249
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Genome-Wide Epigenetic Landscape of Pig lincRNAs and their Evolution During Porcine Domestication

, , , , , , , , & show all
Pages 1603-1618 | Received 11 Sep 2017, Accepted 07 Feb 2018, Published online: 29 Oct 2018

References

  • Zhou ZY , LiA , WangLGet al. DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues . Sci. Rep.5 , 15435 ( 2015 ).
  • Spurlock ME , GablerNK . The development of porcine models of obesity and the metabolic syndrome . J. Nutr.138 ( 2 ), 397 – 402 ( 2008 ).
  • Schachtschneider KM , MadsenO , ParkC , RundLA , GroenenMAM , SchookLB . Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model . BMC Genomics16 , 743 ( 2015 ).
  • Yang S , LiX , LiK , FanB , TangZ . A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds . BMC Genet.15 , 7 ( 2014 ).
  • Giuffra E , KijasJM , AmargerV , CarlborgO , JeonJT , AnderssonL . The origin of the domestic pig: independent domestication and subsequent introgression . Genetics154 ( 4 ), 1785 – 1791 ( 2000 ).
  • Groenen MAM , ArchibaldAL , SchookLB . Analyses of pig genomes provide insight into porcine demography and evolution . Nature491 ( 7424 ), 393 – 398 ( 2012 ).
  • Watanabe T , HayashiY , KimuraJet al. Pig mitochondrial DNA: polymorphism, restriction map orientation, and sequence data . Biochem. Genet.24 ( 5–6 ), 385 – 396 ( 1986 ).
  • Okumura N , IshiguroN , NakanoM , HiraiK , MatsuiA , SaharaM . Geographic population structure and sequence divergence in the mitochondrial DNA control region of the Japanese wild boar (Sus scrofa leucomystax), with reference to those of domestic pigs . Biochem. Genet.34 ( 5–6 ), 179 – 189 ( 1996 ).
  • Li XL , YangS , TangZet al. Genome-wide scans to detect positive selection in Large White and Tongcheng pigs . Animal Genet.45 ( 3 ), 329 – 339 ( 2014 ).
  • Ramos-Onsins SE , Burgos-PazW , ManunzaA , AmillsM . Mining the pig genome to investigate the domestication process . Heredity (Edinb.)113 ( 6 ), 471 – 484 ( 2014 ).
  • Rubin CJ , MegensHJ , Martinez BarrioAet al. Strong signatures of selection in the domestic pig genome . Proc. Natl Acad. Sci. USA109 ( 48 ), 19529 – 19536 ( 2012 ).
  • Wilkinson S , LuZH , MegensHJ . Signatures of diversifying selection in European pig breeds . PLoS Genet.9 ( 4 ), e1003453 ( 2013 ).
  • Andersson L . Studying phenotypic evolution in domestic animals: a walk in the footsteps of Charles Darwin . Cold Spring Harb. Symp. Quant. Biol.74 , 319 – 325 ( 2009 ).
  • Ai H , FangX , YangBet al. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing . Nat. Genet.47 ( 3 ), 217 – 225 ( 2015 ).
  • Fang MY , LarsonG , RibeiroHS , LiN , AnderssonL . Contrasting mode of evolution at a coat color locus in wild and domestic pigs . PLoS Genet.5 ( 1 ), e1000341 ( 2009 ).
  • Li C , WangX , CaiHet al. Molecular microevolution and epigenetic patterns of the long non-coding gene H19 show its potential function in pig domestication and breed divergence . BMC Evol. Biol.16 , 87 ( 2016 ).
  • Zhao W , MuY , MaLet al. Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development . Sci. Rep.5 , 8957 ( 2015 ).
  • Zhou ZY , LiAM , AdeolaACet al. Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs . Genome Biol. Evol.6 ( 6 ), 1387 – 1392 ( 2014 ).
  • Vance KW , PontingCP . Transcriptional regulatory functions of nuclear long noncoding RNAs . Trends Genet.30 ( 8 ), 348 – 355 ( 2014 ).
  • Tsai MC , ManorO , WanYet al. Long noncoding RNA as modular scaffold of histone modification complexes . Science329 ( 5992 ), 689 – 693 ( 2010 ).
  • Gupta RA , ShahN , WangKCet al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis . Nature464 ( 7291 ), 1071 – 1076 ( 2010 ).
  • Orom UA , DerrienT , BeringerMet al. Long noncoding RNAs with enhancer-like function in human cells . Cell143 ( 1 ), 46 – 58 ( 2010 ).
  • Sleutels F , ZwartR , BarlowDP . The non-coding Air RNA is required for silencing autosomal imprinted genes . Nature415 ( 6873 ), 810 – 813 ( 2002 ).
  • Loewer S , CabiliMN , GuttmanMet al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells . Nat. Genet.42 ( 12 ), 1113 – 1117 ( 2010 ).
  • Guttman M , DonagheyJ , CareyBWet al. lincRNAs act in the circuitry controlling pluripotency and differentiation . Nature477 ( 7364 ), 295 – 300 ( 2011 ).
