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Research Article

DNA Ethylation Changes and Evolution of RNA-Based Duplication in Sus Scrofa: Based on a Two-Step Strategy

, , , , , , & show all
Pages 199-218 | Received 05 Jun 2017, Accepted 13 Oct 2017, Published online: 15 Jan 2018

References

  • Kaessmann H . Origins, evolution, and phenotypic impact of new genes . Genome Res.20 ( 10 ), 1313 – 1326 ( 2010 ).
  • Long MY , VankurenNW , ChenSD , VibranovskiMD . New gene evolution: little did we know . Ann. Rev. Genetics47 , 307 – 333 ( 2013 ).
  • Chen SD , KrinskyBH , LongMY . New genes as drivers of phenotypic evolution . Nat. Rev. Genet.14 ( 9 ), 645 – 660 ( 2013 ).
  • Esnault C , MaestreJ , HeidmannT . Human LINE retrotransposons generate processed pseudogenes . Nat. Genet.24 ( 4 ), 363 – 367 ( 2000 ).
  • Gogvadze EV , BuzdinAA . New mechanism of retrogene formation in mammalian genomes: in vivo recombination during RNA reverse transcription . Mol. Biol. (Mosk.)39 ( 3 ), 364 – 373 ( 2005 ).
  • Marques AC , DupanloupI , VinckenboschN , ReymondA , KaessmannH . Emergence of young human genes after a burst of retroposition in primates . PLoS Biol.3 ( 11 ), e357 ( 2005 ).
  • Vinckenbosch N , DupanloupI , KaessmannH . Evolutionary fate of retroposed gene copies in the human genome . Proc. Natl Acad. Sci. USA103 ( 9 ), 3220 – 3225 ( 2006 ).
  • Fu B , ChenM , ZouM , LongM , HeS . The rapid generation of chimerical genes expanding protein diversity in zebrafish . BMC Genomics11 , 657 ( 2010 ).
  • Pan D , ZhangL . Burst of young retrogenes and independent retrogene formation in mammals . PLoS ONE4 ( 3 ), e5040 ( 2009 ).
  • De Cubas AA , KorpershoekE , Inglada-PerezLet al. DNA methylation profiling in pheochromocytoma and paraganglioma reveals diagnostic and prognostic markers . Clin. Cancer Res.21 ( 13 ), 3020 – 3030 ( 2015 ).
  • Lowdon RF , JangHS , WangT . Evolution of epigenetic regulation in vertebrate genomes . Trends Genet.32 ( 5 ), 269 – 283 ( 2016 ).
  • Khulan B , LiuL , RoseCM , BoyleAK , ManningJR , DrakeAJ . Glucocorticoids accelerate maturation of the heme pathway in fetal liver through effects on transcription and DNA methylation . Epigenetics11 ( 2 ), 103 – 109 ( 2016 ).
  • Carrel L , WillardHF . X-inactivation profile reveals extensive variability in X-linked gene expression in females . Nature434 ( 7031 ), 400 – 404 ( 2005 ).
  • Ehrlich M . DNA hypomethylation in cancer cells . Epigenomics1 ( 2 ), 239 – 259 ( 2009 ).
  • Weber M , HellmannI , StadlerMBet al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome . Nat. Genet.39 ( 4 ), 457 – 466 ( 2007 ).
  • Sasaki H , MatsuiY . Epigenetic events in mammalian germ-cell development: reprogramming and beyond . Nat. Rev. Genet.9 ( 2 ), 129 – 140 ( 2008 ).
  • Suzuki MM , BirdA . DNA methylation landscapes: provocative insights from epigenomics . Nat. Rev. Genet.9 ( 6 ), 465 – 476 ( 2008 ).
  • Meissner A , MikkelsenTS , GuHet al. Genome-scale DNA methylation maps of pluripotent and differentiated cells . Nature454 ( 7205 ), 766 – 770 ( 2008 ).
  • Goldberg AD , AllisCD , BernsteinE . Epigenetics: a landscape takes shape . Cell128 ( 4 ), 635 – 638 ( 2007 ).
  • Lou S , LeeHM , QinHet al. Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation . Genome Biol.15 ( 7 ), 408 ( 2014 ).
  • Maunakea AK , NagarajanRP , BilenkyMet al. Conserved role of intragenic DNA methylation in regulating alternative promoters . Nature466 ( 7303 ), 253 – 257 ( 2010 ).
  • Guo JU , SuY , ShinJHet al. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain . Nat. Neurosci.17 ( 2 ), 215 – 222 ( 2014 ).
  • Laine VN , GossmannTI , SchachtschneiderKMet al. Evolutionary signals of selection on cognition from the great tit genome and methylome . Nat. Commun.7 , 10474 ( 2016 ).
