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Molecular mechanisms of genomic imprinting and clinical implications for cancer

Published online by Cambridge University Press:  25 January 2011

Santiago Uribe-Lewis
Affiliation:
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK.
Kathryn Woodfine
Affiliation:
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK.
Lovorka Stojic
Affiliation:
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK.
Adele Murrell*
Affiliation:
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK.
*
*Corresponding author: Adele Murrell, Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK. E-mail: adele.murrell@cancer.org.uk

Abstract

Genomic imprinting is an epigenetic marking of genes in the parental germline that ensures the stable transmission of monoallelic gene expression patterns in a parent-of-origin-specific manner. Epigenetic marking systems are thus able to regulate gene activity independently of the underlying DNA sequence. Several imprinted gene products regulate cell proliferation and fetal growth; loss of their imprinted state, which effectively alters their dosage, might promote or suppress tumourigenic processes. Conversely, global epigenetic changes that underlie tumourigenesis might affect imprinted gene expression. Here, we review imprinted genes with regard to their roles in epigenetic predisposition to cancer, and discuss acquired epigenetic changes (DNA methylation, histone modifications and chromatin conformation) either as a result of cancer or as an early event in neoplasia. We also address recent work showing the potential role of noncoding RNA in modifying chromatin and affecting imprinted gene expression, and summarise the effects of loss of imprinting in cancer with regard to the roles that imprinted genes play in regulating growth signalling cascades. Finally, we speculate on the clinical applications of epigenetic drugs in cancer.

Type
Review Article
Copyright
Copyright © Cambridge University Press 2011

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References

References

1Cremer, T. and Cremer, M. (2010) Chromosome territories. Cold Spring Harbor Perspectives in Biology 2, a003889CrossRefGoogle ScholarPubMed
2Schoenfelder, S., Clay, I. and Fraser, P. (2010) The transcriptional interactome: gene expression in 3D. Current Opinion in Genetics and Development 20, 127-133CrossRefGoogle ScholarPubMed
3Kouzarides, T. (2007) Chromatin modifications and their function. Cell 128, 693-705CrossRefGoogle ScholarPubMed
4Jones, P.A. and Baylin, S.B. (2007) The epigenomics of cancer. Cell 128, 683-692CrossRefGoogle ScholarPubMed
5Filion, G.J. et al. (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143, 212-224CrossRefGoogle ScholarPubMed
6Rinn, J.L. et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129, 1311-1323CrossRefGoogle ScholarPubMed
7Varmuza, S. and Mann, M. (1994) Genomic imprinting – defusing the ovarian time bomb. Trends in Genetics 10, 118-123CrossRefGoogle ScholarPubMed
8Daponte, A. et al. (2008) Immature teratoma in pregnancy: a case report and literature review. European Journal of Gynaecological Oncology 29, 300-304Google ScholarPubMed
9Cheung, A.N. et al. (2009) Pathogenesis of choriocarcinoma: clinical, genetic and stem cell perspectives. Future Oncology 5, 217-231CrossRefGoogle ScholarPubMed
10Weksberg, R., Shuman, C. and Beckwith, J.B. (2010) Beckwith–Wiedemann syndrome. European Journal of Human Genetics 18, 8-14CrossRefGoogle ScholarPubMed
11Engel, J.R. et al. (2000) Epigenotype–phenotype correlations in Beckwith–Wiedemann syndrome. Journal of Medical Genetics 37, 921-926CrossRefGoogle ScholarPubMed
12Brown, K.W. et al. (2008) Frequency and timing of loss of imprinting at 11p13 and 11p15 in Wilms' tumor development. Molecular Cancer Research 6, 1114-1123CrossRefGoogle ScholarPubMed
13Murrell, A. (2006) Genomic imprinting and cancer: from primordial germ cells to somatic cells. ScientificWorldJournal 6, 1888-1910CrossRefGoogle ScholarPubMed
14Davies, H.D. et al. (2003) Myeloid leukemia in Prader–Willi syndrome. Jornal de Pediatria 142, 174-178CrossRefGoogle ScholarPubMed
15Kanber, D. et al. (2009) The human retinoblastoma gene is imprinted. PLoS Genetics 5, e1000790CrossRefGoogle ScholarPubMed
16Toguchida, J. et al. (1989) Preferential mutation of paternally derived RB gene as the initial event in sporadic osteosarcoma. Nature 338, 156-158CrossRefGoogle ScholarPubMed
17Kato, M.V. et al. (1994) Parental origin of germ-line and somatic mutations in the retinoblastoma gene. Human Genetics 94, 31-38CrossRefGoogle ScholarPubMed
18Schuler, A. et al. (2005) Age at diagnosis of isolated unilateral retinoblastoma does not distinguish patients with and without a constitutional RB1 gene mutation but is influenced by a parent-of-origin effect. European Journal of Cancer 41, 735-740CrossRefGoogle Scholar
19Kong, A. et al. (2009) Parental origin of sequence variants associated with complex diseases. Nature 462, 868-874CrossRefGoogle ScholarPubMed
20Murrell, A. et al. (2008) Distinct methylation changes at the IGF2-H19 locus in congenital growth disorders and cancer. PLoS One 3, e1849CrossRefGoogle Scholar