  • Borsani G , TonlorenziR , SimmlerMCet al. Characterization of a murine gene expressed from the inactive X chromosome . Nature351 ( 6324 ), 325 – 329 ( 1991 ).
  • Lakhotia SC . Divergent actions of long noncoding RNAs on X-chromosome remodelling in mammals and Drosophila achieve the same end result: dosage compensation . J. Genet.94 ( 4 ), 575 – 84 ( 2015 ).
  • Wang Y , HuT , WuL , LiuX , XueS , LeiM . Identification of non-coding and coding RNAs in porcine endometrium . Genomics109 ( 1 ), 43 – 50 ( 2017 ).
  • Yang Y , ZhouR , ZhuSet al. Systematic identification and molecular characteristics of long noncoding RNAs in pig tissues . Biomed. Res. Int.2017 , 6152582 ( 2017 ).
  • Zhao P , ZhengX , FengWet al. Profiling long noncoding RNA of multi-tissue transcriptome enhances porcine noncoding genome annotation . Epigenomics10 ( 3 ), 301 – 320 ( 2018 ).
  • Zou C , LiS , DengLet al. Transcriptome analysis reveals long intergenic noncoding RNAs contributed to growth and meat quality differences between Yorkshire and Wannanhua pig . Genes (Basel)8 ( 8 ), 8080203 ( 2017 ).
  • Li M , TianS , JinLet al. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars . Nat. Genet.45 ( 12 ), 1431 – 1438 ( 2013 ).
  • Schachtschneider KM , MadsenO , ParkC , RundLA , GroenenMAM , SchookLB . Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model . BMC Genomics16 ( 1 ), 743 ( 2015 ).
  • Pollier J , RombautsS , GoossensA . Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures . Methods Mol. Biol.1011 , 305 – 315 ( 2013 ).
  • Trapnell C , WilliamsBA , PerteaGet al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation . Nat. Biotechnol.28 ( 5 ), 511 – 515 ( 2010 ).
  • Trapnell C , RobertsA , GoffLet al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks . Nat. Protoc.7 ( 3 ), 562 – 578 ( 2012 ).
  • Kong L , ZhangY , YeZQet al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine . Nucleic Acids Res.35 ( Web Server issue ), W345 – W349 ( 2007 ).
  • Anders S , PylPT , HuberW . HTSeq – a Python framework to work with high-throughput sequencing data . Bioinformatics31 ( 2 ), 166 – 169 ( 2015 ).
  • McCarthy DJ , ChenY , SmythGK . Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation . Nucleic Acids Res.40 ( 10 ), 4288 – 4297 ( 2012 ).
  • Wang L , FengZ , WangX , WangX , ZhangX . DEGseq: an R package for identifying differentially expressed genes from RNA-seq data . Bioinformatics26 ( 1 ), 136 – 138 ( 2010 ).
  • Yanai I , BenjaminH , ShmoishMet al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification . Bioinformatics21 ( 5 ), 650 – 659 ( 2005 ).
  • Liao BY , ZhangJ . Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution . Mol. Biol. Evol.23 ( 6 ), 1119 – 1128 ( 2006 ).
  • Xiang H , ZhuJ , ChenQet al. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map . Nat. Biotechnol.28 ( 5 ), 516 – 520 ( 2010 ).
  • Quinlan AR , HallIM . BEDTools: a flexible suite of utilities for comparing genomic features . Bioinformatics26 ( 6 ), 841 – 842 ( 2010 ).
  • Huang da W , ShermanBT , ZhengXet al. Extracting biological meaning from large gene lists with DAVID . Curr. Protoc. Bioinformatics Chapter 13: p. Unit 13 11 ( 2009 ).
  • Krueger F , AndrewsSR . Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications . Bioinformatics27 ( 11 ), 1571 – 1572 ( 2011 ).
  • Li H , DurbinR . Fast and accurate short read alignment with Burrows–Wheeler transform . Bioinformatics25 ( 14 ), 1754 – 1760 ( 2009 ).
  • McKenna A , HannaM , BanksEet al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data . Genome Res.20 ( 9 ), 1297 – 1303 ( 2010 ).
  • Wu H , XuT , FengHet al. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates . Nucleic Acids Res.43 ( 21 ), e141 ( 2015 ).
  • Wu Y , ChengT , LiuCet al. Systematic identification and characterization of long non-coding RNAs in the silkworm, Bombyx mori . PLoS ONE11 ( 1 ), e0147147 ( 2016 ).
  • Cooper DN , YoussoufianH . The CpG dinucleotide and human genetic disease . Hum. Genet.78 ( 2 ), 151 – 155 ( 1988 ).
  • Sati S , GhoshS , JainV , ScariaV , SenguptaS . Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci . Nucleic Acids Res.40 ( 20 ), 10018 – 1031 ( 2012 ).
  • Cabili MN , TrapnellC , GoffLet al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses . Genes Dev.25 ( 18 ), 1915 – 1927 ( 2011 ).
  • Luo H , SunS , LiP , BuD , CaoH , ZhaoY . Comprehensive characterization of 10,571 mouse large intergenic noncoding RNAs from whole transcriptome sequencing . PLoS ONE8 ( 8 ), e70835 ( 2013 ).
