayward, Caroline, Simonsick, Eleanor, van Duijn, Cornelia M, Jin, Zi-Bing, Lu, Fan, Hishigaki, Haretsugu, Lin, Xu, März, Winfried, Gudnason, Vilmundur, Tardif, Jean-Claude, Lettre, Guillaume, T Hart, Leen M, Elders, Petra J M, Rader, Daniel J, Damrauer, Scott M, Kumari, Meena, Kivimaki, Mika, van der Harst, Pim, Spector, Tim D, Loos, Ruth J F, Province, Michael A, Parra, Esteban J, Cruz, Miguel, Psaty, Bruce M, Brandslund, Ivan, Pramstaller, Peter P, Rotimi, Charles N, Christensen, Kaare, Ripatti, Samuli, Widén, Elisabeth, Hakonarson, Hakon, Grant, Struan F A, Kiemeney, Lambertus, de Graaf, Jacqueline, Loeffler, Markus, Kronenberg, Florian, Gu, Dongfeng, Erdmann, Jeanette, Schunkert, Heribert, Franks, Paul W, Linneberg, Allan, Jukema, J Wouter, Khera, Amit V, Männikkö, Minna, Jarvelin, Marjo-Riitta, Kutalik, Zoltan, Francesco, Cucca, Mook-Kanamori, Dennis O, Willems van Dijk, Ko, Watkins, Hugh, Strachan, David P, Grarup, Niels, Sever, Peter, Poulter, Neil, Huey-Herng Sheu, Wayne, Rotter, Jerome I, Dantoft, Thomas M, Karpe, Fredrik, Neville, Matt J, Timpson, Nicholas J, Cheng, Ching-Yu, Wong, Tien-Yin, Khor, Chiea Chuen, Li, Hengtong, Sabanayagam, Charumathi, Peters, Annette, Gieger, Christian, Hattersley, Andrew T, Pedersen, Nancy L, Magnusson, Patrik K E, Boomsma, Dorret I, de Geus, Eco J C, Cupples, L Adrienne, van Meurs, Joyce B J, Ikram, Arfan, Ghanbari, Mohsen, Gordon-Larsen, Penny, Huang, Wei, Kim, Young Jin, Tabara, Yasuharu, Wareham, Nicholas J, Langenberg, Claudia, Zeggini, Eleftheria, Tuomilehto, Jaakko, Kuusisto, Johanna, Laakso, Markku, Ingelsson, Erik, Abecasis, Goncalo, Chambers, John C, Kooner, Jaspal S, de Vries, Paul S, Morrison, Alanna C, Hazelhurst, Scott, Ramsay, Michèle, North, Kari E, Daviglus, Martha, Kraft, Peter, Martin, Nicholas G, Whitfield, John B, Abbas, Shahid, Saleheen, Danish, Walters, Robin G, Holmes, Michael V, Black, Corri, Smith, Blair H, Baras, Aris, Justice, Anne E, Buring, Julie E, Ridker, Paul M, Chasman, Daniel I, Kooperberg, Charles, Tamiya, Gen, Yamamoto, Masayuki, van Heel, David A, Trembath, Richard C, Wei, Wei-Qi, Jarvik, Gail P, Namjou, Bahram, Hayes, M Geoffrey, Ritchie, Marylyn D, Jousilahti, Pekka, Salomaa, Veikko, Hveem, Kristian, Åsvold, Bjørn Olav, Kubo, Michiaki, Kamatani, Yoichiro, Okada, Yukinori, Murakami, Yoshinori, Kim, Bong-Jo, Thorsteinsdottir, Unnur, Stefansson, Kari, Zhang, Jifeng, Chen, Y Eugene, Ho, Yuk-Lam, Lynch, Julie A, Tsao, Philip S, Chang, Kyong-Mi, Cho, Kelly, O'Donnell, Christopher J, Gaziano, John M, Wilson, Peter, Mohlke, Karen L, Frayling, Timothy M, Hirschhorn, Joel N, Kathiresan, Sekar, Boehnke, Michael, Million Veterans Program, Global Lipids Genetics Consortium, Struan Grant, Natarajan, Pradeep, Sun, Yan V, Morris, Andrew P, Deloukas, Panos, Peloso, Gina, Assimes, Themistocles L, Willer, Cristen J, Zhu, Xiang, Brown, Christopher D

