Genome-wide identification of new imprinted genes

Briefings in Functional Genomics and Proteomics

Volumn 9, Issue 4, 2010, Pages 304-314

  Henckel, Amandine ^a   Arnaud, Philippe ^b  

^a MAX PLANCK INSTITUTE   (Germany)

^b CNRS   (France)

Author keywords

Allelic transcription; Chromatin signature; Imprinted genes; Whole genome screen

Indexed keywords

TRANSCRIPTOME;

ARTICLE; EPIGENETICS; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC SCREENING; GENOME; HUMAN; METHYLATION; NONHUMAN;

ALLELES; ANIMALS; CHROMATIN; EPIGENESIS, GENETIC; GENOMIC IMPRINTING; HUMANS; MODELS, GENETIC; TRANSCRIPTION, GENETIC;

EID: 77955350720     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/elq016     Document Type: Article

References (74)

1. Barton SC, Surani MA, Norris ML. Role of paternal and maternal genomes in mouse development. Nature 1984;311:374-6.
2. McGrath J, Solter D. Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell 1984;37:179-83.
3. Barlow DP, Stoger R, Herrmann BG, et al. The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus. Nature 1991;349:84-7.
4. Bartolomei MS, Zemel S, Tilghman SM. Parental imprinting of the mouse H19 gene. Nature 1991;351:153-5.
5. DeChiara TM, Robertson EJ, Efstratiadis A. Parental imprinting of the mouse insulin-like growth factor II gene. Cell 1991;64:849-59.
6. Monk D, Arnaud P, Apostolidou S, et al. Limited evolutionary conservation of imprinting in the human placenta. Proc Natl Acad Sci USA 2006;103:6623-8.
7. Morison IM, Ramsay JP, Spencer HG. A census of mammalian imprinting. Trends Genet 2005;21:457-65.
8. Barlow DP. Gametic imprinting in mammals. Science 1995;270:1610-3.
9. Nikaido I, Saito C, Mizuno Y, et al. Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Genome Res 2003;13:1402-9.
10. Smith FM, Garfield AS, Ward A. Regulation of growth and metabolism by imprinted genes. Cytogenet Genome Res 2006;113:279-91.
11. Wilkinson LS, Davies W, Isles AR. Genomic imprinting effects on brain development and function. Nat Rev Neurosci 2007;8:832-43.
12. Arnaud P, Feil R. Epigenetic deregulation of genomic imprinting in human disorders and following assisted reproduction. Birth Defects Res C EmbryoToday 2005; 75:81-97.
13. Feinberg AP, Cui H, Ohlsson R. DNA methylation and genomic imprinting: insights from cancer into epigenetic mechanisms. Semin Cancer Biol 2002;12:389-98.
14. Bourc'his D, Xu GL, Lin CS, et al. Dnmt3L and the establishment of maternal genomic imprints. Science 2001;294:2536-9.
15. Li E, Beard C, Jaenisch R. Role for DNA methylation in genomic imprinting. Nature 1993;366:362-5.
16. Kaneda M, Okano M, Hata K, et al. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 2004;429:900-3.
17. 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.
18. Cattanach BM, Kirk M. Differential activity of maternally and paternally derived chromosome regions in mice. Nature 1985;315:496-8.
19. Williamson CM, Blake A, Thomas S, et al. World Wide Website-Mouse. MRC Harwell: Oxfordshire, 2009.
20. Greally JM. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. Proc Natl Acad Sci USA 2002;99:327-32.
21. Ke X, Thomas NS, Robinson DO, Collins A. A novel approach for identifying candidate imprinted genes through sequence analysis of imprinted and control genes. Hum Genet 2002;111:511-20.
22. Ke X, Thomas NS, Robinson DO, Collins A. The distinguishing sequence characteristics of mouse imprinted genes. Mamm Genome 2002;13:639-45.
23. Wang Z, Fan H, Yang HH, et al. Comparative sequence analysis of imprinted genes between human and mouse to reveal imprinting signatures. Genomics 2004;83:395-401.
24. Wood AJ, Roberts RG, Monk D, et al. A screen for retrotransposed imprinted genes reveals an association between X chromosome homology and maternal germ-line methylation. PLoS Genet 2007;3:e20.
