Extensive variation between tissues in allele specific expression in an outbred mammal
作者： Amanda J. Chamberlain , Christy J. Vander Jagt , Benjamin J. Hayes , Majid Khansefid , Leah C. Marett
DOI: 10.1186/S12864-015-2174-0
关键词:
摘要: Allele specific gene expression (ASE), with the paternal allele more expressed than maternal or vice versa, appears to be a common phenomenon in humans and mice. In other species extent of ASE is unknown, even mice there are several outstanding questions. These include; what tissue specific? how often does direction imbalance reverse between tissues? only one two alleles expressed? genome wide bias towards allele; finally do genes that nearby on chromosome share same ASE? Here we use data (RNASeq) from 18 tissues single cow investigate each these questions turn, then validate some findings 20 cows. Between 40 100 million sequence reads were generated per across three replicate samples for eighteen (the discovery dataset). A bovine atlas was created first RNASeq data), differentially identified. To analyse ASE, had access unambiguously phased genotypes all heterozygous variants cow’s whole sequence, where homozygous her sire, as result able map parental genomes, determine SNP showing tissue. total 25,251 within 7985 tested at least pervasive, 89 % significant This large proportion displaying confirmed validation dataset. For individual varied low 8–16 % those thymus high 71–82 % lung. There number cases reversed tissues. example SPTY2D1 showed almost complete kidney thymus, brain caudal lobe cerebellum. Mono allelic (MAE) common, 1349 4856 (28 %) MAE. Across tissues, 54.17 % favoured allele. Genes closely linked likely show higher (paternal maternal) expected by chance. We identified long runs neighbouring either five adjacent (GIMAP8, GIMAP7 copy1, GIMAP4, copy 2 GIMAP5) exclusive lobe. Investigating cows demonstrated 1) pervasive cattle, 2) MAE but ranges slight overexpression major allele, 3) most half time displays divergent patterns 4) 5) expressing clustered together chance, numbers
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David L. A. Wood, Katia Nones, Anita Steptoe, Angelika Christ, Ivon Harliwong, Felicity Newell, Timothy J. C. Bruxner, David Miller, Nicole Cloonan, Sean M. Grimmond, Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data PLOS ONE. ,vol. 10, pp. e0126911- ,(2015) , 10.1371/JOURNAL.PONE.0126911
GTEx Consortium, Kristin G Ardlie, David S Deluca, Ayellet V Segrè, Timothy J Sullivan, Taylor R Young, Ellen T Gelfand, Casandra A Trowbridge, Julian B Maller, Taru Tukiainen, Monkol Lek, Lucas D Ward, Pouya Kheradpour, Benjamin Iriarte, Yan Meng, Cameron D Palmer, Tõnu Esko, Wendy Winckler, Joel N Hirschhorn, Manolis Kellis, Daniel G MacArthur, Gad Getz, Andrey A Shabalin, Gen Li, Yi-Hui Zhou, Andrew B Nobel, Ivan Rusyn, Fred A Wright, Tuuli Lappalainen, Pedro G Ferreira, Halit Ongen, Manuel A Rivas, Alexis Battle, Sara Mostafavi, Jean Monlong, Michael Sammeth, Marta Mele, Ferran Reverter, Jakob M Goldmann, Daphne Koller, Roderic Guigó, Mark I McCarthy, Emmanouil T Dermitzakis, Eric R Gamazon, Hae Kyung Im, Anuar Konkashbaev, Dan L Nicolae, Nancy J Cox, Timothée Flutre, Xiaoquan Wen, Matthew Stephens, Jonathan K Pritchard, Zhidong Tu, Bin Zhang, Tao Huang, Quan Long, Luan Lin, Jialiang Yang, Jun Zhu, Jun Liu, Amanda Brown, Bernadette Mestichelli, Denee Tidwell, Edmund Lo, Mike Salvatore, Saboor Shad, Jeffrey A Thomas, John T Lonsdale, Michael T Moser, Bryan M Gillard, Ellen Karasik, Kimberly Ramsey, Christopher Choi, Barbara A Foster, John Syron, Johnell Fleming, Harold Magazine, Rick Hasz, Gary D Walters, Jason P Bridge, Mark Miklos, Susan Sullivan, Laura K Barker, Heather M Traino, Maghboeba Mosavel, Laura A Siminoff, Dana R Valley, Daniel C Rohrer, Scott D Jewell, Philip A Branton, Leslie H Sobin, Mary Barcus, Liqun Qi, Jeffrey McLean, Pushpa Hariharan, Ki Sung Um, Shenpei Wu, David Tabor, Charles Shive, Anna M Smith, Stephen A Buia, Anita H Undale, Karna L Robinson, Nancy Roche, Kimberly M Valentino, Angela Britton, Robin Burges, Debra Bradbury, Kenneth W Hambright, John Seleski, Greg E Korzeniewski, Kenyon Erickson, Yvonne Marcus, Jorge Tejada, Mehran Taherian, Chunrong Lu, Margaret Basile, Deborah C Mash, Simona Volpi, Jeffery P Struewing, Gary F Temple, Joy Boyer, Deborah Colantuoni, Roger Little, Susan Koester, Latarsha J Carithers, Helen M Moore, Ping Guan, Carolyn Compton, Sherilyn J Sawyer, Joanne P Demchok, Jimmie B Vaught, Chana A Rabiner, Nicole C Lockhart, Kristin G Ardlie, Gad Getz, Fred A Wright, Manolis Kellis, Simona Volpi, Emmanouil T Dermitzakis, None, The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans Science. ,vol. 348, pp. 648- 660 ,(2015) , 10.1126/SCIENCE.1262110
