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Epigenomics Volume 4, 2012 - Issue 5
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Review

Epigenetic Implication of Gene-Adjacent Retroelements in Helicobacter Pylori-Infected Adults

Mun-Gan Rhyu1 Department of Microbiology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong Socho-gu, Seoul137–701, KoreaView further author information
,
Jung-Hwan Oh2 Department of Internal Medicine, College of Medicine, The Catholic University of Korea, 505 Banpo-dong Socho-gu, Seoul137–701, KoreaView further author information
&
Seung-Jin Hong1 Department of Microbiology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong Socho-gu, Seoul137–701, KoreaCorrespondence[email protected]
View further author information
Pages 527-535 | Published online: 06 Nov 2012

References

  • Mills JC , ShivdasaniRA. Gastric epithelial stem cells. Gastroenterology140(2) , 412–424 (2010).
  • Correa P , HoughtonJ. Carcinogenesis of Helicobacter pylori. Gastroenterology133(2) , 659–672 (2007).
  • Mcdonald SA , GreavesLC, Gutierrez-GonzalezLet al. Mechanisms of field cancerization in the human stomach: the expansion and spread of mutated gastric stem cells. Gastroenterology 134(2) , 500–510 (2008).
  • Houghton J , StoicovC, NomuraSet al. Gastric cancer originating from bone marrow-derived cells. Science 306(5701) , 1568–1571 (2004).
  • Gardiner-Garden M , FrommerM. CpG islands in vertebrate genomes. J. Mol. Biol.196(2) , 261–282 (1987).
  • Yoder JA , WalshCP, BestorTH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet.13(8) , 335–340 (1997).
  • Pennisi E . Behind the scenes of gene expression. Science293(5532) , 1064–1067 (2001).
  • Bird A . DNA methylation patterns and epigenetic memory. Genes Dev.16(1) , 6–21 (2002).
  • She X , RohlCA, CastleJC, KulkarniAV, JohnsonJM, ChenR. Definition, conservation and epigenetics of housekeeping and tissue-enriched genes. BMC Genomics10 , 269 (2009).
  • Maekita T , NakazawaK, MiharaMet al. High levels of aberrant DNA methylation in Helicobacter pylori-infected gastric mucosae and its possible association with gastric cancer risk. Clin. Cancer Res. 12(3 Pt 1) , 989–995 (2006).
  • Nakajima T , YamashitaS, MaekitaT, NiwaT, NakazawaK, UshijimaT. The presence of a methylation fingerprint of Helicobacter pylori infection in human gastric mucosae. Int. J. Cancer124(4) , 905–910 (2009).
  • Park SY , YooEJ, ChoNY, KimN, KangGH. Comparison of CpG island hypermethylation and repetitive DNA hypomethylation in premalignant stages of gastric cancer, stratified for Helicobacter pylori infection. J. Pathol.219(4) , 410–416 (2009).
  • Hong SJ , OhJH, JeonEJet al. The overmethylated genes in Helicobacter pylori-infected gastric mucosa are demethylated in gastric cancers. .BMC Gastroenterol. 10 , 137 (2010).
  • Van De Bovenkamp JH , Korteland-Van Male AM, Buller HA, Einerhand AW, Dekker J. Infection with Helicobacter pylori affects all major secretory cell populations in the human antrum. Dig. Dis. Sci.50(6) , 1078–1086 (2005).
  • Kang MI , RhyuMG, KimYHet al. The length of CpG islands is associated with the distribution of Alu and L1 retroelements. Genomics 87(5) , 580–590 (2006).
  • Kim YH , HongSJ, JungYCet al. The 5´-end transitional CpGs between the CpG islands and retroelements are hypomethylated in association with loss of heterozygosity in gastric cancers. BMC Cancer 6 , 180 (2006).
  • Kang MI , KimHS, JungYCet al. Transitional CpG methylation between promoters and retroelements of tissue-specific genes during human mesenchymal cell differentiation. J. Cell. Biochem. 102(1) , 224–239 (2007).
  • Jung YC , HongSJ, KimYHet al. Chromosomal losses are associated with hypomethylation of the gene-control regions in the stomach with a low number of active genes. J. Korean Med. Sci. 23(6) , 1068–1089 (2008).
  • Hong SJ , KangMI, OhJHet al. DNA methylation and expression patterns of key tissue-specific genes in adult stem cells and stomach tissues. J. Korean Med. Sci. 24(5) , 918–929 (2009).
  • Okumura T , WangSS, TakaishiSet al. Identification of a bone marrow-derived mesenchymal progenitor cell subset that can contribute to the gastric epithelium. Lab. Invest. 89(12) , 1410–1422 (2009).
  • Iglesias-Bartolome R , GutkindJS. Signaling circuitries controlling stem cell fate: to be or not to be. Curr. Opin Cell. Biol.23(6) , 716–723 (2011).
  • Misteli T . Beyond the sequence: cellular organization of genome function. Cell128(4) , 787–800 (2007).
  • Qu K , OrtolevaP. Understanding stem cell differentiation through self-organization theory. J. Theor. Biol.250(4) , 606–620 (2008).
  • Rajapakse I , PerlmanMD, ScalzoD, KooperbergC, GroudineM, KosakST. The emergence of lineage-specific chromosomal topologies from coordinate gene regulation. Proc. Natl Acad. Sci. USA106(16) , 6679–6684 (2009).
  • Li M , LiuGH, Izpisua Belmonte JC. Navigating the epigenetic landscape of pluripotent stem cells. Nat. Rev. Mol. Cell. Biol.13(8) , 524–535 (2012).