  • Schachtschneider KM , MadsenO , ParkC , RundLA , GroenenMA , SchookLB . Adult porcine genome-wide DNA methylation patterns support pigs as a biomedical model . BMC Genomics16 , 743 ( 2015 ).
  • Ball MP , LiJB , GaoYet al. Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells . Nat. Biotechnol.27 ( 4 ), 361 – 368 ( 2009 ).
  • Anderson OS , SantKE , DolinoyDC . Nutrition and epigenetics: an interplay of dietary methyl donors, one-carbon metabolism and DNA methylation . J. Nutr. Biochem.23 ( 8 ), 853 – 859 ( 2012 ).
  • Waterland RA . Epigenetic mechanisms and gastrointestinal development . J. Pediatr.149 ( 5 Suppl. ), S137 – S142 ( 2006 ).
  • Keller TE , YiSV . DNA methylation and evolution of duplicate genes . Proc. Natl Acad. Sci. USA111 ( 16 ), 5932 – 5937 ( 2014 ).
  • Zhong Z , DuK , YuQ , ZhangYE , HeS . Divergent DNA methylation provides insights into the evolution of duplicate genes in zebrafish . G3 (Bethesda)6 ( 11 ), 3581 – 3591 ( 2016 ).
  • Wang H , BeyeneG , ZhaiJet al. CG gene body DNA methylation changes and evolution of duplicated genes in cassava . Proc. Natl Acad. Sci. USA112 ( 44 ), 13729 – 13734 ( 2015 ).
  • Schroeder DI , JayashankarK , DouglasKCet al. Early developmental and evolutionary origins of gene body DNA methylation patterns in mammalian placentas . PLoS Genet.11 ( 8 ), e1005442 ( 2015 ).
  • Akram M , JamilMS , MehmoodZet al. Fast alignment (FASTA): a review article . J. Med. Plants Res.5 ( 32 ), 6931 – 6933 ( 2011 ).
  • Birney E , ClampM , DurbinR . Genewise and genomewise . Genome Res.14 ( 5 ), 988 – 995 ( 2004 ).
  • Yang Z . PAML 4: phylogenetic analysis by maximum likelihood . Mol. Biol. Evol.24 ( 8 ), 1586 – 1591 ( 2007 ).
  • Choi M , LeeJ , LeMTet al. Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing . DNA Res.22 ( 5 ), 343 – 355 ( 2015 ).
  • Krueger F , AndrewsSR . Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications . Bioinformatics27 ( 11 ), 1571 – 1572 ( 2011 ).
  • Kim D , LangmeadB , SalzbergSL . HISAT: a fast spliced aligner with low memory requirements . Nat. Methods12 ( 4 ), 357 – 360 ( 2015 ).
  • Pertea M , KimD , PerteaGM , LeekJT , SalzbergSL . Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown . Nat. Protoc.11 ( 9 ), 1650 – 1667 ( 2016 ).
  • Deng W , WangY , LiuZ , ChengH , XueY . HemI: a toolkit for illustrating heatmaps . PLoS ONE9 ( 11 ), e111988 ( 2014 ).
  • Hedges SB , DudleyJ , KumarS . TimeTree: a public knowledge-base of divergence times among organisms . Bioinformatics22 ( 23 ), 2971 – 2972 ( 2006 ).
  • Hardison RC , RoskinKM , YangSet al. Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution . Genome Res.13 ( 1 ), 13 – 26 ( 2003 ).
  • Emerson JJ , KaessmannH , BetranE , LongM . Extensive gene traffic on the mammalian X chromosome . Science303 ( 5657 ), 537 – 540 ( 2004 ).
  • Vibranovski MD , ZhangY , LongM . General gene movement off the X chromosome in the Drosophila genus . Genome Res.19 ( 5 ), 897 – 903 ( 2009 ).
  • Betran E , ThorntonK , LongM . Retroposed new genes out of the X in Drosophila . Genome Res.12 ( 12 ), 1854 – 1859 ( 2002 ).
  • Groenen MAM , ArchibaldAL , UenishiHet al. Analyses of pig genomes provide insight into porcine demography and evolution . Nature491 ( 7424 ), 393 – 398 ( 2012 ).
  • Wang W , ZhengH , FanCet al. High rate of chimeric gene origination by retroposition in plant genomes . Plant Cell18 ( 8 ), 1791 – 1802 ( 2006 ).
  • Zhang YE , LongMY . New genes contribute to genetic and phenotypic novelties in human evolution . Curr. Opin. Gene. Dev.29 , 90 – 96 ( 2014 ).
  • Okamura K , FeukL , Marques-BonetT , NavarroA , SchererSW . Frequent appearance of novel protein-coding sequences by frameshift translation . Genomics88 ( 6 ), 690 – 697 ( 2006 ).
  • Chen SD , ZhangYE , LongMY . New genes in drosophila quickly become essential . Science330 ( 6011 ), 1682 – 1685 ( 2010 ).
