1. Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
- Author
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KyungSu Kim, Chen Ping Fu, John P. Didion, Leonard McMillan, Corey R. Quackenbush, James Holt, Yunjung Kim, William Valdar, Mark Calaway, Fernando Pardo-Manuel de Villena, Timothy A. Bell, Lisa M. Tarantino, Yuying Xie, Ginger D. Shaw, Cordelia J. Barrick, Darla R. Miller, Alan B. Lenarcic, James J. Crowley, Terry J. Gooch, Jeremy Wang, Vasyl Zhabotynsky, Zhishan Guo, Zhaojun Zhang, John D. Calaway, Patrick F. Sullivan, Wei Wang, Stephanie D. Hansen, Shunping Huang, Zaining Yun, David W. Threadgill, Wei Sun, Fei Zou, Jason S. Spence, James G. Xenakis, Randal J. Nonneman, Ryan J. Buus, David L. Aylor, Andrew P. Morgan, Nashiya N. Robinson, Isa Kemal Pakatci, and Catherine E. Welsh
- Subjects
Male ,Genetic Speciation ,1.1 Normal biological development and functioning ,Knockout ,Gene Expression ,Single-nucleotide polymorphism ,Biology ,Crosses ,Allelic Imbalance ,eQTL ,Polymorphism, Single Nucleotide ,Medical and Health Sciences ,Article ,Mice ,Genetic ,Phylogenetics ,Dosage Compensation, Genetic ,Genetics ,Animals ,Humans ,Imprinting (psychology) ,Allele ,Polymorphism ,Gene ,Crosses, Genetic ,mouse ,Phylogeny ,Alleles ,Mice, Knockout ,Dosage compensation ,Human Genome ,Single Nucleotide ,Biological Sciences ,allelic imbalance ,Expression quantitative trait loci ,dosage compensation ,Dosage Compensation ,Female ,Generic health relevance ,imprinting ,Biotechnology ,Developmental Biology - Abstract
Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a new global allelic imbalance in expression favoring the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.
- Published
- 2015