title: Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-Altitude Adaptation of Tibetan Pig.
abstract: Tibetan pigs have survived at high altitude for millennia and they have a suite of adaptive features to tolerate the hypoxic environment. However, the molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes have not been completely elucidated. In this study, we analyzed differentially expressed genes (DEGs), biological pathways and constructed co-expression regulation networks using whole-transcriptome microarrays from lung tissues of Tibetan and Duroc pigs both at high and low altitude. A total of 3,066 DEGs were identified and this list was over-represented for the ontology terms including metabolic process, catalytic activity, and KEGG pathway including metabolic pathway and PI3K-Akt signaling pathway. The regulatory (RIF) and phenotypic (PIF) impact factor analysis identified several known and several potentially novel regulators of hypoxia adaption, including: IKBKG, KLF6 and RBPJ (RIF1), SF3B1, EFEMP1, HOXB6 and ATF6 (RIF2). These findings provide new details of the regulatory architecture of hypoxia-adaptive genes and also insight into which genes may undergo epigenetic modification for further study in the high-altitude adaptation.
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Cunling
authors.initials: C
authors.lastname: Jia
authors.affiliation: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Kong
authors.affiliation: Department of Animal Science, University of Arkansas, Fayetteville, AR, United States of America.
authors.forename: James E
authors.initials: JE
authors.lastname: Koltes
authors.affiliation: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Gou
authors.affiliation: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
authors.forename: Shuli
authors.initials: S
authors.lastname: Yang
authors.affiliation: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
authors.forename: Dawei
authors.initials: D
authors.lastname: Yan
authors.affiliation: College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China.
authors.forename: Shaoxiong
authors.initials: S
authors.lastname: Lu
authors.affiliation: College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
authors.forename: Zehui
authors.identifier: http://orcid.org/0000-0003-2532-5218
authors.initials: Z
authors.lastname: Wei
mesh_terms: D000222:Adaptation, Physiological; D000531:Altitude; D000818:Animals; D005786:Gene Expression Regulation; D000860:Hypoxia / Q000235:genetics; D013552:Swine / Q000235:genetics* / Q000502:physiology; D014158:Transcription, Genetic