蓝塘猪和长白猪骨骼肌差异表达cis-NATs基因鉴定
详细信息    查看全文 | 推荐本文 |
  • 英文篇名:Comparison Study of Differential Expression Genes and cis-NATs of Skeletal Muscle Between Lantang and Landrace Pig
  • 作者:许月园 ; 齐晓龙 ; 候晔 ; 赵云霞 ; 栾宇 ; 周焕焕 ; 赵书红 ; 李新云
  • 英文作者:XU YueYuan;QI XiaoLong;HOU Ye;ZHAO YunXia;LUAN Yu;ZHOU HuanHuan;ZHAO ShuHong;LI XinYun;Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education;The Cooperative Innovation Center for Sustainable Pig Production;Key Laboratory of Pig Healthy Breeding, Ministry of Agriculture,Guangxi Yangxiang Co Ltd;
  • 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
  • 英文关键词:Lantang;;Landrace;;cis-natural antisense transcripts;;differential expression;;energy metabolism
  • 中文刊名:ZNYK
  • 英文刊名:Scientia Agricultura Sinica
  • 机构:华中农业大学农业动物遗传育种与繁殖教育部重点实验室;生猪健康养殖协同创新中心;农业部猪健康养殖重点实验室广西扬翔股份有限公司;
  • 出版日期:2018-05-14 16:37
  • 出版单位:中国农业科学
  • 年:2018
  • 期:v.51
  • 基金:国家自然科学基金项目(31672391,31601920);; 国家“863”项目(2013AA102502)
  • 语种:中文;
  • 页:ZNYK201809016
  • 页数:11
  • CN:09
  • ISSN:11-1328/S
  • 分类号:184-194
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。
        【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(|log2 FC|>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.
引文
[1]OSATO N,SUZUKI Y,IKEO K,GOJOBORI T.Transcriptional interferences in cis natural antisense transcripts of humans and mice.Genetics,2007,176(2):1299-1306.DOI:10.1534/genetics.106.069484.
    [2]CHEN J,SUN M,KENT W J,HUANG X,XIE H,WANG W,ZHOU G,SHI R Z,ROWLEY J D.Over 20%of human transcripts might form sense-antisense pairs.Nucleic Acids Research,2004,32(16):4812-4820.DOI:10.1093/nar/gkh818.
    [3]VANHéE-BROSSOLLET C,VAQUERO C.Do natural antisense transcripts make sense in eukaryotes.Gene,1998,211(1):1-9.
    [4]CHEN C,WEI R,QIAO R,REN J,YANG H,LIU C,HUANG L.A genome-wide investigation of expression characteristics of natural antisense transcripts in liver and muscle samples of pigs.PLo S ONE,2012,7(12):e52433.DOI:10.1371/journal.pone.0052433.
    [5]ZHANG J,ZHOU C,MA J,CHEN L,JIANG A,ZHU L,SHUAI S,WANG J,LI M,LI X.Breed,sex and anatomical location-specific gene expression profiling of the porcine skeletal muscles.BMC Genet,2013,14:53.DOI:10.1186/1471-2156-14-53.
    [6]BRAUNSCHWEIG M H,VAN LAERE A S,BUYS N,ANDERSSON L,ANDERSSON G.IGF2 antisense transcript expression in porcine postnatal muscle is affected by a quantitative trait nucleotide in intron 3.Genomics,2004,84(6):1021-1029.
    [7]SUN L,YU S,WANG H,FAN B,LIU B.NUDT6,the FGF-2's antisense gene,showed associations with fat deposition related traits in pigs.Molecular Biology Reports,2012,39(4):4119-4126.DOI:10.1007/s11033-011-1194-3.
    [8]PANDORF C E,HADDAD F,ROY R R,QIN A X,EDGERTON V R,BALDWIN K M.Dynamics of myosin heavy chain gene regulation in slow skeletal muscle:role of natural antisense RNA.Journal of Biological Chemistry,2006,281(50):38330-42.DOI:10.1074/jbc.M607249200.
    [9]PRESCOTT E M,PROUDFOOT N J.Transcriptional collision between convergent genes in budding yeast.Proceedings of the National Academy of Sciences of the United States of America,2002,99(13):8796-8801.DOI:10.1073/pnas.132270899.
    [10]BELTRAN M,PUIG I,PENA C,GARCIA J M,ALVAREZ A B,PENA R,BONILLA F,DE HERREROS A G.A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition.Genes Development,2008,22(6):756-769.DOI:10.1101/gad.455708.
    [11]BASS B L.RNA editing by adenosine deaminases that act on RNA.Annual Review of Biochemistry,2002,71:817-846.DOI:10.1146/annurev.biochem.71.110601.135501.
    [12]ROBB G B,CARSON A R,TAI S C,FISH J E,SINGH S,YAMADA T,SCHERER S W,NAKABAYASHI K,MARSDEN P A.Post-transcriptional regulation of endothelial nitric-oxide synthase by an overlapping antisense m RNA transcript.Journal of Biological Chemistry,2004,279(36):37982-37996.DOI:10.1074/jbc.M400271200.
    [13]SCHEELE C,PETROVIC N,FAGHIHI M A,LASSMANN T,FREDRIKSSON K,ROOYACKERS O,WAHLESTEDT C,GOOD L,TIMMONS J A.The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function.BMC Genomics,2007,8:74.DOI:10.1186/1471-2164-8-74.
    [14]OHHATA T,HOKI Y,SASAKI H,SADO T.Crucial role of antisense transcription across the Xist promoter in Tsix-mediated Xist chromatin modification.Development,2008,135(2):227-235.DOI:10.1242/dev.008490.