21Edwards, C.A. and Ferguson-Smith, A.C. (2007) Mechanisms regulating imprinted genes in clusters. Current Opinion in Cell Biology 19, 281-289CrossRefGoogle ScholarPubMed
22Feng, W. et al. (2008) Imprinted tumor suppressor genes ARHI and PEG3 are the most frequently down-regulated in human ovarian cancers by loss of heterozygosity and promoter methylation. Cancer 112, 1489-1502CrossRefGoogle ScholarPubMed
23Riemenschneider, M.J., Reifenberger, J. and Reifenberger, G. (2008) Frequent biallelic inactivation and transcriptional silencing of the DIRAS3 gene at 1p31 in oligodendroglial tumors with 1p loss. International Journal of Cancer 122, 2503-2510CrossRefGoogle ScholarPubMed
24Weber, F. et al. (2005) Silencing of the maternally imprinted tumor suppressor ARHI contributes to follicular thyroid carcinogenesis. Journal of Clinical Endocrinology and Metabolism 90, 1149-1155CrossRefGoogle ScholarPubMed
25Yuan, J. et al. (2003) Aberrant methylation and silencing of ARHI, an imprinted tumor suppressor gene in which the function is lost in breast cancers. Cancer Research 63, 4174-4180Google ScholarPubMed
26Kamikihara, T. et al. (2005) Epigenetic silencing of the imprinted gene ZAC by DNA methylation is an early event in the progression of human ovarian cancer. International Journal of Cancer 115, 690-700CrossRefGoogle ScholarPubMed
27Martinez, R. et al. (2009) A microarray-based DNA methylation study of glioblastoma multiforme. Epigenetics 4, 255-264CrossRefGoogle ScholarPubMed
28Li, Y., Meng, G. and Guo, Q.N. (2008) Changes in genomic imprinting and gene expression associated with transformation in a model of human osteosarcoma. Experimental and Molecular Pathology 84, 234-239CrossRefGoogle Scholar
29Ulaner, G.A. et al. (2003) Loss of imprinting of IGF2 and H19 in osteosarcoma is accompanied by reciprocal methylation changes of a CTCF-binding site. Human Molecular Genetics 12, 535-549CrossRefGoogle ScholarPubMed
30Cui, H. et al. (2002) Loss of imprinting in colorectal cancer linked to hypomethylation of H19 and IGF2. Cancer Research 62, 6442-6446Google ScholarPubMed
31Byun, H.M. et al. (2007) Examination of IGF2 and H19 loss of imprinting in bladder cancer. Cancer Research 67, 10753-10758CrossRefGoogle ScholarPubMed
32Takai, D. et al. (2001) Large scale mapping of methylcytosines in CTCF-binding sites in the human H19 promoter and aberrant hypomethylation in human bladder cancer. Human Molecular Genetics 10, 2619-2626CrossRefGoogle ScholarPubMed
33Wu, J. et al. (2008) Hypomethylated and hypermethylated profiles of H19DMR are associated with the aberrant imprinting of IGF2 and H19 in human hepatocellular carcinoma. Genomics 91, 443-450CrossRefGoogle ScholarPubMed
34Furukawa, S. et al. (2009) Yolk sac tumor but not seminoma or teratoma is associated with abnormal epigenetic reprogramming pathway and shows frequent hypermethylation of various tumor suppressor genes. Cancer Science 100, 698-708CrossRefGoogle ScholarPubMed
35Kondo, M. et al. (1995) Frequent loss of imprinting of the H19 gene is often associated with its overexpression in human lung cancers. Oncogene 10, 1193-1198Google ScholarPubMed
36Douc-Rasy, S. et al. (1996) High incidence of loss of heterozygosity and abnormal imprinting of H19 and IGF2 genes in invasive cervical carcinomas. Uncoupling of H19 and IGF2 expression and biallelic hypomethylation of H19. Oncogene 12, 423-430Google ScholarPubMed
37Hashimoto, K. et al. (1997) Loss of H19 imprinting and up-regulation of H19 and SNRPN in a case with malignant mixed Mullerian tumor of the uterus. Human Pathology 28, 862-865CrossRefGoogle Scholar
38Lynch, C.A. et al. (2002) Reactivation of a silenced H19 gene in human rhabdomyosarcoma by demethylation of DNA but not by histone hyperacetylation. Molecular Cancer 1, 2CrossRefGoogle Scholar
39Sun, Y. et al. (2006) IGF2 is critical for tumorigenesis by synovial sarcoma oncoprotein SYT-SSX1. Oncogene 25, 1042-1052CrossRefGoogle ScholarPubMed
40Kawakami, T. et al. (2006) Erasure of methylation imprint at the promoter and CTCF-binding site upstream of H19 in human testicular germ cell tumors of adolescents indicate their fetal germ cell origin. Oncogene 25, 3225-3236CrossRefGoogle ScholarPubMed
41Cui, H. et al. (2001) Loss of imprinting of insulin-like growth factor-II in Wilms' tumor commonly involves altered methylation but not mutations of CTCF or its binding site. Cancer Research 61, 4947-4950Google ScholarPubMed
42Yuan, E. et al. (2005) Genomic profiling maps loss of heterozygosity and defines the timing and stage dependence of epigenetic and genetic events in Wilms' tumors. Molecular Cancer Research 3, 493-502CrossRefGoogle ScholarPubMed
43Nakagawa, H. et al. (2001) Loss of imprinting of the insulin-like growth factor II gene occurs by biallelic methylation in a core region of H19-associated CTCF-binding sites in colorectal cancer. Proceedings of the National Academy of Sciences of the United States of America 98, 591-596CrossRefGoogle Scholar
