Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq

BMC Genomics

Research Article

Seoae Cho¹  Sojeong Ka²  Kelsey Caetano-Anolles³  Sandra Rodriguez-Zas³  Whan-Gook Nho⁴  Sungkwon Park⁵  Min Ji Kim⁵  Jin Young Jeong⁶  Minseok Seo⁷  Heebal Kim⁸  Hyun-Jeong Lee⁹ 

[1] CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, 151-919, Seoul, Republic of Korea;Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Republic of Korea;Department of Animal Sciences, University of Illinois, 61801, Urbana, IL, USA;Department of Swine & Poultry Science, National College of Agriculture and Fisheries, #1515 Kongjwipatjwi-ro, Wansan-gu, 560-500, Jeonju-si, Jeollabuk-do, Republic of Korea;Department of food science and technology, Sejong University, 98 Gun-Ja-Dong, 143-747, Seoul, Republic of Korea;Division of Animal Products R&D, National Institute of Animal science, #1500 Kongjwipatjwi-ro, Wansan-gu, 565-851, Jeonju-si, Jeollabuk-do, Republic of Korea;Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, 151-741, Seoul, South Korea, Republic of Korea;CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, 151-919, Seoul, Republic of Korea;Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, 151-741, Seoul, South Korea, Republic of Korea;CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, 151-919, Seoul, Republic of Korea;Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life Sciences, Seoul National University, 151-921, Seoul, Republic of Korea;Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, 151-741, Seoul, South Korea, Republic of Korea;Division of Animal Products R&D, National Institute of Animal science, #1500 Kongjwipatjwi-ro, Wansan-gu, 565-851, Jeonju-si, Jeollabuk-do, Republic of Korea;

关键词: RNA-seq;    Sexual dimorphism;    Tissue-specific gene expression;    ANODEV;   

DOI  :  10.1186/s12864-016-2400-4

 received in 2015-05-20, accepted in 2016-01-18,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundMolecular mechanisms associated with sexual dimorphism in cattle have not been well elucidated. Furthermore, as recent studies have implied that gene expression patterns are highly tissue specific, it is essential to investigate gene expression in a variety of tissues using RNA-seq. Here, we employed and compared two statistical methods, a simple two group test and Analysis of deviance (ANODEV), in order to investigate bovine sexually dimorphic genes in 40 RNA-seq samples distributed across two factors: sex and tissue.ResultsAs a result, we detected 752 sexually dimorphic genes across tissues from two statistical approaches and identified strong tissue-specific patterns of gene expression. Additionally, significantly detected sex-related genes shared between two mammal species (cattle and rat) were identified using qRT-PCR.ConclusionsResults of our analyses reveal that sexual dimorphism of metabolic tissues and pituitary gland in cattle involves various biological processes. Several differentially expressed genes between sexes in cattle and rat species are shared, but show tissue-specific patterns. Finally, we concluded that two distinct statistical approaches have their advantages and disadvantages in RNA-seq studies investigating multiple tissues.

【 授权许可】

CC BY   
© Seo et al. 2016