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Multi-tissue integrative analysis of personal epigenomes

Rozowsky, Joel and Drenkow, Jorg and Yang, Yucheng and Gursoy, Gamze and Galeev, Timur and Borsari, Beatrice and Epstein, Charles and Xiong, Kun and Xu, Jinrui and Gao, Jiahao and Yu, Keyang and Berthel, Ana and Chen, Zhanlin and Navarro, Fabio and Liu, Jason and Sun, Maxwell and Wright, James and Chang, Justin and Cameron, Christopher and Shoresh, Noam and Gaskell, Elizabeth and Adrian, Jessika and Aganezov, Sergey and Balderrama-Gutierrez, Gabriela and Banskota, Samridhi and Corona, Guillermo and Chee, Sora and Chhetri, Surya and Martins, Gabriel and Danyko, Cassidy and Davis, Carrie and Farid, Daniel and Farrell, Nina and Gabdank, Idan and Gofin, Yoel and Gorkin, David and Gu, Mengting and Hecht, Vivian and Hitz, Benjamin and Issner, Robbyn and Kirsche, Melanie and Kong, Xiangmeng and Lam, Bonita and Li, Shantao and Li, Bian and Li, Tianxiao and Li, Xiqi and Lin, Khine and Luo, Ruibang and Mackiewicz, Mark and Moore, Jill and Mudge, Jonathan and Nelson, Nicholas and Nusbaum, Chad and Popov, Ioann and Pratt, Henry and Qiu, Yunjiang and Ramakrishnan, Srividya and Raymond, Joe and Salichos, Leonidas and Scavelli, Alexandra and Schreiber, Jacob and Sedlazeck, Fritz and See, Lei and Sherman, Rachel and Shi, Xu and Shi, Minyi and Sloan, Cricket and Strattan, J. Seth and Tan, Zhen and Tanaka, Forrest and Vlasova, Anna and Wang, Jun and Werner, Jonathan and Williams, Brian and Xu, Min and Yan, Chengfei and Yu, Lu and Zaleski, Christopher and Zhang, Jing and Cherry, J. Michael and Mendenhall, Eric and Noble, William and Weng, Zhiping and Levine, Morgan and Dobin, Alexander and Wold, Barbara and Mortazavi, Ali and Ren, Bing and Gillis, Jesse and Myers, Richard and Snyder, Michael and Choudhary, Jyoti and Milosavljevic, Aleksandar and Schatz, Michael and Guigo, Roderic and Bernstein, Bradley and Gingeras, Thomas and Gerstein, Mark (2021) Multi-tissue integrative analysis of personal epigenomes. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210430-100605150

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Abstract

Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for four cadaveric donors (using long-read sequencing) and systematically charted noncoding regulatory elements and transcriptional activity across more than 25 tissues from these donors. Integrative analysis revealed over a million variants with allele-specific activity, coordinated, locus-scale allelic imbalances, and structural variants impacting proximal chromatin structure. We relate the personal genome analysis to the ENCODE encyclopedia, annotating allele- and tissue-specific elements that are strongly enriched for variants impacting expression and disease phenotypes. These experimental and statistical approaches, and the corresponding EN-TEx resource, provide a framework for personalized functional genomics.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.04.26.441442DOIDiscussion Paper
ORCID:
AuthorORCID
Rozowsky, Joel0000-0002-3565-0762
Epstein, Charles0000-0001-8358-8345
Balderrama-Gutierrez, Gabriela0000-0002-5794-4518
Gorkin, David0000-0003-4944-4107
Mackiewicz, Mark0000-0002-7088-1902
Moore, Jill0000-0002-3023-0806
Cherry, J. Michael0000-0001-9163-5180
Mendenhall, Eric0000-0002-7395-6295
Weng, Zhiping0000-0002-3032-7966
Wold, Barbara0000-0003-3235-8130
Mortazavi, Ali0000-0002-4259-6362
Ren, Bing0000-0002-5435-1127
Gillis, Jesse0000-0002-0936-9774
Snyder, Michael0000-0003-0784-7987
Bernstein, Bradley0000-0002-5726-6278
Gerstein, Mark0000-0002-9746-3719
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. This version posted April 26, 2021. The authors have declared no competing interest.
Record Number:CaltechAUTHORS:20210430-100605150
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210430-100605150
Official Citation:Multi-tissue integrative analysis of personal epigenomes. Joel Rozowsky, Jorg Drenkow, Yucheng T Yang, Gamze Gursoy, Timur Galeev, Beatrice Borsari, Charles B Epstein, Kun Xiong, Jinrui Xu, Jiahao Gao, Keyang Yu, Ana Berthel, Zhanlin Chen, Fabio Navarro, Jason Liu, Maxwell S Sun, James Wright, Justin Chang, Christopher JF Cameron, Noam Shoresh, Elizabeth Gaskell, Jessika Adrian, Sergey Aganezov, Gabriela Balderrama-Gutierrez, Samridhi Banskota, Guillermo Barreto Corona, Sora Chee, Surya B Chhetri, Gabriel Conte Cortez Martins, Cassidy Danyko, Carrie A Davis, Daniel Farid, Nina P Farrell, Idan Gabdank, Yoel Gofin, David U Gorkin, Mengting Gu, Vivian Hecht, Benjamin C Hitz, Robbyn Issner, Melanie Kirsche, Xiangmeng Kong, Bonita R Lam, Shantao Li, Bian Li, Tianxiao Li, Xiqi Li, Khine Zin Lin, Ruibang Luo, Mark Mackiewicz, Jill E Moore, Jonathan Mudge, Nicholas Nelson, Chad Nusbaum, Ioann Popov, Henry E Pratt, Yunjiang Qiu, Srividya Ramakrishnan, Joe Raymond, Leonidas Salichos, Alexandra Scavelli, Jacob M Schreiber, Fritz J Sedlazeck, Lei Hoon See, Rachel M Sherman, Xu Shi, Minyi Shi, Cricket Alicia Sloan, J Seth Strattan, Zhen Tan, Forrest Y Tanaka, Anna Vlasova, Jun Wang, Jonathan Werner, Brian Williams, Min Xu, Chengfei Yan, Lu Yu, Christopher Zaleski, Jing Zhang, J Michael Cherry, Eric M Mendenhall, William S Noble, Zhiping Weng, Morgan E Levine, Alexander Dobin, Barbara Wold, Ali Mortazavi, Bing Ren, Jesse Gillis, Richard M Myers, Michael P Snyder, Jyoti Choudhary, Aleksandar Milosavljevic, Michael C Schatz, Roderic Guigó, Bradley E Bernstein, Thomas R Gingeras, Mark Gerstein. bioRxiv 2021.04.26.441442; doi: https://doi.org/10.1101/2021.04.26.441442
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:108899
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:30 Apr 2021 17:28
Last Modified:30 Apr 2021 17:28

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