44De Castro Valente Esteves, L.I. et al. (2006) H19-DMR allele-specific methylation analysis reveals epigenetic heterogeneity of CTCF binding site 6 but not of site 5 in head-and-neck carcinomas: a pilot case-control analysis. International Journal of Molecular Medicine 17, 397-404Google Scholar
45Honda, S. et al. (2008) Loss of imprinting of IGF2 correlates with hypermethylation of the H19 differentially methylated region in hepatoblastoma. British Journal of Cancer 99, 1891-1899CrossRefGoogle ScholarPubMed
46Li, X. et al. (1998) Promoter-specific methylation and expression alterations of igf2 and h19 are involved in human hepatoblastoma. International Journal of Cancer 75, 176-1803.0.CO;2-R>CrossRefGoogle ScholarPubMed
47Paradowska, A. et al. (2009) Aberrant epigenetic modifications in the CTCF binding domain of the IGF2/H19 gene in prostate cancer compared with benign prostate hyperplasia. International Journal of Oncology 35, 87-96CrossRefGoogle ScholarPubMed
48Arima, T. et al. (1997) Association of IGF2 and H19 imprinting with choriocarcinoma development. Cancer Genetics and Cytogenetics 93, 39-47CrossRefGoogle ScholarPubMed
49Dammann, R.H. et al. (2010) Frequent aberrant methylation of the imprinted IGF2/H19 locus and LINE1 hypomethylation in ovarian carcinoma. International Journal of Oncology 36, 171-179Google ScholarPubMed
50Cheng, Y.W. et al. (2010) Loss of imprinting and marked gene elevation are 2 forms of aberrant IGF2 expression in colorectal cancer. International Journal of Cancer 127, 568-577CrossRefGoogle ScholarPubMed
51Eriksson, T. et al. (2001) Methylation changes in the human IGF2 p3 promoter parallel IGF2 expression in the primary tumor, established cell line, and xenograft of a human hepatoblastoma. Experimental Cell Research 270, 88-95CrossRefGoogle ScholarPubMed
52Poirier, K. et al. (2003) Loss of parental-specific methylation at the IGF2 locus in human hepatocellular carcinoma. Journal of Pathology 201, 473-479CrossRefGoogle ScholarPubMed
53Sullivan, M.J. et al. (1999) Relaxation of IGF2 imprinting in Wilms tumours associated with specific changes in IGF2 methylation. Oncogene 18, 7527-7534CrossRefGoogle ScholarPubMed
54Ito, Y. et al. (2008) Somatically acquired hypomethylation of IGF2 in breast and colorectal cancer. Human Molecular Genetics 17, 2633-2643CrossRefGoogle ScholarPubMed
55Baba, Y. et al. (2010) Hypomethylation of the IGF2 DMR in colorectal tumors, detected by bisulfite pyrosequencing, is associated with poor prognosis. Gastroenterology Aug 2; [Epub ahead of print]CrossRefGoogle ScholarPubMed
56Li, Y. et al. (2009) Hypomethylation of the P3 promoter is associated with up-regulation of IGF2 expression in human osteosarcoma. Human Pathology 40, 1441-1447CrossRefGoogle ScholarPubMed
57Issa, J.P. et al. (1996) Switch from monoallelic to biallelic human IGF2 promoter methylation during aging and carcinogenesis. Proceedings of the National Academy of Sciences of the United States of America 93, 11757-11762CrossRefGoogle ScholarPubMed
58Xu, W. et al. (2006) LOI of IGF2 is associated with esophageal cancer and linked to methylation status of IGF2 DMR. Journal of Experiments and Clinical Cancer Research 25, 543-547Google ScholarPubMed
59El-Maarri, O. et al. (2003) Maternal alleles acquiring paternal methylation patterns in biparental complete hydatidiform moles. Human Molecular Genetics 12, 1405-1413CrossRefGoogle ScholarPubMed
60Dejeux, E. et al. (2009) Hypermethylation of the IGF2 differentially methylated region 2 is a specific event in insulinomas leading to loss-of-imprinting and overexpression. Endocrine-related Cancer 16, 939-952CrossRefGoogle ScholarPubMed
61Nakano, S. et al. (2006) Expression profile of LIT1/KCNQ1OT1 and epigenetic status at the KvDMR1 in colorectal cancers. Cancer Science 97, 1147-1154CrossRefGoogle ScholarPubMed
62Kuang, S.Q. et al. (2007) Differential tumor suppressor properties and transforming growth factor-beta responsiveness of p57KIP2 in leukemia cells with aberrant p57KIP2 promoter DNA methylation. Oncogene 26, 1439-1448CrossRefGoogle ScholarPubMed
63Pike, B.L. et al. (2008) DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status. Leukemia 22, 1035-1043CrossRefGoogle ScholarPubMed
64Astuti, D. et al. (2005) Epigenetic alteration at the DLK1-GTL2 imprinted domain in human neoplasia: analysis of neuroblastoma, phaeochromocytoma and Wilms' tumour. British Journal of Cancer 92, 1574-1580CrossRefGoogle ScholarPubMed
65Kawakami, T. et al. (2006) Imprinted DLK1 is a putative tumor suppressor gene and inactivated by epimutation at the region upstream of GTL2 in human renal cell carcinoma. Human Molecular Genetics 15, 821-830CrossRefGoogle ScholarPubMed
66Huang, J. et al. (2007) Up-regulation of DLK1 as an imprinted gene could contribute to human hepatocellular carcinoma. Carcinogenesis 28, 1094-1103CrossRefGoogle ScholarPubMed
67Gejman, R. et al. (2008) Selective loss of MEG3 expression and intergenic differentially methylated region hypermethylation in the MEG3/DLK1 locus in human clinically nonfunctioning pituitary adenomas. Journal of Clinical Endocrinology and Metabolism 93, 4119-4125CrossRefGoogle ScholarPubMed