  • Birchler JA , BhadraU, BhadraMP, AugerDL. Dosage-dependent gene regulation in multicellular eukaryotes: implications for dosage compensation, aneuploid syndromes, and quantitative traits. Dev. Biol.234(2) , 275–288 (2001).
  • Easwaran HP , SchermellehL, LeonhardtH, CardosoMC. Replication-independent chromatin loading of Dnmt1 during G2 and M phases. EMBO Rep.5(12) , 1181–1186 (2004).
  • Deininger PL , BatzerMA. Mammalian retroelements. Genome Res.12(10) , 1455–1465 (2002).
  • Smit AF . The origin of interspersed repeats in the human genome. Curr. Opin Genet. Dev.6(6) , 743–748 (1996).
  • Lander ES , LintonLM, BirrenBet al. Initial sequencing and analysis of the human genome. Nature 409(6822) , 860–921 (2001).
  • Kim TM , HongSJ, RhyuMG. Periodic explosive expansion of human retroelements associated with the evolution of the hominoid primate. J. Korean Med. Sci.19(2) , 177–185 (2004).
  • Cordaux R , BatzerMA. The impact of retrotransposons on human genome evolution. Nat. Rev. Genet.10(10) , 691–703 (2009).
  • Kim TM , JungYC, RhyuMG. Alu and L1 retroelements are correlated with the tissue extent and peak rate of gene expression, respectively. J. Korean Med. Sci.19(6) , 783–792 (2004).
  • Medstrand P , Van De Lagemaat LN, Mager DL. Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res.12(10) , 1483–1495 (2002).
  • Jones PA . The DNA methylation paradox. Trends Genet.15(1) , 34–37 (1999).
  • Arnaud P , GoubelyC, PelissierT, DeragonJM. SINE retroposons can be used in vivo as nucleation centers for de novo methylation. Mol. Cell. Biol.20(10) , 3434–3441 (2000).
  • Turker MS . Gene silencing in mammalian cells and the spread of DNA methylation. Oncogene21(35) , 5388–5393 (2002).
  • Zhang Y , ShuJ, SiJ, ShenL, EstecioMR, IssaJP. Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island. Nucleic Acids Res.40(15) , 7257–7268 (2012).
  • Liu WM , ChuWM, ChoudaryPV, SchmidCW. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res.23(10) , 1758–1765 (1995).
  • Pandey R , MandalAK, JhaV, MukerjiM. Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism. Genome Biol.12(11) , R117 (2011).
  • Mathieu O , BenderJ. RNA-directed DNA methylation. J. Cell Sci.117(Pt 21) , 4881–4888 (2004).
  • Varon C , DubusP, MazurierFet al. Helicobacter pylori infection recruits bone marrow-derived cells that participate in gastric preneoplasia in mice. Gastroenterology142(2) , 281–291 (2012).
  • 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).
  • Eckhardt F , LewinJ, CorteseRet al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38(12) , 1378–1385 (2006).
  • Irizarry RA , Ladd-AcostaC, WenBet al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet. 41(2) , 178–186 (2009).
  • Doi A , ParkIH, WenBet al. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat. Genet. 41(12) , 1350–1353 (2009).
  • Ji H , EhrlichLI, SeitaJet al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 467(7313) , 338–342 (2010).
  • Hodges E , MolaroA, Dos Santos CO et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell.44(1) , 17–28 (2011).
  • Hansen KD , TimpW, BravoHCet al. Increased methylation variation in epigenetic domains across cancer types. Nat. Genet. 43(8) , 768–775 (2011).
  • Xie H , WangM, Bonaldo Mde F et al. Epigenomic analysis of Alu repeats in human ependymomas. Proc. Natl Acad. Sci. USA107(15) , 6952–6957 (2011).
  • Boumber YA , KondoY, ChenXet al. An Sp1/Sp3 binding polymorphism confers methylation protection. PLoS Genet. 4(8) , e1000162 (2008).
  • Estecio MR , GallegosJ, VallotCet al. Genome architecture marked by retrotransposons modulates predisposition to DNA methylation in cancer. Genome Res. 20(10) , 1369–1382 (2010).
  • Takeshima H , YamashitaS, ShimazuT, UshijimaT. Effects of genome architecture and epigenetic factors on susceptibility of promoter CpG islands to aberrant DNA methylation induction. Genomics98(3) , 182–188 (2011).
  • Walsh CP , BestorTH. Cytosine methylation and mammalian development. Genes Dev.13(1) , 26–34 (1999).
  • Yatabe Y , TavareS, ShibataD. Investigating stem cells in human colon by using methylation patterns. Proc. Natl Acad. Sci. USA98(19) , 10839–10844 (2001).
  • Beckmann J , ScheitzaS, WernetP, FischerJC, GiebelB. Asymmetric cell division within the human hematopoietic stem and progenitor cell compartment: identification of asymmetrically segregating proteins. Blood109(12) , 5494–5501 (2007).
  • Shibata D . Inferring human stem cell behaviour from epigenetic drift. J. Pathol.217(2) , 199–205 (2009).
  • Shin CM , KimN, JungYet al. Role of Helicobacter pylori infection in aberrant DNA methylation along multistep gastric carcinogenesis. Cancer Sci. 101(6) , 1337–1346 (2010).
  • Hong SJ , KimYH, ChoiYD, MinKO, ChoiSW, RhyuMG. Relationship between the extent of chromosomal losses and the pattern of CpG methylation in gastric carcinomas. J. Korean Med. Sci.20(5) , 790–805 (2005).
  • Hong SJ , OhJH, JungYCet al. DNA methylation patterns of ulcer-healing genes associated with the normal gastric mucosa of gastric cancers. J. Korean Med. Sci. 25(3) , 405–417 (2010).

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