  • Betran E , WangW , JinL , LongM . Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene . Mol. Biol. Evol.19 ( 5 ), 654 – 663 ( 2002 ).
  • Wang S , RobinetP , SmithJD , GulshanK . ORMDL orosomucoid-like proteins are degraded by free-cholesterol-loading-induced autophagy . Proc. Natl Acad. Sci. USA112 ( 12 ), 3728 – 3733 ( 2015 ).
  • Yuneva M , ZamboniN , OefnerP , SachidanandamR , LazebnikY . Deficiency in glutamine but not glucose induces MYC-dependent apoptosis in human cells . J. Cell Biol.178 ( 1 ), 93 – 105 ( 2007 ).
  • Gouw AM , ToalGG , FelsherDW . Metabolic vulnerabilities of MYC-induced cancer . Oncotarget7 ( 21 ), 29879 – 29880 ( 2016 ).
  • Corbet C , FeronO . Metabolic and mind shifts: from glucose to glutamine and acetate addictions in cancer . Curr. Opin. Clin. Nutr. Metab. Care18 ( 4 ), 346 – 353 ( 2015 ).
  • Yamamoto T , ShimoyamaT , KuriyamaM . Dietary and enteral interventions for Crohn’s disease . Curr. Opin. Biotechnol.44 , 69 – 73 ( 2016 ).
  • Hunt BG , BrissonJA , YiSV , GoodismanMA . Functional conservation of DNA methylation in the pea aphid and the honeybee . Genome Biol. Evol.2 , 719 – 728 ( 2010 ).
  • Ji L , NeumannDA , SchmitzRJ . Crop epigenomics: identifying, unlocking, and harnessing cryptic variation in crop genomes . Mol. Plant8 ( 6 ), 860 – 870 ( 2015 ).
  • Su J , WangY , XingX , LiuJ , ZhangY . Genome-wide analysis of DNA methylation in bovine placentas . BMC Genomics15 , 12 ( 2014 ).
  • Chang AY , LiaoBY . DNA methylation rebalances gene dosage after mammalian gene duplications . Mol. Biol. Evol.29 ( 1 ), 133 – 144 ( 2012 ).
  • Rodin SN , RiggsAD . Epigenetic silencing may aid evolution by gene duplication . J. Mol. Evol.56 ( 6 ), 718 – 729 ( 2003 ).
  • Shukla S , KavakE , GregoryMet al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing . Nature479 ( 7371 ), 74 – 79 ( 2011 ).
  • Miura A , YonebayashiS , WatanabeK , ToyamaT , ShimadaH , KakutaniT . Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis . Nature411 ( 6834 ), 212 – 214 ( 2001 ).
  • Slotkin RK , MartienssenR . Transposable elements and the epigenetic regulation of the genome . Nat. Rev. Genet.8 ( 4 ), 272 – 285 ( 2007 ).
  • Yoder JA , WalshCP , BestorTH . Cytosine methylation and the ecology of intragenomic parasites . Trends Genet.13 ( 8 ), 335 – 340 ( 1997 ).
  • Huh I , ZengJ , ParkT , YiSV . DNA methylation and transcriptional noise . Epigenetics & Chromatin6 ( 1 ), 9 ( 2013 ).
  • Willing EM , RawatV , MandakovaTet al. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation . Nat. Plants1 , 14023 ( 2015 ).
  • Wicker T , SabotF , Hua-VanAet al. A unified classification system for eukaryotic transposable elements . Nat. Rev. Genet.8 ( 12 ), 973 – 982 ( 2007 ).
  • Fryxell KJ , MoonWJ . CpG mutation rates in the human genome are highly dependent on local GC content . Mol. Biol. Evol.22 ( 3 ), 650 – 658 ( 2005 ).
  • Nachman MW , CrowellSL . Estimate of the mutation rate per nucleotide in humans . Genetics156 ( 1 ), 297 – 304 ( 2000 ).
  • Wiebauer K , NeddermannP , HughesM , JiricnyJ . The repair of 5-methylcytosine deamination damage . EXS64 , 510 – 522 ( 1993 ).
  • Jjingo D , ConleyAB , YiSV , LunyakVV , JordanIK . On the presence and role of human gene-body DNA methylation . Oncotarget3 ( 4 ), 462 – 474 ( 2012 ).
  • Sarda S , ZengJ , HuntBG , YiSV . The evolution of invertebrate gene body methylation . Mol. Biol. Evol.29 ( 8 ), 1907 – 1916 ( 2012 ).
  • Buckler EST , HoltsfordTP . Zea ribosomal repeat evolution and substitution patterns . Mol. Biol. Evol.13 ( 4 ), 623 – 632 ( 1996 ).
  • Messeguer R , GanalMW , SteffensJC , TanksleySD . Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA . Plant Mol. Biol.16 ( 5 ), 753 – 770 ( 1991 ).

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