68Benetatos, L. et al. (2008) Promoter hypermethylation of the MEG3 (DLK1/MEG3) imprinted gene in multiple myeloma. Clinical Lymphoma and Myeloma 8, 171-175CrossRefGoogle ScholarPubMed
69Benetatos, L. et al. (2010) CpG methylation analysis of the MEG3 and SNRPN imprinted genes in acute myeloid leukemia and myelodysplastic syndromes. Leukemia Research 34, 148-153CrossRefGoogle ScholarPubMed
70Zhao, J. et al. (2005) Hypermethylation of the promoter region is associated with the loss of MEG3 gene expression in human pituitary tumors. Journal of Clinical Endocrinology and Metabolism 90, 2179-2186CrossRefGoogle ScholarPubMed
71Savage, S.A. et al. (2007) Analysis of genes critical for growth regulation identifies insulin-like growth factor 2 receptor variations with possible functional significance as risk factors for osteosarcoma. Cancer Epidemiology, Biomarkers and Prevention 16, 1667-1674CrossRefGoogle ScholarPubMed
72Huang, Z. et al. (2006) High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer. Nucleic Acids Research 34, 555-563CrossRefGoogle ScholarPubMed
73Maegawa, S. et al. (2001) Epigenetic silencing of PEG3 gene expression in human glioma cell lines. Molecular Carcinogenesis 31, 1-9CrossRefGoogle ScholarPubMed
74Otsuka, S. et al. (2009) Aberrant promoter methylation and expression of the imprinted PEG3 gene in glioma. Proceedings of the Japan Academy – Series B: Physical and Biological Science 85, 157-165CrossRefGoogle ScholarPubMed
75Dowdy, S.C. et al. (2005) Biallelic methylation and silencing of paternally expressed gene 3 (PEG3) in gynecologic cancer cell lines. Gynecologic Oncology 99, 126-134CrossRefGoogle ScholarPubMed
76Kuerbitz, S.J. et al. (2002) Hypermethylation of the imprinted NNAT locus occurs frequently in pediatric acute leukemia. Carcinogenesis 23, 559-564CrossRefGoogle ScholarPubMed
77Revill, K. et al. (2009) Loss of neuronatin expression is associated with promoter hypermethylation in pituitary adenoma. Endocrine-related Cancer 16, 537-548CrossRefGoogle ScholarPubMed
78Li, J. et al. (2004) Imprinting of the human L3MBTL gene, a polycomb family member located in a region of chromosome 20 deleted in human myeloid malignancies. Proceedings of the National Academy of Sciences of the United States of America 101, 7341-7346CrossRefGoogle Scholar
79Kacem, S. and Feil, R. (2009) Chromatin mechanisms in genomic imprinting. Mammalian Genome 20, 544-556CrossRefGoogle ScholarPubMed
80Azuara, V. et al. (2006) Chromatin signatures of pluripotent cell lines. Nature Cell Biology 8, 532-538CrossRefGoogle ScholarPubMed
81Monk, D. et al. (2009) Reciprocal imprinting of human GRB10 in placental trophoblast and brain: evolutionary conservation of reversed allelic expression. Human Molecular Genetics 18, 3066-3074CrossRefGoogle ScholarPubMed
82Sanz, L.A. et al. (2008) A mono-allelic bivalent chromatin domain controls tissue-specific imprinting at Grb10. EMBO Journal 27, 2523-2532CrossRefGoogle ScholarPubMed
83McEwen, K.R. and Ferguson-Smith, A.C. (2010) Distinguishing epigenetic marks of developmental and imprinting regulation. Epigenetics and Chromatin 3, 2CrossRefGoogle ScholarPubMed
84Feinberg, A.P. and Vogelstein, B. (1983) Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301, 89-92CrossRefGoogle ScholarPubMed
85Fatemi, M. et al. (2001) The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. Journal of Molecular Biology 309, 1189-1199CrossRefGoogle Scholar
86Weaver, J.R., Susiarjo, M. and Bartolomei, M.S. (2009) Imprinting and epigenetic changes in the early embryo. Mammalian Genome 20, 532-543CrossRefGoogle ScholarPubMed
87Li, X. et al. (2008) A maternal-zygotic effect gene, Zfp57, maintains both maternal and paternal imprints. Developmental Cell 15, 547-557CrossRefGoogle ScholarPubMed
88Mackay, D.J. et al. (2008) Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57. Nature Genetics 40, 949-951CrossRefGoogle ScholarPubMed
89Nakamura, T. et al. (2007) PGC7/Stella protects against DNA demethylation in early embryogenesis. Nature Cell Biology 9, 64-71CrossRefGoogle ScholarPubMed
90Schoenherr, C.J., Levorse, J.M. and Tilghman, S.M. (2003) CTCF maintains differential methylation at the Igf2/H19 locus. Nature Genetics 33, 66-69CrossRefGoogle ScholarPubMed
91Rhee, I. et al. (2002) DNMT1 and DNMT3b cooperate to silence genes in human cancer cells. Nature 416, 552-556CrossRefGoogle ScholarPubMed
92Wu, S.C. and Zhang, Y. (2010) Active DNA demethylation: many roads lead to Rome. Nature Reviews. Molecular Cell Biology 11, 607-620CrossRefGoogle ScholarPubMed
93Lucci-Cordisco, E. and Neri, G. (2009) Silent beginning: early silencing of the MED1/MBD4 gene in colorectal tumorigenesis. Cancer Biology and Therapy 8, 192-193Google ScholarPubMed
94Tahiliani, M. et al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930-935CrossRefGoogle ScholarPubMed
95Sparmann, A. and van Lohuizen, M. (2006) Polycomb silencers control cell fate, development and cancer. Nature Reviews. Cancer 6, 846-856CrossRefGoogle ScholarPubMed