Publikováno v: American Journal of Human Genetics, 109(8), 1366-1387. CELL PRESS
Million Veterans Program, Ramdas, S, Judd, J, Graham, S E, Kanoni, S, Wang, Y, Surakka, I, Wenz, B, Clarke, S L, Chesi, A, Wells, A, Bhatti, K F, Vedantam, S, Winkler, T W, Locke, A E, Marouli, E, Zajac, G J M, Wu, K-H H, Ntalla, I, Hui, Q, Klarin, D, Hilliard, A T, Wang, Z, Xue, C, Thorleifsson, G, Helgadottir, A, Gudbjartsson, D F, Holm, H, Olafsson, I, Hwang, M Y, Han, S, Akiyama, M, Sakaue, S, Terao, C, Kanai, M, Zhou, W, Brumpton, B M, Rasheed, H, Havulinna, A S, Veturi, Y, Pacheco, J A, Weir, D R, Brown, M R, Smyth, L J, Cañadas-Garre, M, Li, X, Nelson, C P, McKnight, A J, Kee, F, Wilson, P & Brown, C D 2022, ' A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ', The American Journal of Human Genetics, vol. 109, no. 8, pp. 1366-1387 . https://doi.org/10.1016/j.ajhg.2022.06.012
Ramdas, S, Judd, J, Graham, S E, Hottenga, J J, Penninx, B, Boomsma, D I, de Geus, E J C, Million Veterans Program & Global Lipids Genetics Consortium 2022, ' A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ', American Journal of Human Genetics, vol. 109, no. 8, pp. 1366-1387 . https://doi.org/10.1016/j.ajhg.2022.06.012
Million Veterans Program & Global Lipids Genetics Consortium 2022, ' A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ', American journal of human genetics, vol. 109, no. 8, pp. 1366-1387 . https://doi.org/10.1016/j.ajhg.2022.06.012
Am J Hum Genet
American journal of human genetics, vol 109, iss 8
AMERICAN JOURNAL OF HUMAN GENETICS
r-IIB SANT PAU. Repositorio Institucional de Producción Científica del Instituto de Investigación Biomédica Sant Pau
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American Journal of Human Genetics
American journal of human genetics, 109(8), 1366-1387. Cell Press
American journal of human genetics, vol. 109, no. 8, pp. 1366-1387
Ramdas, S, Judd, J, Graham, S E, Kanoni, S, Wang, Y, Surakka, I, Wenz, B, Clarke, S L, Brumpton, B M, Rasheed, H, Haworth, S J, Mitchell, R E, Zhu, X & Brown, C D & et, A 2022, ' A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ', American Journal of Human Genetics, vol. 109, no. 8, pp. 1366-1387 . https://doi.org/10.1016/j.ajhg.2022.06.012
2022, ' A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids ', American Journal of Human Genetics, vol. 109, no. 8, pp. 1366-1387 . https://doi.org/10.1016/j.ajhg.2022.06.012
American Journal of Human Genetics, 109, 8, pp. 1366-1387
American Journal of Human Genetics, 109, 1366-1387
American Journal of Human Genetics, 109(8), 1366-1387. Cell Press

A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce85872de65cda3bd9b22e7d06fabeed
https://doi.org/10.1016/j.ajhg.2022.06.012

Whole-genome doubling drives oncogenic loss of chromatin segregation

Autor: Ruxandra A. Lambuta, Luca Nanni, Yuanlong Liu, Juan Diaz-Miyar, Arvind Iyer, Daniele Tavernari, Natalya Katanayeva, Giovanni Ciriello, Elisa Oricchio

Publikováno v: Nature, vol. 615, no. 7954, pp. 925-933

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies1–8. However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic ph

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b11fba28aced476b059177419410557e
https://serval.unil.ch/resource/serval:BIB_4691B7A968A0.P001/REF.pdf

Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis

Autor: Zhenhui Zhong, Yafei Wang, Ming Wang, Fan Yang, Quentin Angelo Thomas, Yan Xue, Yaxin Zhang, Wanlu Liu, Yasaman Jami-Alahmadi, Linhao Xu, Suhua Feng, Sebastian Marquardt, James A. Wohlschlegel, Israel Ausin, Steven E. Jacobsen

Publikováno v: Nature communications, vol 13, iss 1
Zhong, Z, Wang, Y, Wang, M, Yang, F, Thomas, Q A, Xue, Y, Zhang, Y, Liu, W, Jami-Alahmadi, Y, Xu, L, Feng, S, Marquardt, S, Wohlschlegel, J A, Ausin, I & Jacobsen, S E 2022, ' Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis ', Nature Communications, vol. 13, 6970 . https://doi.org/10.1038/s41467-022-34648-0

Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated repl

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf83fac8a22dca9e7877f0ae98c283a5
https://escholarship.org/uc/item/0hb8m6p0

Cohesin is required for long-range enhancer action at the Shh locus

Autor: Lauren Kane, Iain Williamson, Ilya M. Flyamer, Yatendra Kumar, Robert E. Hill, Laura A. Lettice, Wendy A. Bickmore

Publikováno v: Kane, L, Williamson, I, Flyamer, I, Kumar, Y, Hill, R E, Lettice, L A & Bickmore, W A 2022, ' Cohesin is required for long-range enhancer action at the Shh locus ', Nature Structural & Molecular Biology, vol. 29, no. 9, pp. 891-897 . https://doi.org/10.1038/s41594-022-00821-8
Nat Struct Mol Biol

The regulatory landscapes of developmental genes in mammals can be complex, with enhancers spread over many hundreds of kilobases. It has been suggested that three-dimensional genome organisation, particularly topologically associating domains formed

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::005cf46e25b276610ee986e6f1825e97
https://www.pure.ed.ac.uk/ws/files/288068812/Kane_NSMB_accepted.pdf

Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

Autor: Niels J. Rinzema, Konstantinos Sofiadis, Sjoerd J. D. Tjalsma, Marjon J. A. M. Verstegen, Yuva Oz, Christian Valdes-Quezada, Anna-Karina Felder, Teodora Filipovska, Stefan van der Elst, Zaria de Andrade dos Ramos, Ruiqi Han, Peter H. L. Krijger, Wouter de Laat

Publikováno v: Nature Structural & Molecular Biology, 29(6), 563-574. Nature Publishing Group

Developmental gene expression is often controlled by distal regulatory DNA elements called enhancers. Distant enhancer action is restricted to structural chromosomal domains that are flanked by CTCF-associated boundaries and formed through cohesin ch

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::68cd2cc4773e8b4dbb0a1e6367bd7058
https://pure.knaw.nl/portal/en/publications/d8e1f888-d14c-4139-a769-885db924b103