    [15]LI N,JOSKA T M,RUESCH C E,COSTER S J,BELDEN W J.The frequency natural antisense transcript first promotes,then represses,frequency gene expression via facultative heterochromatin.Proceedings of the National Academy of Sciences of the United States of America,2015,112(14):4357-62.DOI:10.1073/pnas.1406130112.
    [16]李加琪,张豪,刘小红,高萍,王翀,吴秋豪,张细权,陈瑶生.长白-蓝塘猪资源群第6号染色体的QTL检测.中国农业科学,2004,37(1):130-135.LI J Q,ZHANG H,LIU X H,GAO P,WANG C,WU Q H.QTL detection on chromosome 6 in Landrace-Lantang Pig resource population.Scientia Agricultura Sinica,2004,37(1):130-135,(in Chinses)
    [17]ZHAO X,MO D,LI A,GONG W,XIAO S,ZHANG Y,QIN L,NIU Y,GUO Y,LIU X,CONG P,HE Z,WANG C,LI J,CHEN Y.Comparative analyses by sequencing of transcriptomes during skeletal muscle development between pig breeds differing in muscle growth rate and fatness.PLo S ONE,2011,6(5):e19774.DOI:10.1371/journal.pone.0019774.
    [18]ZHAO Y,HOU Y,ZHAO C,LIU F,LUAN Y,JING L,LI X,ZHU M,ZHAO S.Cis-natural antisense transcripts are mainly Co-expressed with their sense transcripts and primarily related to energy metabolic pathways during muscle development.International Journal of Biological Sciences,2016,12(8):1010-1021.DOI:10.7150/ijbs.14825.
    [19]ROBINSON M D,MCCARTHY D J,SMYTH G K.edge R:a Bioconductor package for differential expression analysis of digital gene expression data.Bioinformatics,2010,26(1):139-140.DOI:10.1093/bioinformatics/btp616.
    [20]HUANG DA W,SHERMAN B T,LEMPICKI R A.Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.Nature Protocols,2009,4(1):44-57.DOI:10.1038/nprot.2008.211.
    [21]SHANNON P,MARKIEL A,OZIER O,BALIGA N S,WANG J T,RAMAGE D,AMIN N,SCHWIKOWSKI B,IDEKER T.Cytoscape:a software environment for integrated models of biomolecular interaction networks.Genome Research,2003,13(11):2498-504.DOI:10.1101/gr.1239303.
    [22]WANG X Q,YANG W J,YANG Z,SHU G,WANG S B,JIANG Q Y,YUAN L,WU T S.The differential proliferative ability of satellite cells in Lantang and Landrace pigs.PLo S ONE,2012,7(3):e32537.DOI:10.1371/journal.pone.0032537.
    [23]GUO J,SHAN T,WU T,ZHU L N,REN Y,AN S,WANG Y.Comparisons of different muscle metabolic enzymes and muscle fiber types in Jinhua and Landrace pigs.Journal of Animal Sciences,2011,89(1):185-191.DOI:10.2527/jas.2010-2983.
    [24]TE PAS M F,DE WIT A A,PRIEM J,CAGNAZZO M,DAVOLI R,RUSSO V,POOL M H.Transcriptome expression profiles in prenatal pigs in relation to myogenesis.Journal of Muscle Research and Cell Motility,2005,26(2-3):157-165.DOI:10.1007/s10974-005-7004-6.
    [25]李伯江,李平华,吴望军,李齐发,黄瑞华,刘红林.骨骼肌肌纤维形成机制的研究进展.中国农业科学,2014,47(6):1200-1207.LI B J,LI P H,WU W J,LI Q F,HUANG R H,LIU H L.Progresses in research of the mechanisms of skeletal muscle fiber formation.Scientia Agricultura Sinica,2014,47(6):1200-1207.(in Chinses)
    [26]BERCHTOLD M W,BRINKMEIER H,MUNTENER M.Calcium ion in skeletal muscle:its crucial role for muscle function,plasticity,and disease.Physiological Reviews,2000,80(3):1215-1265.DOI:10.1152/physrev.2000.80.3.1215.
    [27]LEFAUCHEUR L,ECOLAN P,LOSSEC G,GABILLARD J C,BUTLER-BROWNE G S,HERPIN P.Influence of early postnatal cold exposure on myofiber maturation in pig skeletal muscle.Journal of Muscle Research and Cell Motility,2001,22(5):439-452.DOI:10.1023/A:1014591818870.
    [28]赵晓,莫德林,张悦,龚雯,李安宁,陈瑶生.猪的骨骼肌生长发育研究进展.生命科学,2011,23(1):37-44.ZHAO X,MO D L,ZHANG Y,GONG W,LI A N,CHEN Y S.Progress in research on skeletal muscle growth and development in swine.Chinese Bulletin of Life Sciences,2011,23(1):37-44.(in Chinses)
    [29]PETTE D,STARON R S.Myosin isoforms,muscle fiber types,and transitions.Microscopy Research and Technique,2000,50(6):500-509.DOI:10.1002/1097-0029(20000915)50:6<500::AID-JEMT7>3.0.CO;2-7.
    [30]PICARD B,LEFAUCHEUR L,BERRI C,DUCLOS M J.Muscle fibre ontogenesis in farm animal species.Reproduction Nutrition Development,2002,42(5):415-431.DOI:10.1051/rnd:2002035.
    [31]WANK V,FISCHER M S,WALTER B,BAUER R.Muscle growth and fiber type composition in hind limb muscles during postnatal development in pigs.Cells Tissues Organs,2006,182(3/4):171-181.DOI:10.1159/000093966.

© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号

地址:北京市海淀区学院路29号 邮编:100083

电话:办公室:(+86 10)66554848;文献借阅、咨询服务、科技查新:66554700