96Simon, J.A. and Kingston, R.E. (2009) Mechanisms of polycomb gene silencing: knowns and unknowns. Nature Reviews. Molecular Cell Biology 10, 697-708CrossRefGoogle Scholar
97Cao, R. et al. (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298, 1039-1043CrossRefGoogle ScholarPubMed
98Schwartz, Y.B. and Pirrotta, V. (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nature Reviews. Genetics 8, 9-22CrossRefGoogle ScholarPubMed
99Wang, J. et al. (2001) Imprinted X inactivation maintained by a mouse polycomb group gene. Nature Genetics 28, 371-375CrossRefGoogle ScholarPubMed
100Pandey, R.R. et al. (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Molecular Cell 32, 232-246CrossRefGoogle ScholarPubMed
101Terranova, R. et al. (2008) Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Developmental Cell 15, 668-679CrossRefGoogle ScholarPubMed
102Redrup, L. et al. (2009) The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development 136, 525-530CrossRefGoogle Scholar
103Bracken, A.P. and Helin, K. (2009) Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nature Reviews. Cancer 9, 773-784CrossRefGoogle ScholarPubMed
104Pasini, D. et al. (2008) Regulation of stem cell differentiation by histone methyltransferases and demethylases. Cold Spring Harbor Symppsia on Quantitative Biology 73, 253-263CrossRefGoogle ScholarPubMed
105Ohm, J.E. et al. (2007) A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nature Genetics 39, 237-242CrossRefGoogle ScholarPubMed
106Vire, E. et al. (2006) The polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871-874CrossRefGoogle ScholarPubMed
107Tiwari, V.K. et al. (2008) A novel 6C assay uncovers Polycomb-mediated higher order chromatin conformations. Genome Research 18, 1171-1179CrossRefGoogle ScholarPubMed
108Smallwood, A. et al. (2007) Functional cooperation between HP1 and DNMT1 mediates gene silencing. Genes and Development 21, 1169-1178CrossRefGoogle ScholarPubMed
109Esteve, P.O. et al. (2006) Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes and Development 20, 3089-3103CrossRefGoogle ScholarPubMed
110Tachibana, M. et al. (2008) G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription. EMBO Journal 27, 2681-2690CrossRefGoogle ScholarPubMed
111Wagschal, A. et al. (2008) G9a histone methyltransferase contributes to imprinting in the mouse placenta. Molecular and Cellular Biology 28, 1104-1113CrossRefGoogle ScholarPubMed
112Nagano, T. et al. (2008) The air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322, 1717-1720CrossRefGoogle ScholarPubMed
113Ueda, J. et al. (2006) Zinc finger protein Wiz links G9a/GLP histone methyltransferases to the co-repressor molecule CtBP. Journal of Biological Chemistry 281, 20120-20128CrossRefGoogle Scholar
114Huang, J. et al. (2010) G9a and Glp methylate lysine 373 in the tumor suppressor p53. Journal of Biological Chemistry 285, 9636-9641CrossRefGoogle ScholarPubMed
115Pannetier, M. et al. (2008) PR-SET7 and SUV4-20H regulate H4 lysine-20 methylation at imprinting control regions in the mouse. EMBO Report 9, 998-1005CrossRefGoogle ScholarPubMed
116Nielsen, S.J. et al. (2001) Rb targets histone H3 methylation and HP1 to promoters. Nature 412, 561-565CrossRefGoogle ScholarPubMed
117Sewalt, R.G. et al. (2002) Selective interactions between vertebrate polycomb homologs and the SUV39H1 histone lysine methyltransferase suggest that histone H3-K9 methylation contributes to chromosomal targeting of polycomb group proteins. Molecular and Cellular Biology 22, 5539-5553CrossRefGoogle ScholarPubMed
118Frontelo, P. et al. (2004) Suv39h histone methyltransferases interact with Smads and cooperate in BMP-induced repression. Oncogene 23, 5242-5251CrossRefGoogle ScholarPubMed
119Peters, A.H. et al. (2001) Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability. Cell 107, 323-337CrossRefGoogle ScholarPubMed
120Ayton, P.M. and Cleary, M.L. (2001) Molecular mechanisms of leukemogenesis mediated by MLL fusion proteins. Oncogene 20, 5695-5707CrossRefGoogle ScholarPubMed
121Patel, A. et al. (2009) On the mechanism of multiple lysine methylation by the human mixed lineage leukemia protein-1 (MLL1) core complex. Journal of Biological Chemistry 284, 24242-24256CrossRefGoogle ScholarPubMed
122Esteve, P.O. et al. (2009) Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells. Proceedings of the National Academy of Sciences of the United States of America 106, 5076-5081CrossRefGoogle ScholarPubMed
123Ciccone, D.N. et al. (2009) KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. Nature 461, 415-418CrossRefGoogle ScholarPubMed
124Wang, Y. et al. (2009) LSD1 is a subunit of the NuRD complex and targets the metastasis programs in breast cancer. Cell 138, 660-672CrossRefGoogle ScholarPubMed
125Zhang, Y. et al. (1999) Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes and Development 13, 1924-1935CrossRefGoogle Scholar
126Reese, K.J. et al. (2007) Maintenance of paternal methylation and repression of the imprinted H19 gene requires MBD3. PLoS Genetics 3, e137CrossRefGoogle ScholarPubMed
127Klose, R.J. et al. (2007) The retinoblastoma binding protein RBP2 is an H3K4 demethylase. Cell 128, 889-900CrossRefGoogle ScholarPubMed