James J Crowley, Vasyl Zhabotynsky, Wei Sun, Shunping Huang, Isa Kemal Pakatci, Yunjung Kim, Jeremy R Wang, Andrew P Morgan, John D Calaway, David L Aylor, Zaining Yun, Timothy A Bell, Ryan J Buus, Mark E Calaway, John P Didion, Terry J Gooch, Stephanie D Hansen, Nashiya N Robinson, Ginger D Shaw, Jason S Spence, Corey R Quackenbush, Cordelia J Barrick, Randal J Nonneman, Kyungsu Kim, James Xenakis, Yuying Xie, William Valdar, Alan B Lenarcic, Wei Wang, Catherine E Welsh, Chen-Ping Fu, Zhaojun Zhang, James Holt, Zhishan Guo, David W Threadgill, Lisa M Tarantino, Darla R Miller, Fei Zou, Leonard McMillan, Patrick F Sullivan, Fernando Pardo-Manuel de Villena, None, Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance Nature Genetics. ,vol. 47, pp. 353- 360 ,(2015) , 10.1038/NG.3222
Christelle Borel, Pedro G. Ferreira, Federico Santoni, Olivier Delaneau, Alexandre Fort, Konstantin Y. Popadin, Marco Garieri, Emilie Falconnet, Pascale Ribaux, Michel Guipponi, Ismael Padioleau, Piero Carninci, Emmanouil T. Dermitzakis, Stylianos E. Antonarakis, Biased Allelic Expression in Human Primary Fibroblast Single Cells American Journal of Human Genetics. ,vol. 96, pp. 70- 80 ,(2015) , 10.1016/J.AJHG.2014.12.001
C. Gregg, J. Zhang, B. Weissbourd, S. Luo, G. P. Schroth, D. Haig, C. Dulac, High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain Science. ,vol. 329, pp. 643- 648 ,(2010) , 10.1126/SCIENCE.1190830
Hans D Daetwyler, Aurélien Capitan, Hubert Pausch, Paul Stothard, Rianne van Binsbergen, Rasmus F Brøndum, Xiaoping Liao, Anis Djari, Sabrina C Rodriguez, Cécile Grohs, Diane Esquerré, Olivier Bouchez, Marie-Noëlle Rossignol, Christophe Klopp, Dominique Rocha, Sébastien Fritz, André Eggen, Phil J Bowman, David Coote, Amanda J Chamberlain, Charlotte Anderson, Curt P VanTassell, Ina Hulsegge, Mike E Goddard, Bernt Guldbrandtsen, Mogens S Lund, Roel F Veerkamp, Didier A Boichard, Ruedi Fries, Ben J Hayes, Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle Nature Genetics. ,vol. 46, pp. 858- 865 ,(2014) , 10.1038/NG.3034
Catherine A Guenther, Bosiljka Tasic, Liqun Luo, Mary A Bedell, David M Kingsley, A molecular basis for classic blond hair color in Europeans Nature Genetics. ,vol. 46, pp. 748- 752 ,(2014) , 10.1038/NG.2991
Thomas M. Keane, Leo Goodstadt, Petr Danecek, Michael A. White, Kim Wong, Binnaz Yalcin, Andreas Heger, Avigail Agam, Guy Slater, Martin Goodson, Nicholas A. Furlotte, Eleazar Eskin, Christoffer Nellåker, Helen Whitley, James Cleak, Deborah Janowitz, Polinka Hernandez-Pliego, Andrew Edwards, T. Grant Belgard, Peter L. Oliver, Rebecca E. McIntyre, Amarjit Bhomra, Jérôme Nicod, Xiangchao Gan, Wei Yuan, Louise van der Weyden, Charles A. Steward, Sendu Bala, Jim Stalker, Richard Mott, Richard Durbin, Ian J. Jackson, Anne Czechanski, José Afonso Guerra-Assunção, Leah Rae Donahue, Laura G. Reinholdt, Bret A. Payseur, Chris P. Ponting, Ewan Birney, Jonathan Flint, David J. Adams, Mouse genomic variation and its effect on phenotypes and gene regulation Nature. ,vol. 477, pp. 289- 294 ,(2011) , 10.1038/NATURE10413
Wenshan Wang, Na Lv, Shasha Zhang, Guanghou Shui, Hui Qian, Jingfeng Zhang, Yuanying Chen, Jing Ye, Yuansheng Xie, Yuemao Shen, Markus R Wenk, Peng Li, Cidea is an essential transcriptional coactivator regulating mammary gland secretion of milk lipids Nature Medicine. ,vol. 18, pp. 235- 243 ,(2012) , 10.1038/NM.2614
Else Marie Vestergaard, Ebba Nexo, Anke Wendt, Florian Guthmann, Trefoil factors in human milk Early Human Development. ,vol. 84, pp. 631- 635 ,(2008) , 10.1016/J.EARLHUMDEV.2008.04.001