25. Luedi PP, Hartemink AJ, Jirtle RL. Genome-wide prediction of imprinted murine genes. Genome Res 2005;15: 875-84.
26. Luedi PP, Dietrich FS, Weidman JR, et al. Computational and experimental identification of novel human imprinted genes. Genome Res 2007;17:1723-30.
27. Ruf N, Bahring S, Galetzka D, et al. Sequence-based bioinformatic prediction and QUASEP identify genomic imprinting of the KCNK9 potassium channel gene in mouse and human. Hum Mol Genet 2007;16:2591-9.
28. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A. Widespread monoallelic expression on human autosomes. Science 2007;318:1136-40.
29. Pant PV, Tao H, Beilharz EJ, et al. Analysis of allelic differential expression in human white blood cells. Genome Res 2006;16:331-9.
30. Serre D, Gurd S, Ge B, etal. Differential allelic expression in the human genome: a robust approach to identify genetic and epigenetic cis-acting mechanisms regulating gene expression. PLoS Genet 2008;4:e1000006.
31. Kaneko-Ishino T, Kuroiwa Y, Miyoshi N, et al. Peg1/Mest imprinted gene on chromosome 6 identified by cDNA subtraction hybridization. Nat Genet 1995;11:52-9.
32. Mizuno Y, Sotomaru Y, Katsuzawa Y, et al. Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray. Biochem Biophys Res Commun 2002;290:1499-505.
33. Piras G, El Kharroubi A, Kozlov S, et al. Zac1 (Lot1), a potential tumor suppressor gene, and the gene for epsilonsarcoglycan are maternally imprinted genes: identification by a subtractive screen of novel uniparental fibroblast lines. MolCellBiol2000;20:3308-15.
34. Kobayashi H, Yamada K, Morita S, 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.
35. Ruf N, Dunzinger U, Brinckmann A, et al. Expression profiling of uniparental mouse embryos is inefficient in identifying novel imprinted genes. Genomics 2006;87:509-19.
36. Cattanach BM, Beechey CV. Genomic imprinting in the mouse: possible final analysis. In: Reik W, Surani A (eds). Genomic Imprinting. New York: Oxford University Press Inc., 1997:118-45.
37. Choi JD, Underkoffler LA, Collins JN, et al. Microarray expression profiling of tissues from mice with uniparental duplications of chromosomes 7 and 11 to identify imprinted genes. Mamm Genome 2001;12:758-64.
38. Choi JD, Underkoffler LA, Wood AJ, et al. A novel variant of Inpp5f is imprinted in brain, and its expression is correlated with differential methylation of an internal CpG island. Mol Cell Biol 2005;25:5514-22.
39. Menheniott TR, Woodfine K, Schulz R, et al. Genomic imprinting of Dopa decarboxylase in heart and reciprocal allelic expression with neighboring Grb10. Mol Cell Biol 2008;28:386-96.
40. Ogata T, Kagami M, Ferguson-Smith AC. Molecular mechanisms regulating phenotypic outcome in paternal and maternal uniparental disomy for chromosome 14. Epigenetics 2008;3:181-7.
41. Schulz R, Menheniott TR, Woodfine K, et al. Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies. Nucleic Acids Res 2006;34:e88.
42. Lo HS, Wang Z, Hu Y, et al. Allelic variation in gene expression is common in the human genome. Genome Res 2003;13:1855-62.
43. Bjornsson HT, Albert TJ, Ladd-Acosta CM, et al. SNP-specific array-based allele-specific expression analysis. Genome Res 2008;18:771-9.
44. Pollard KS, Serre D, Wang X, et al. A genome-wide approach to identifying novel-imprinted genes. Hum Genet 2008;122:625-34.
45. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009;10:57-63.
46. Wang X, Sun Q, McGrath SD, et al. Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS One 2008;3:e3839.
47. Babak T, Deveale B, Armour C, et al. Global survey of genomic imprinting by transcriptome sequencing. Curr Biol 2008;18:1735-41.