128Schotta, G. et al. (2004) A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes and Development 18, 1251-1262CrossRefGoogle ScholarPubMed
129Nishioka, K. et al. (2002) PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Molecular Cell 9, 1201-1213CrossRefGoogle ScholarPubMed
130Fraga, M.F. et al. (2005) Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nature Genetics 37, 391-400CrossRefGoogle ScholarPubMed
131Tryndyak, V.P., Kovalchuk, O. and Pogribny, I.P. (2006) Loss of DNA methylation and histone H4 lysine 20 trimethylation in human breast cancer cells is associated with aberrant expression of DNA methyltransferase 1, Suv4-20h2 histone methyltransferase and methyl-binding proteins. Cancer Biology and Therapy 5, 65-70CrossRefGoogle ScholarPubMed
132Wu, M.Y., Tsai, T.F. and Beaudet, A.L. (2006) Deficiency of Rbbp1/Arid4a and Rbbp1l1/Arid4b alters epigenetic modifications and suppresses an imprinting defect in the PWS/AS domain. Genes and Development 20, 2859-2870CrossRefGoogle ScholarPubMed
133Zhao, Q. et al. (2009) PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nature Structural and Molecular Biology 16, 304-311CrossRefGoogle ScholarPubMed
134Jelinic, P., Stehle, J.C. and Shaw, P. (2006) The testis-specific factor CTCFL cooperates with the protein methyltransferase PRMT7 in H19 imprinting control region methylation. PLoS Biology 4, e355CrossRefGoogle ScholarPubMed
135Ohlsson, R., Lobanenkov, V. and Klenova, E. (2010) Does CTCF mediate between nuclear organization and gene expression? Bioessays 32, 37-50CrossRefGoogle ScholarPubMed
136Nguyen, P. et al. (2008) CTCFL/BORIS is a methylation-independent DNA-binding protein that preferentially binds to the paternal H19 differentially methylated region. Cancer Research 68, 5546-5551CrossRefGoogle Scholar
137Zilberman, D. et al. (2008) Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature 456, 125-129CrossRefGoogle ScholarPubMed
138Barski, A. et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837CrossRefGoogle ScholarPubMed
139Costanzi, C. et al. (2000) Histone macroH2A1 is concentrated in the inactive X chromosome of female preimplantation mouse embryos. Development 127, 2283-2289CrossRefGoogle ScholarPubMed
140Choo, J.H. et al. (2006) Allele-specific deposition of macroH2A1 in imprinting control regions. Human Molecular Genetics 15, 717-724CrossRefGoogle ScholarPubMed
141Rasmussen, T.P. et al. (1999) Messenger RNAs encoding mouse histone macroH2A1 isoforms are expressed at similar levels in male and female cells and result from alternative splicing. Nucleic Acids Research 27, 3685-3689CrossRefGoogle ScholarPubMed
142Zhang, R. et al. (2005) Formation of MacroH2A-containing senescence-associated heterochromatin foci and senescence driven by ASF1a and HIRA. Developmental Cell 8, 19-30CrossRefGoogle ScholarPubMed
143Sporn, J.C. et al. (2009) Histone macroH2A isoforms predict the risk of lung cancer recurrence. Oncogene 28, 3423-3428CrossRefGoogle ScholarPubMed
144Nativio, R. et al. (2009) Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus. PLoS Genetics 5, e1000739CrossRefGoogle ScholarPubMed
145Vu, T.H., Nguyen, A.H. and Hoffman, A.R. (2010) Loss of IGF2 imprinting is associated with abrogation of long-range intrachromosomal interactions in human cancer cells. Human Molecular Genetics 19, 901-919CrossRefGoogle ScholarPubMed
146Hadjur, S. et al. (2009) Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 460, 410-413CrossRefGoogle ScholarPubMed
147Mishiro, T. et al. (2009) Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster. EMBO Journal 28, 1234-1245CrossRefGoogle ScholarPubMed
148Taft, R.J. et al. (2010) Non-coding RNAs: regulators of disease. Journal of Pathology 220, 126-139CrossRefGoogle ScholarPubMed
149Ng, K. et al. (2007) Xist and the order of silencing. EMBO Report 8, 34-39CrossRefGoogle ScholarPubMed
150Sleutels, F., Zwart, R. and Barlow, D.P. (2002) The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415, 810-813CrossRefGoogle ScholarPubMed
151Thakur, N. et al. (2004) An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region. Molecular and Cellular Biology 24, 7855-7862CrossRefGoogle ScholarPubMed
152Williamson, C.M. et al. (2006) Identification of an imprinting control region affecting the expression of all transcripts in the Gnas cluster. Nature Genetics 38, 350-355CrossRefGoogle ScholarPubMed
153Le Meur, E. et al. (2005) Dynamic developmental regulation of the large non-coding RNA associated with the mouse 7C imprinted chromosomal region. Developmental Biology 286, 587-600CrossRefGoogle ScholarPubMed
154Peters, J. and Robson, J.E. (2008) Imprinted noncoding RNAs. Mammalian Genome 19, 493-502CrossRefGoogle ScholarPubMed
155Latos, P.A. and Barlow, D.P. (2009) Regulation of imprinted expression by macro non-coding RNAs. RNA Biology 6, 100-106CrossRefGoogle ScholarPubMed
156Wang, X. et al. (2008) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454, 126-130CrossRefGoogle ScholarPubMed
157Hudson, Q.J. et al. (2010) Genomic imprinting mechanisms in embryonic and extraembryonic mouse tissues. Heredity 105, 45-56CrossRefGoogle ScholarPubMed