  • Chen X , QiG , QinMet al. DNA methylation directly downregulates human cathelicidin antimicrobial peptide gene (CAMP) promoter activity . Oncotarget8 ( 17 ), 27943 – 27952 ( 2017 ).
  • Wei JW , HuangK , YangC , KangCS . Non-coding RNAs as regulators in epigenetics (review) . Oncol. Rep.37 ( 1 ), 3 – 9 ( 2017 ).
  • Li X , ZhuJ , HuFet al. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression . BMC Genomics13 , 300 ( 2012 ).
  • Guo H , ZhuP , YanLet al. The DNA methylation landscape of human early embryos . Nature511 ( 7511 ), 606 – 610 ( 2014 ).
  • Wang KC , YangYW , LiuBet al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression . Nature472 ( 7341 ), 120 – 124 ( 2011 ).
  • Cai L , ChangH , FangY , LiG . A comprehensive characterization of the function of LincRNAs in transcriptional regulation through long-range chromatin interactions . Sci. Rep.6 , 36572 ( 2016 ).
  • Cusick JK , MustianA , GoldbergK , ReylandME . RELT induces cellular death in HEK 293 epithelial cells . Cell Immunol.261 ( 1 ), 1 – 8 ( 2010 ).
  • Moua P , CheckettsM , XuLG , ShuHB , ReylandME , CusickJK . RELT family members activate p38 and induce apoptosis by a mechanism distinct from TNFR1 . Biochem. Biophys. Res. Commun.491 ( 1 ), 25 – 32 ( 2017 ).
  • He Z , BammannH , HanD , XieG , KhaitovichP . Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation . RNA20 ( 7 ), 1103 – 1111 ( 2014 ).
  • Ward M , McEwanC , MillsJD , JanitzM . Conservation and tissue-specific transcription patterns of long noncoding RNAs . J. Hum. Transcr.1 ( 1 ), 2 – 9 ( 2015 ).
  • Feschotte C . Transposable elements and the evolution of regulatory networks . Nat. Rev. Genet.9 ( 5 ), 397 – 405 ( 2008 ).
  • Necsulea A , SoumillonM , WarneforsMet al. The evolution of lncRNA repertoires and expression patterns in tetrapods . Nature505 ( 7485 ), 635 – 640 ( 2014 ).
  • Li A , ZhouZY , HeiXet al. Genome-wide discovery of long intergenic noncoding RNAs and their epigenetic signatures in the rat . Sci. Rep.7 ( 1 ), 14817 ( 2017 ).
  • Keller TE , YiSV . DNA methylation and evolution of duplicate genes . Proc. Natl Acad. Sci. USA111 ( 16 ), 5932 – 5937 ( 2014 ).
  • Nelson BR , MakarewichCA , AndersonDMet al. A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle . Science351 ( 6270 ), 271 – 275 ( 2016 ).
  • Wilusz JE , SunwooH , SpectorDL . Long noncoding RNAs: functional surprises from the RNA world . Genes Dev.23 ( 13 ), 1494 – 1504 ( 2009 ).
  • Song X , CaoG , JingLet al. Analysing the relationship between lncRNA and protein-coding gene and the role of lncRNA as ceRNA in pulmonary fibrosis . J. Cell Mol. Med.18 ( 6 ), 991 – 1003 ( 2014 ).
  • Yang Y , ZhouR , MuY , HouX , TangZ , LiK . Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds . Sci. Rep.6 , 30160 ( 2016 ).
  • Omenn GS . Evolution in health and medicine Sackler colloquium: evolution and public health . Proc. Natl Acad. Sci. USA107 ( Suppl. 1 ), 1702 – 1709 ( 2010 ).
  • Bykov IL , VakevaA , JarvelainenHA , MeriS , LindrosKO . Protective function of complement against alcohol-induced rat liver damage . Int. Immunopharmacol.4 ( 12 ), 1445 – 1454 ( 2004 ).
  • Liao JH , LiCC , WuSH , FanJW , GuHT , WangZW . Gene variations of sixth complement component affecting tacrolimus metabolism in patients with liver transplantation for hepatocellular carcinoma . Chin. Med. J. (Engl.)130 ( 14 ), 1670 – 1676 ( 2017 ).
  • Brauer RB , BaldwinWM3rd , WangDet al. Hepatic and extrahepatic biosynthesis of complement factor C6 in the rat . J. Immunol.153 ( 7 ), 3168 – 3176 ( 1994 ).
  • Wang Z , LiaoJ , WuS , LiC , FanJ , PengZ . Recipient C6 rs9200 genotype is associated with hepatocellular carcinoma recurrence after orthotopic liver transplantation in a Han Chinese population . Cancer Gene Ther.23 ( 6 ), 157 – 161 ( 2016 ).
  • Pasaje CF , BaeJS , ParkBLet al. Association analysis of C6 genetic variations and aspirin hypersensitivity in Korean asthmatic patients . Hum. Immunol.72 ( 10 ), 973 – 978 ( 2011 ).

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.