Research Papers:

Analysis of Bos taurus and Sus scrofa X and Y chromosome transcriptome highlights reproductive driver genes

Faheem Ahmed Khan, Hui Liu, Hao Zhou, Kai Wang, Muhammad Tahir Ul Qamar, Nuruliarizki Shinta Pandupuspitasari and Zhang Shujun _

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Oncotarget. 2017; 8:54416-54433. https://doi.org/10.18632/oncotarget.17081

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Faheem Ahmed Khan1, Hui Liu1, Hao Zhou1, Kai Wang1, Muhammad Tahir Ul Qamar2, Nuruliarizki Shinta Pandupuspitasari1,3 and Zhang Shujun1

1Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education China, College of Animal Science and Technology Huazhong Agricultural University, Wuhan, China

2College of Informatics, Huazhong Agricultural University, Wuhan, China

3The Center for Biomedical Research, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China

Correspondence to:

Zhang Shujun, email: [email protected]

Keywords: spermatogenesis, spermiogenesis, fertilization, WGCNA, reproduction

Received: February 06, 2017     Accepted: March 08, 2017     Published: April 13, 2017


The biology of sperm, its capability of fertilizing an egg and its role in sex ratio are the major biological questions in reproductive biology. To answer these question we integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa and identified reproductive driver genes based on Weighted Gene Co-Expression Network Analysis (WGCNA) algorithm. Our strategy resulted in 11007 and 10445 unique genes consisting of 9 and 11 reproductive modules in Bos taurus and Sus scrofa, respectively. The consensus module calculation yields an overall 167 overlapped genes which were mapped to 846 DEGs in Bos taurus to finally get a list of 67 dual feature genes. We develop gene co-expression network of selected 67 genes that consists of 58 nodes (27 down-regulated and 31 up-regulated genes) enriched to 66 GO biological process (BP) including 6 GO annotations related to reproduction and two KEGG pathways. Moreover, we searched significantly related TF (ISRE, AP1FJ, RP58, CREL) and miRNAs (bta-miR-181a, bta-miR-17-5p, bta-miR-146b, bta-miR-146a) which targeted the genes in co-expression network. In addition we performed genetic analysis including phylogenetic, functional domain identification, epigenetic modifications, mutation analysis of the most important reproductive driver genes PRM1, PPP2R2B and PAFAH1B1 and finally performed a protein docking analysis to visualize their therapeutic and gene expression regulation ability.

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