158Yu, W. et al. (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451, 202-206CrossRefGoogle ScholarPubMed
159Morris, K.V. et al. (2008) Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genetics 4, e1000258CrossRefGoogle ScholarPubMed
160Watanabe, T. et al. (2008) Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature 453, 539-543CrossRefGoogle ScholarPubMed
161Tam, O.H. et al. (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453, 534-538CrossRefGoogle ScholarPubMed
162Guttman, M. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458, 223-227CrossRefGoogle Scholar
163Khalil, A.M. et al. (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences of the United States of America 106, 11667-11672CrossRefGoogle ScholarPubMed
164Gupta, R.A. et al. (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464, 1071-1076CrossRefGoogle ScholarPubMed
165Yoshimizu, T. et al. (2008) The H19 locus acts in vivo as a tumor suppressor. Proceedings of the National Academy of Sciences of the United States of America 105, 12417-12422CrossRefGoogle ScholarPubMed
166Tsang, W.P. et al. (2010) Oncofetal H19-derived miR-675 regulates tumor suppressor RB in human colorectal cancer. Carcinogenesis 31, 350-358CrossRefGoogle ScholarPubMed
167Zhou, Y. et al. (2007) Activation of p53 by MEG3 non-coding RNA. Journal of Biological Chemistry 282, 24731-24742CrossRefGoogle ScholarPubMed
168Zhang, X. et al. (2010) Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions. Endocrinology 151, 939-947CrossRefGoogle ScholarPubMed
169Baek, D. et al. (2008) The impact of microRNAs on protein output. Nature 455, 64-71CrossRefGoogle ScholarPubMed
170Seitz, H. et al. (2004) A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Research 14, 1741-1748CrossRefGoogle ScholarPubMed
171Glazov, E.A. et al. (2008) Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Molecular Biology and Evolution 25, 939-948CrossRefGoogle ScholarPubMed
172Saito, Y. et al. (2006) Specific activation of microRNA-127 with downregulation of the proto-oncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell 9, 435-443CrossRefGoogle ScholarPubMed
173Lee, J.W. et al. (2008) Altered MicroRNA expression in cervical carcinomas. Clinical Cancer Research 14, 2535-2542CrossRefGoogle ScholarPubMed
174Yu, J. et al. (2006) Human microRNA clusters: genomic organization and expression profile in leukemia cell lines. Biochemical and Biophysical Research Communications 349, 59-68CrossRefGoogle ScholarPubMed
175Guo, L. et al. (2010) Gene expression profiling of drug-resistant small cell lung cancer cells by combining microRNA and cDNA expression analysis. European Journal of Cancer 46, 1692-1702CrossRefGoogle ScholarPubMed
176Guled, M. et al. (2009) CDKN2A, NF2, and JUN are dysregulated among other genes by miRNAs in malignant mesothelioma – a miRNA microarray analysis. Genes, Chromosomes and Cancer 48, 615-623CrossRefGoogle ScholarPubMed
177Veronese, A. et al. (2010) Oncogenic role of miR-483-3p at the IGF2/483 locus. Cancer Research 70, 3140-3149CrossRefGoogle ScholarPubMed
178Malzkorn, B. et al. (2009) Identification and functional characterization of microRNAs involved in the malignant progression of gliomas. Brain Pathology 20, 539-550CrossRefGoogle Scholar
179Wong, T.S. et al. (2008) Mature miR-184 as potential oncogenic microRNA of squamous cell carcinoma of tongue. Clinical Cancer Research 14, 2588-2592CrossRefGoogle ScholarPubMed
180Liu, C. et al. (2010) Epigenetic regulation of miR-184 by MBD1 governs neural stem cell proliferation and differentiation. Cell Stem Cell 6, 433-444CrossRefGoogle ScholarPubMed
181Stubbs, M. and Griffiths, J.R. (2010) The altered metabolism of tumors: HIF-1 and its role in the Warburg effect. Advances in Enzyme Regulation 50, 44-55CrossRefGoogle ScholarPubMed
182Timp, W., Levchenko, A. and Feinberg, A.P. (2009) A new link between epigenetic progenitor lesions in cancer and the dynamics of signal transduction. Cell Cycle 8, 383-390CrossRefGoogle ScholarPubMed
183Young, A.R. and Narita, M. (2009) SASP reflects senescence. EMBO Report 10, 228-230CrossRefGoogle ScholarPubMed
184Tezuka, N., Brown, A.M. and Yanagawa, S. (2007) GRB10 binds to LRP6, the Wnt co-receptor and inhibits canonical Wnt signaling pathway. Biochemical and Biophysical Research Communications 356, 648-654CrossRefGoogle ScholarPubMed
185Jiang, X. et al. (2010) The imprinted gene PEG3 inhibits Wnt signaling and regulates glioma growth. Journal of Biological Chemistry 285, 8472-8480CrossRefGoogle ScholarPubMed
186Kobayashi, S. et al. (2002) Paternal expression of a novel imprinted gene, Peg12/Frat3, in the mouse 7C region homologous to the Prader–Willi syndrome region. Biochemical and Biophysical Research Communications 290, 403-408CrossRefGoogle Scholar
187Jubb, A.M. et al. (2006) Achaete-scute like 2 (ascl2) is a target of Wnt signalling and is upregulated in intestinal neoplasia. Oncogene 25, 3445-3457CrossRefGoogle ScholarPubMed
188Zhu, W. et al. (2008) IGFBP-4 is an inhibitor of canonical Wnt signalling required for cardiogenesis. Nature 454, 345-349CrossRefGoogle ScholarPubMed
