A screen for retrotransposed imprinted genes reveals an association between x chromosome homology and maternal germ-line methylation

PLoS Genetics

Volumn 3, Issue 2, 2007, Pages 0192-0203

  Wood, Andrew J ^a   Roberts, Roland G ^a   Monk, David ^b   Moore, Gudrun E ^b   Schulz, Reiner ^a   Oakey, Rebecca J ^a  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CHROMOSOME; CHROMOSOME 2; CORRELATION ANALYSIS; EPIGENETICS; FEMALE; GAMETOGENESIS; GENE SEQUENCE; GENETIC TRANSCRIPTION; GERM LINE; HUMAN; MALE; METHYLATION; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; RETROPOSON; SEQUENCE HOMOLOGY; X CHROMOSOME; ANIMAL; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; EXON; GENETICS; GENOME IMPRINTING; INTRON; METABOLISM; MOLECULAR GENETICS; OOCYTE; PHYLOGENY;

MAMMALIA;

ASPARTIC PROTEINASE; INOSITOL 1,4,5 TRISPHOSPHATE 5 PHOSPHATASE; INOSITOL-1,4,5-TRISPHOSPHATE 5-PHOSPHATASE; NERVE PROTEIN; ONCOPROTEIN; PHOSPHATASE; SIGNAL PEPTIDE PEPTIDASE; UNCLASSIFIED DRUG;

ANIMALS; ASPARTIC ENDOPEPTIDASES; BASE SEQUENCE; CPG ISLANDS; DNA METHYLATION; EXONS; FEMALE; GENOMIC IMPRINTING; HUMANS; INTRONS; MICE; MOLECULAR SEQUENCE DATA; NERVE TISSUE PROTEINS; ONCOGENE PROTEINS; OVUM; PHOSPHORIC MONOESTER HYDROLASES; PHYLOGENY; RETROELEMENTS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; X CHROMOSOME;

EID: 33847251033     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030020     Document Type: Article

References (57)