48. Maynard ND, Chen J, Stuart RK, et al. Genome-wide mapping of allele-specific protein-DNA interactions in human cells. Nat Methods 2008;5:307-9.
49. Delaval K, Govin J, Cerqueira F, et al. Differential histone modifications mark mouse imprinting control regions during spermatogenesis. EMBO J 2007;26:720-9.
50. Fournier C, Goto Y, Ballestar E, et al. Allele-specific histone lysine methylation marks regulatory regions at imprinted mouse genes. EMBOJ 2002;21:6560-70.
51. Henckel A, Nakabayashi K, Sanz LA, et al. Histone methylation is mechanistically linked to DNA methylation at imprinting control regions in mammals. Hum Mol Genet 2009;18:3375-83.
52. Yang Y, Li T, Vu TH, et al. The histone code regulating expression of the imprinted mouse Igf2r gene. Endocrinology 2003;144:5658-70.
53. Guibert S, Forne T, Weber M. Dynamic regulation of DNA methylation during mammalian development. Epigenomics 2009;1:81-9.
54. Huang YW, Huang TH, Wang LS. Profiling DNA methylomes from microarray to genome-scale sequencing. Technol Cancer ResTreat 2010;9:139-47.
55. Weber M, Davies JJ, Wittig D, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005;37:853-62.
56. Cokus SJ, Feng S, Zhang X, et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 2008;452:215-9.
57. Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009;10:669-80.
58. Hayashizaki Y, Shibata H, Hirotsune S, et al. Identification of an imprinted U2af binding protein related sequence on mouse chromosome 11 using the RLGS method. NatGenet 1994;6:33-40.
59. Kelsey G, Bodle D, Miller HJ, et al. Identification of imprinted loci by methylation-sensitive representational difference analysis: application to mouse distal chromosome 2. Genomics 1999;62:129-38.
60. Maeda N, Hayashizaki Y. Genome-wide survey of imprinted genes. Cytogenet Genome Res 2006;113:144-52.
61. Peters J, Beechey C. Identification and characterisation of imprinted genes in the mouse. Brief Funct Genomic Proteomic 2004;2:320-33.
62. Smith RJ, Arnaud P, Kelsey G. Identification and properties of imprinted genes and their control elements. Cytogenet Genome Res 2004;105:335-45.
63. Strichman-Almashanu LZ, Lee RS, Onyango PO, et al.A genome-wide screen for normally methylated human CpG islands that can identify novel imprinted genes. Genome Res 2002;12:543-54.
64. Yamada Y, Watanabe H, Miura F, et al.A comprehensive analysis of allelic methylation status of 314 Henckel and Arnaud CpG islands on human chromosome 21q. Genome Res 2004;14:247-66.
65. Lister R, Pelizzola M, Dowen RH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009;462:315-22.
66. Popp C, Dean W, Feng S, et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 2010;463:1101-5.
67. Kanber D, Berulava T, Ammerpohl O, et al. The human retinoblastoma gene is imprinted. PLoS Genet 2009;5:e1000790.
68. McEwen KR, Ferguson-Smith AC. Distinguishing epigenetic marks of developmental and imprinting regulation. Epigenetics Chromatin 2010;3:2.
69. Mikkelsen TS, Ku M, Jaffe DB, etal. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007;448:553-60.
70. Barski A, Cuddapah S, Cui K, et al. High-resolution profiling of histone methylations in the human genome. Cell 2007;129:823-37.
71. Hon G, Ren B, Wang W. ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol 2008;4:e1000201.
72. Hon G, Wang W, Ren B. Discovery and annotation of functional chromatin signatures in the human genome. PLoS Comput Biol 2009;5:e1000566.
73. Dindot SV, Person R, Strivens M, et al. Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions. Genome Res 2009;19:1374-83.
74. Wen B, Wu H, Bjornsson H, et al. Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification. Genome Res 2008;18:1806-13.