189Wick, K.R. et al. (2003) Grb10 inhibits insulin-stimulated insulin receptor substrate (IRS)-phosphatidylinositol 3-kinase/Akt signaling pathway by disrupting the association of IRS-1/IRS-2 with the insulin receptor. Journal of Biological Chemistry 278, 8460-8467CrossRefGoogle ScholarPubMed
190Langlais, P. et al. (2004) Negative regulation of insulin-stimulated mitogen-activated protein kinase signaling by Grb10. Molecular Endocrinology 18, 350-358CrossRefGoogle ScholarPubMed
191Charalambous, M. et al. (2010) Maternally-inherited Grb10 reduces placental size and efficiency. Developmental Biology 337, 1-8CrossRefGoogle Scholar
192Playford, M.P. et al. (2000) Insulin-like growth factor 1 regulates the location, stability, and transcriptional activity of beta-catenin. Proceedings of the National Academy of Sciences of the United States of America 97, 12103-12108CrossRefGoogle ScholarPubMed
193Wade, M., Wang, Y.V. and Wahl, G.M. (2010) The p53 orchestra: Mdm2 and Mdmx set the tone. Trends in Cell Biology 20, 299-309CrossRefGoogle ScholarPubMed
194Kaghad, M. et al. (1997) Monoallelically expressed gene related to p53 at 1p36, a region frequently deleted in neuroblastoma and other human cancers. Cell 90, 809-819CrossRefGoogle ScholarPubMed
195Kim, J.W. et al. (2008) TIP60 represses transcriptional activity of p73beta via an MDM2-bridged ternary complex. Journal of Biological Chemistry 283, 20077-20086CrossRefGoogle ScholarPubMed
196Yu, Y. et al. (2006) Biochemistry and biology of ARHI (DIRAS3), an imprinted tumor suppressor gene whose expression is lost in ovarian and breast cancers. Methods in Enzymology 407, 455-468CrossRefGoogle ScholarPubMed
197Nishimoto, A. et al. (2005) A Ras homologue member I directly inhibits signal transducers and activators of transcription 3 translocation and activity in human breast and ovarian cancer cells. Cancer Research 65, 6701-6710CrossRefGoogle ScholarPubMed
198Huang, S. et al. (2010) ARHI (DIRAS3), an imprinted tumour suppressor gene, binds to importins and blocks nuclear import of cargo proteins. Bioscience Reports 30, 159-168CrossRefGoogle Scholar
199Ferres-Marco, D. et al. (2006) Epigenetic silencers and Notch collaborate to promote malignant tumours by Rb silencing. Nature 439, 430-436CrossRefGoogle ScholarPubMed
200Bray, S.J. et al. (2008) The atypical mammalian ligand Delta-like homologue 1 (Dlk1) can regulate Notch signalling in Drosophila. BMC Developmental Biology 8, 11CrossRefGoogle ScholarPubMed
201Ikushima, H. and Miyazono, K. (2010) TGFbeta signalling: a complex web in cancer progression. Nature Reviews. Cancer 10, 415-424CrossRefGoogle ScholarPubMed
202Bergstrom, R. et al. (2010) Transforming growth factor beta promotes complexes between Smad proteins and CTCF on the H19 imprinting control region chromatin. Journal of Biological Chemistry 285, 19727-19737CrossRefGoogle ScholarPubMed
203Scandura, J.M. et al. (2004) Transforming growth factor beta-induced cell cycle arrest of human hematopoietic cells requires p57KIP2 up-regulation. Proceedings of the National Academy of Sciences of the United States of America 101, 15231-15236CrossRefGoogle ScholarPubMed
204Lux, A. et al. (2005) Human retroviral gag- and gag-pol-like proteins interact with the transforming growth factor-beta receptor activin receptor-like kinase 1. Journal of Biological Chemistry 280, 8482-8493CrossRefGoogle ScholarPubMed
205Li, C.M. et al. (2006) PEG10 is a c-MYC target gene in cancer cells. Cancer Research 66, 665-672CrossRefGoogle ScholarPubMed
206Okabe, H. et al. (2003) Involvement of PEG10 in human hepatocellular carcinogenesis through interaction with SIAH1. Cancer Research 63, 3043-3048Google ScholarPubMed
207Zhang, P. et al. (1998) Cooperation between the Cdk inhibitors p27(KIP1) and p57(KIP2) in the control of tissue growth and development. Genes and Development 12, 3162-3167CrossRefGoogle ScholarPubMed
208Montgomery, S.B. et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464, 773-777CrossRefGoogle Scholar
209Dawson, M.A. et al. (2009) JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin. Nature 461, 819-822CrossRefGoogle ScholarPubMed
210Saito, Y. and Jones, P.A. (2006) Epigenetic activation of tumor suppressor microRNAs in human cancer cells. Cell Cycle 5, 2220-2222CrossRefGoogle ScholarPubMed
211Klisovic, R.B. et al. (2008) A phase I biological study of MG98, an oligodeoxynucleotide antisense to DNA methyltransferase 1, in patients with high-risk myelodysplasia and acute myeloid leukemia. Clinical Cancer Research 14, 2444-2449CrossRefGoogle ScholarPubMed
212Ptak, C. and Petronis, A. (2008) Epigenetics and complex disease: from etiology to new therapeutics. Annual Review of Pharmacology and Toxicology 48, 257-276CrossRefGoogle ScholarPubMed

Further reading, resources and contacts

The Epigenome Network of Excellence gathers European laboratories dedicated to research in epigenetics:

http://www.ncrn.org.uk/ (National Cancer Research Network, UK)Google Scholar
http://www.eortc.be/ (European Organisation for Research and Treatment of Cancer)Google Scholar