1,458
Views
20
CrossRef citations to date
0
Altmetric
Research Paper

Epigenetic and transcriptional features of the novel human imprinted lncRNA GPR1AS suggest it is a functional ortholog to mouse Zdbf2linc

, , , , , , , , & show all
Pages 635-645 | Received 19 Mar 2013, Accepted 01 May 2013, Published online: 09 May 2013

References

  • Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, et al, ENCODE Project Consortium, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children’s Hospital Oakland Research Institute. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007; 447:799 - 816; http://dx.doi.org/10.1038/nature05874; PMID: 17571346
  • Kapranov P, Willingham AT, Gingeras TR. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet 2007; 8:413 - 23; http://dx.doi.org/10.1038/nrg2083; PMID: 17486121
  • Esteller M. Non-coding RNAs in human disease. Nat Rev Genet 2011; 12:861 - 74; http://dx.doi.org/10.1038/nrg3074; PMID: 22094949
  • Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, et al, Mouse Genome Sequencing Consortium. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol 2009; 7:e1000112; http://dx.doi.org/10.1371/journal.pbio.1000112; PMID: 19468303
  • Chodroff RA, Goodstadt L, Sirey TM, Oliver PL, Davies KE, Green ED, et al. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol 2010; 11:R72; http://dx.doi.org/10.1186/gb-2010-11-7-r72; PMID: 20624288
  • Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 2008; 105:716 - 21; http://dx.doi.org/10.1073/pnas.0706729105; PMID: 18184812
  • Ponting CP, Oliver PL, Reik W. Evolution and functions of long noncoding RNAs. Cell 2009; 136:629 - 41; http://dx.doi.org/10.1016/j.cell.2009.02.006; PMID: 19239885
  • Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011; 477:295 - 300; http://dx.doi.org/10.1038/nature10398; PMID: 21874018
  • Reik W, Walter J. Genomic imprinting: parental influence on the genome. Nat Rev Genet 2001; 2:21 - 32; http://dx.doi.org/10.1038/35047554; PMID: 11253064
  • Sasaki H, Matsui Y. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet 2008; 9:129 - 40; http://dx.doi.org/10.1038/nrg2295; PMID: 18197165
  • Sleutels F, Zwart R, Barlow DP. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 2002; 415:810 - 3; http://dx.doi.org/10.1038/415810a; PMID: 11845212
  • Mancini-Dinardo D, Steele SJ, Levorse JM, Ingram RS, Tilghman SM. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev 2006; 20:1268 - 82; http://dx.doi.org/10.1101/gad.1416906; PMID: 16702402
  • Williamson CM, Ball ST, Dawson C, Mehta S, Beechey CV, Fray M, et al. Uncoupling antisense-mediated silencing and DNA methylation in the imprinted Gnas cluster. PLoS Genet 2011; 7:e1001347; http://dx.doi.org/10.1371/journal.pgen.1001347; PMID: 21455290
  • Latos PA, Pauler FM, Koerner MV, Şenergin HB, Hudson QJ, Stocsits RR, et al. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 2012; 338:1469 - 72; http://dx.doi.org/10.1126/science.1228110; PMID: 23239737
  • Mohammad F, Pandey GK, Mondal T, Enroth S, Redrup L, Gyllensten U, et al. Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing. Development 2012; 139:2792 - 803; http://dx.doi.org/10.1242/dev.079566; PMID: 22721776
  • Williamson CM, Turner MD, Ball ST, Nottingham WT, Glenister P, Fray M, et al. Identification of an imprinting control region affecting the expression of all transcripts in the Gnas cluster. Nat Genet 2006; 38:350 - 5; http://dx.doi.org/10.1038/ng1731; PMID: 16462745
  • Korostowski L, Sedlak N, Engel N. The Kcnq1ot1 long non-coding RNA affects chromatin conformation and expression of Kcnq1, but does not regulate its imprinting in the developing heart. PLoS Genet 2012; 8:e1002956; http://dx.doi.org/10.1371/journal.pgen.1002956; PMID: 23028363
  • Babak T, Deveale B, Armour C, Raymond C, Cleary MA, van der Kooy D, et al. Global survey of genomic imprinting by transcriptome sequencing. Curr Biol 2008; 18:1735 - 41; http://dx.doi.org/10.1016/j.cub.2008.09.044; PMID: 19026546
  • Kobayashi H, Yamada K, Morita S, Hiura H, Fukuda A, Kagami M, et al. Identification of the mouse paternally expressed imprinted gene Zdbf2 on chromosome 1 and its imprinted human homolog ZDBF2 on chromosome 2. Genomics 2009; 93:461 - 72; http://dx.doi.org/10.1016/j.ygeno.2008.12.012; PMID: 19200453
  • Hiura H, Sugawara A, Ogawa H, John RM, Miyauchi N, Miyanari Y, et al. A tripartite paternally methylated region within the Gpr1-Zdbf2 imprinted domain on mouse chromosome 1 identified by meDIP-on-chip. Nucleic Acids Res 2010; 38:4929 - 45; http://dx.doi.org/10.1093/nar/gkq200; PMID: 20385583