1. Li E, Beard C, Jaenisch R (1993) Role for DNA methylation in genomic imprinting. Nature 366: 362-365.
2. Walsh CP, Chaillet JR, Bestor TH (1998) Transcription of IAP endogenous retroviruses is constrained by cytosine methylation. Nat Genet 20: 116-117.
3. Bourc'his D, Bestor TH (2004) Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431: 96-99.
4. Barlow DP (1993) Methylation and imprinting: From host defense to gene regulation? Science 260: 309-310.
5. Yoder JA, Walsh C, Bestor TH (1997) Cytosine methylation and the ecology of intragenomic parasites. Nat Genet 13: 335-340.
6. Paulsen M, Walter J (2003) The potential role of gene duplications in the evolution of imprinting mechanisms. Hum Mol Genet 12: R215-R220.
7. Morison IM, Ramsay JP, Spencer HG (2005) A census of mammalian imprinting. Nat Genet 21: 457-465.
8. Youngson NA, Kocialkowski S, Peel N, Ferguson-Smith AC (2005) A small family of sushi-class retrotransposon-derived genes in mammals and their relation to genomic imprinting. J Mol Evol 61: 481-490.
9. Esnault C, Maestre J, Heidmann T (2000) Human LINE retrotransposons generate processed pseudogenes. Nat Genet 24: 363-367.
10. Vinckenbosch N, Dupanloup I, Kaessmann H (2006) Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A 103: 3220-3225.
11. Bradley J, Baltus A, Skaletsky H, Royce-Tolland M, Dewar K, et al. (2004) An X-to-autosome retrogene is required for spermatogenesis in mice. Nat Genet 36: 872-876.
12. Wang PJ (2004) X chromosomes, retrogenes, and their role in male reproduction. Trends Endocrinol Metab 15: 70-83.
13. Nabetani A, Hatada I, Morisaki H, Oshimura M, Mukai T (1997) Mouse U2af1-rs1 is a neomorphic-imprinted gene. Mol Cell Biol 17: 789-798.
14. Chai JH, Locke DP, Ohta T, Greally JM, Nicholls RD (2001) Retrotransposed genes such as Frat3 in the mouse Chromosome 7C Prader-Willi syndrome region acquire the imprinted status of their insertion site. Mamm Genome 12: 813-821.
15. Zhang Z, Joh K, Yatsuki H, Wang Y, Arai Y, et al. (2006) Comparative analyses of genomic imprinting and CpG island-methylation in mouse Murr1 and human MURR1 loci revealed a putative imprinting control region in mice. Gene 366: 77-86.
16. Beechey CV, Cattanach BM, Blake A, Peters J (2004) Mouse imprinting map. MRC Genetics Unit, Oxfordshire, United Kingdom. Available: http://www.mgu.har. mrc.ac.uk/research/imprinting. Accessed 18 December 2006.
17. Schwartz S, Kent JW, Smit A, Zhang Z, Baertsch R, et al. (2003) Human-mouse alignments with BLASTZ. Genome Res 13: 103-107.
18. Yang T, Adamson TE, Resnick JL, Leff S, Wevrick R, et al. (1998) A mouse model for Prader-Willi syndrome imprinting-centre mutations. Nat Genet 19: 25-31.
19. Lin SP, Youngson N, Takada S, Seitz H, Reik W, et al. (2003) Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gtl2 imprinted cluster on mouse Chromosome 12. Nat Genet 35: 97-102.
20. Smith RJ, Dean W, Konfortova G, Kelsey G (2003) Identification of novel imprinted genes in a genome-wide screen for maternal methylation. Genome Res 13: 558-569.
21. Choi JD, Underkoffler LA, Collins JN, Williams PT, Golden JA, et al. (2005) A novel variant of Inpp5f is imprinted in brain and its expression is correlated with differential methylation of an internal exonic CpG island. Mol Cell Biol 25: 5514-5522.
22. Long M, Betran E, Thornton K, Wang W (2003) The origin of new genes: Glimpses from the young and old. Nat Rev Genet 4: 865-875.
23. Kazazian HHJ (2004) Mobile elements: Drivers of genome evolution. Science 303: 1626-1632.
24. Emerson JJ, Kaessmann H, Betran E, Long M (2004) Extensive gene traffic on the mammalian X chromosome. Science 303: 537-540.
25. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The Human Genome Browser at UCSC http://genome.ucsc.edu. Genome Res 12: 996-1006.
26. Kent JW (2002) BLAT - the BLAST-like alignment tool. Genome Res 12: 656-664.
27. Verona RI, Mann MR, Bartolomei M (2003) Genomic imprinting: Intricacies of epigenetic regulation in clusters. Annu Rev Cell Dev Biol 19: 237-259.
28. Hutter B, Helms V, Paulsen M (2006) Tandem repeats in the CpG islands of imprinted genes. Genomics 88: 323-332.
29. Greally JM (2002) Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. Proc Natl Acad Sci U S A 99: 327-332.
30. Dierov J, Prosniak M, Gallia G, Garterhaus RB (1999) Increased G1 cyclin/cdk activity in cells overexpressing the candidate oncogene, MCT-1. J Cell Biochem 74: 544-550.
