Abstract
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.
Highlights
The sex chromosomes XY or ZW in case of mammals or birds varies both phylogenetically and structurally among different taxonomical classes with many similar features and is under selective pressure that shapes their evolution [1, 2, 3]
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 Gene Ontology (GO) biological process (BP) including 6 GO annotations related to reproduction and two Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways
The 33-residue LIS1 homology (LisH) motif is found in eukaryotic intracellular proteins that is involved in microtubule dynamics, cell migration, nucleokinesis and most importantly in chromosome segregation when we look for its function in reproduction
Summary
The sex chromosomes XY or ZW in case of mammals or birds varies both phylogenetically and structurally among different taxonomical classes with many similar features and is under selective pressure that shapes their evolution [1, 2, 3]. Reproduction is the fundamental biological process by which animals produce their offspring In mammals it is done by sexual reproduction where a haploid sperm from male fertilizes a haploid oocyte to restore the chromosome number. The recent advances in sequencing technologies and its analysis have a strong potential to find out genes that can improve the overall reproductive performance of farm animals including cow and pig. To this end, we first integrated X and Y chromosome transcriptome across different species: Bos taurus and Sus scrofa to identify reproductive driver genes based on Weighted Gene www.impactjournals.com/oncotarget
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