蓝塘猪和长白猪骨骼肌差异表达cis-NATs基因鉴定

doi:10.3864/j.issn.0578-1752.2018.09.016

摘要/Abstract

摘要： 【目的】通过分析蓝塘猪和长白猪生长发育过程中品种间骨骼肌组织差异表达基因及顺式天然反义转录本（cis-natural antisense transcripts, cis-NATs），并以此为基础进行整合分析，探索cis-NATs调控猪骨骼肌生长发育的分子机理。【方法】使用差异表达分析鉴定蓝塘猪和长白猪胚胎期35 d至出生后180 d共10个时间点品种间差异表达基因及cis-NATs（|log₂FC|≥1且 FDR＜0.01）；然后通过功能富集分析注释出差异表达基因及cis-NATs对应的正义基因主要参与的GO生物学过程（P＜0.01）及KEGG通路(P＜0.05)；再根据与cis-NATs相关表达的基因数目筛选出cis-NATs主要参与的GO生物学过程和KEGG通路，并根据通路间的相同基因数目对所有KEGG通路进行整合；最后基于通路内cis-NATs及其正义基因在品种间的差异表达倍数进行通路可视化分析。【结果】在蓝塘和长白猪骨骼肌发育的10个时间点共鉴定出5 350个品种间差异表达基因和738个差异表达cis-NATs；GO分析结果显示品种间骨骼肌组织差异表达cis-NATs主要与肌肉发育及能量代谢等GO生物学过程中的基因相关表达；KEGG通路整合分析发现能量代谢通路之间关联性最强；其中线粒体三羧酸循环通路中基因及其相关表达的cis-NATs在仔猪出生后早期表达量较高；通路可视化分析发现在肌纤维生长的两个关键时间点即胚胎期49 d和77 d，蓝塘猪能量代谢相关通路中基因及其相关表达的cis-NATs显著高表达于长白猪，而出生后品种间表达模式的变化则主要集中在出生后2—90 d的出生后早期阶段。【结论】在蓝塘猪和长白猪骨骼肌发育的10个时间点，共鉴定出738个品种间差异表达的cis-NATs，功能注释结果表明这些cis-NATs主要通过与能量代谢通路中的基因相关表达从而参与影响蓝塘猪和长白猪品种间骨骼肌纤维发育差异。

关键词: 蓝塘猪, 长白猪, 顺势天然反义转录本, 差异表达, 能量代谢

Abstract: 【Objective】 This study was designed to analyze the molecular mechanism of pig skeletal muscle development regulated by cis-natural antisense transcripts (cis-NATs) by comparing the differential expression genes and cis-NATs between Lantang and Landrace pig during their skeletal muscle development. 【Method】In this study, the following steps were adopted: (i) The differential expression genes (DEGs) and cis-NATs comparing Lantang (LT) and Landrace (LR) pig breeds at 10 time-points distributed from 35 days-post-coitus (dpc) to 180 days-post-natum (dpn) were identified (|log₂FC|＞1 and FDR＜0.01). (ii) The significant biological process Gene Ontology (GO) terms (P＜0.01) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (P＜0.05) of the DEGs and the sense gene of differential expression cis-NATs were enriched via function enrichment analysis. (iii) Then the significant biological process GO terms and KEGG pathways that cis-NATS participated were filtered by the number of related genes of cis-NATs, and KEGG pathways were integrated by the number of same genes between pathways. Finally, visual analyses was conducted based on fold change of differential expression cis-NATs and their sense gene between breeds within pathways.【Result】A total of 5 350 DEGs and 738 differential expression cis-NATs were identified between LT and LR at 10 time points in this study. GO analysis showed that the expression of differential expression cis-NATs between LT and LR in skeletal muscle was primarily concerned with genes in biological process, including muscle development and energy metabolism. The integrated analysis of KEGG pathways found that energy metabolism pathways were strongly related by DE genes and their correlated cis-NATs. Moreover the expression of genes and their correlated cis-NATs were higher in pig mitochondrial citrate cycle pathway during early stages of birth than adulthood. The visual analyses of KEGG pathways showed that the expression level of energy metabolism pathway involved genes and their correlated cis-NATs were higher in LT than LR at 49 dpc and 77 dpc, which were two critical points for muscle fibers growth. The differences of expression patterns between LT and LR primarily appear at the early postnatal stages of 2 dpn-90 dpn. 【Conclusion】In this study, 738 differential expression cis-NATs were identified by comparing between LT and LR at 10 time points of skeletal muscle development. Function enrichment analysis showed that cis-NATs played a role in developmental differences of skeletal muscle fibers between LT and LR by interacting with genes expressed in energy metabolism related pathways.

Key words: Lantang, Landrace, cis-natural antisense transcripts, differential expression, energy metabolism

许月园，齐晓龙，侯晔，赵云霞，栾宇，周焕焕，赵书红，李新云. 蓝塘猪和长白猪骨骼肌差异表达cis-NATs基因鉴定[J]. 中国农业科学, 2018, 51(9): 1795-1805.

XU YueYuan, QI XiaoLong, HOU Ye, ZHAO YunXia, LUAN Yu, ZHOU HuanHuan, ZHAO ShuHong, LI XinYun. Comparison Study of Differential Expression Genes and cis-NATs of Skeletal Muscle Between Lantang and Landrace Pig[J]. Scientia Agricultura Sinica, 2018, 51(9): 1795-1805.

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