31. Prosniak M, Dierov J, Okami K, Tilton B, Jameson B, et al. (1998) A novel candidate oncogene, MCT-1, is involved in cell-cycle progression. Cancer Res 58: 4233-4237.
32. Shi B, Hsu HL, Evens AM, Gordon LI, Gartenhaus RB (2003) Expression of the candidate MCT-1 oncogene in B- and T-cell lymphoid malignancies. Blood 102: 297-302.
33. Wilting SM, Snijders PJ, Meijer GA, Ylstra B, van den Ijssel PR, et al. (2006) Increased gene copy numbers at Chromosome 20q are frequent in both squamous cell carcinomas and adenocarcinomas of the cervix. J Pathol 209: 220-230.
34. Tonon G, Wong KK, Maulik G, Brennan C, Feng B, et al. (2005) High-resolution genomic profiles of human lung cancer. Proc Natl Acad Sci U S A 102: 9625-9630.
35. Weihofen A, Binns K, Lemberg MK, Ashman K, Martoglio B (2002) Identification of signal peptide peptidase, a presenilin-type aspartic protease. Science 296: 2215-2218.
36. Snell GD, Cudkowicz G, Bunker HP (1967) Histocompatibility genes of mice. VII. H-13, a new histocompatibility locus in the fifth linkage group. Transplantation 5: 492-503.
37. Mendoza LM, Paz P, Zuberi A, Christianson G, Roopenian D, et al. (1997) Minors held by majors: The H13 minor histocompatibility locus defined as a peptide/MHC class I complex. Immunity 7: 461-472.
38. Loveland B, Wang CR, Yonekawa H, Hermel E, Lindahl KF (1990) Maternally transmitted histocompatibility antigen of mice: A hydrophobic peptide of a mitochondrially encoded protein. Cell 60: 971-980.
39. Bhuyan PK, Young LL, Lindahl KF, Butcher GW (1997) Identification of the rat maternally transmitted minor histocompatibility antigen. J Immunol 158: 3753-3760.
40. Wang Y, Joh K, Masuko S, Yatsuki H, Soejima H, et al. (2004) The mouse Murr1 gene is imprinted in the adult brain, presumably due to transcriptional interference by the antisense-oriented U2af1-rs1 gene. Mol Cell Biol 24: 270-279.
41. Gartler SM, Liskay RM, Gant N (1973) Two functional X chromosomes in human fetal oocytes. Exp Cell Res 82: 464-466.
42. Bourc'his D, Xu GL, Lin CS, Bollman B, Bestor TH (2001) Dnmt3L and the establishment of maternal genomic imprints. Science 294: 2536-2539.
43. McDonald JF, Matzke MA, Matzke AJ (2005) Host defenses to transposable elements and the evolution of genomic imprinting. Cytogenetics and Genome Res 110: 242-249.
44. Hatada I, Nabetani A, Arai Y, Oshishi S, Suzuki M, et al. (1997) Aberrant methylation of an imprinted gene U2af1-rs1(SP2) caused by its own transgene. J Biol Chem 272: 9120-9122.
45. Matzke MA, Aufsatz W, Kanno T, Mette MF, Matzke AJ (2002) Homologydependent gene silencing and host defense in plants. Adv Genet 46: 235-275.
46. Galagan JE, Selker EU (2004) RIP: The evolutionary cost of genome defense. Nat Genet 20: 417-423.
47. Aravin AA, Naumova NM, Tulin AV, Vagin VV, Rozovsky YM, et al. (2001) Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germ-line. Curr Biol 11: 1017-1027.
48. Meunier J, Khelifi A, Navratil V, Duret L (2005) Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci U S A 102: 5471-5476.
49. Rubin CM, VandeVoort CA, Teplitz RL, Schmid CW (1994) Alu repeated DNAs are differentially methylated in primate germ cells. Nucleic Acids Res 22: 5121-5127.
50. Day T, Bonduriansky R (2004) Intralocus sexual conflict can drive the evolution of genomic imprinting. Genetics 167: 1537-1546.
51. McCarrey JR, Thomas K (1987) Human testis-specific PGK gene lacks introns and possesses characteristics of a processed gene. Nature 326: 501-505.
52. Felsenstein J (1989) PHYLIP: Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
53. Olek A, Oswald J, Walter J (1996) A modified and improved method for bisulphate-based cytosine methylation analysis. Nucleic Acids Res 24: 5064-5066.
54. Kriegs JO, Churakov G, Keifmann M, Jordan U, Brosius J, et al. (2006) Retroposed elements as archives for the evolutionary history of placental mammals. PLoS Biol 4: e91. doi:10.1371/journal.pbio.0040091
55. Ono R, Shiura H, Aburatani H, Kohda T, Kaneko-Ishino T, et al. (2003) Identification of a large novel imprinted gene cluster on mouse proximal Chromosome 6. Genome Res 13: 1696-1705.
56. Lucifero D, Mertineit C, Clarke C, Bestor TH, Trasler JM (2002) Methylation dynamics of imprinted genes in mouse germ cells. Genomics 79: 530-538.
57. Takada S, Paulson M, Trevendale M, Tsai CE, Kelsey G, et al. (2002) Epigenetic analysis of the Dlk-Gtl2 imprinted domain on mouse Chromosome 12: Implications for imprinting control from comparisons with Igf2-H19. Hum Mol Genet 11: 77-86.