  • Fang F, Hodges E, Molaro A, Dean M, Hannon GJ, Smith AD. Genomic landscape of human allele-specific DNA methylation. Proc Natl Acad Sci U S A 2012; 109:7332 - 7; http://dx.doi.org/10.1073/pnas.1201310109; PMID: 22523239
  • Kobayashi H, Sakurai T, Imai M, Takahashi N, Fukuda A, Yayoi O, et al. Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet 2012; 8:e1002440; http://dx.doi.org/10.1371/journal.pgen.1002440; PMID: 22242016
  • Kobayashi H, Sakurai T, Sato S, Nakabayashi K, Hata K, Kono T. Imprinted DNA methylation reprogramming during early mouse embryogenesis at the Gpr1-Zdbf2 locus is linked to long cis-intergenic transcription. FEBS Lett 2012; 586:827 - 33; http://dx.doi.org/10.1016/j.febslet.2012.01.059; PMID: 22449967
  • Hata K, Okano M, Lei H, Li E. Dnmt3L cooperates with the Dnmt3 family of de novo DNA methyltransferases to establish maternal imprints in mice. Development 2002; 129:1983 - 93; PMID: 11934864
  • Kagami M, O’Sullivan MJ, Green AJ, Watabe Y, Arisaka O, Masawa N, et al. The IG-DMR and the MEG3-DMR at human chromosome 14q32.2: hierarchical interaction and distinct functional properties as imprinting control centers. PLoS Genet 2010; 6:e1000992; http://dx.doi.org/10.1371/journal.pgen.1000992; PMID: 20585555
  • Hudson QJ, Seidl CI, Kulinski TM, Huang R, Warczok KE, Bittner R, et al. Extra-embryonic-specific imprinted expression is restricted to defined lineages in the post-implantation embryo. Dev Biol 2011; 353:420 - 31; http://dx.doi.org/10.1016/j.ydbio.2011.02.017; PMID: 21354127
  • Okae H, Hiura H, Nishida Y, Funayama R, Tanaka S, Chiba H, et al. Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression. Hum Mol Genet 2012; 21:548 - 58; http://dx.doi.org/10.1093/hmg/ddr488; PMID: 22025075
  • Kobayashi H, Sakurai T, Miura F, Imai M, Mochiduki K, Yanagisawa E, et al. High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res 2013; 23:616 - 27; http://dx.doi.org/10.1101/gr.148023.112; PMID: 23410886
  • Chotalia M, Smallwood SA, Ruf N, Dawson C, Lucifero D, Frontera M, et al. Transcription is required for establishment of germline methylation marks at imprinted genes. Genes Dev 2009; 23:105 - 17; http://dx.doi.org/10.1101/gad.495809; PMID: 19136628
  • Henckel A, Chebli K, Kota SK, Arnaud P, Feil R. Transcription and histone methylation changes correlate with imprint acquisition in male germ cells. EMBO J 2012; 31:606 - 15; http://dx.doi.org/10.1038/emboj.2011.425; PMID: 22117218
  • Smith EY, Futtner CR, Chamberlain SJ, Johnstone KA, Resnick JL. Transcription is required to establish maternal imprinting at the Prader-Willi syndrome and Angelman syndrome locus. PLoS Genet 2011; 7:e1002422; http://dx.doi.org/10.1371/journal.pgen.1002422; PMID: 22242001
  • Lewis A, Mitsuya K, Umlauf D, Smith P, Dean W, Walter J, et al. Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation. Nat Genet 2004; 36:1291 - 5; http://dx.doi.org/10.1038/ng1468; PMID: 15516931
  • Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458:223 - 7; http://dx.doi.org/10.1038/nature07672; PMID: 19182780
  • Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 2011; 25:1915 - 27; http://dx.doi.org/10.1101/gad.17446611; PMID: 21890647
  • Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129:1311 - 23; http://dx.doi.org/10.1016/j.cell.2007.05.022; PMID: 17604720
  • Tian D, Sun S, Lee JT. The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 2010; 143:390 - 403; http://dx.doi.org/10.1016/j.cell.2010.09.049; PMID: 21029862
  • Sado T, Brockdorff N. Advances in understanding chromosome silencing by the long non-coding RNA Xist. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110325; http://dx.doi.org/10.1098/rstb.2011.0325; PMID: 23166390
  • Ohhata T, Senner CE, Hemberger M, Wutz A. Lineage-specific function of the noncoding Tsix RNA for Xist repression and Xi reactivation in mice. Genes Dev 2011; 25:1702 - 15; http://dx.doi.org/10.1101/gad.16997911; PMID: 21852535
  • Vallot C, Huret C, Lesecque Y, Resch A, Oudrhiri N, Bennaceur-Griscelli A, et al. XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells. Nat Genet 2013; 45:239 - 41; http://dx.doi.org/10.1038/ng.2530; PMID: 23334669
  • Sato S, Yoshida W, Soejima H, Nakabayashi K, Hata K. Methylation dynamics of IG-DMR and Gtl2-DMR during murine embryonic and placental development. Genomics 2011; 98:120 - 7; http://dx.doi.org/10.1016/j.ygeno.2011.05.003; PMID: 21620950
  • Kumaki Y, Oda M, Okano M. QUMA: quantification tool for methylation analysis. Nucleic Acids Res 2008; 36:Web Server issue W170-5; http://dx.doi.org/10.1093/nar/gkn294; PMID: 18487274