Silencing of endogenous retroviruses: When and why do histone marks predominate?

Trends in Biochemical Sciences

Volumn 37, Issue 4, 2012, Pages 127-133

  Leung, Danny C ^a   Lorincz, Matthew C ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; CARBON; CYTOSINE; DIOXYGENASE; DNA; HISTONE; OCTAMER TRANSCRIPTION FACTOR 4; TET PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CELL DIFFERENTIATION; CELL TYPE; DEVELOPMENTAL STAGE; DNA METHYLATION; EMBRYO DEVELOPMENT; EMBRYONIC STEM CELL; ENDOGENOUS RETROVIRUS; GENE EXPRESSION; GENE REPRESSION; GENE SILENCING; GENETIC MARKER; HISTONE METHYLATION; HISTONE MODIFICATION; MOUSE; NONHUMAN; OXIDATION; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; RETROPOSON;

5-METHYLCYTOSINE; ANIMALS; DNA METHYLATION; EMBRYO, MAMMALIAN; ENDOGENOUS RETROVIRUSES; HISTONES; MICE; PROTEIN METHYLTRANSFERASES; REPRESSOR PROTEINS;

METAZOA;

EID: 84858412556     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibs.2011.11.006     Document Type: Article

References (53)

1. Waterston R.H., et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562.
2. Maksakova I.A., et al. Retroviral elements and their hosts: insertional mutagenesis in the mouse germ line. PLoS Genet. 2006, 2:e2.
3. Walsh C.P., Bestor T.H. Cytosine methylation and mammalian development. Genes Dev. 1999, 13:26-34.
4. Okano M., et al. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999, 99:247-257.
5. Hemberger M., et al. Epigenetic dynamics of stem cells and cell lineage commitment: digging Waddington's canal. Nat. Rev. Mol. Cell Biol. 2009, 10:526-537.
6. Pannell D., et al. Retrovirus vector silencing is de novo methylase independent and marked by a repressive histone code. EMBO J. 2000, 19:5884-5894.
7. Matsui T., et al. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 2010, 464:927-931.
8. Hutnick L.K., et al. Repression of retrotransposal elements in mouse embryonic stem cells is primarily mediated by a DNA methylation-independent mechanism. J. Biol. Chem. 2010, 285:21082-21091.
9. Dong K.B., et al. DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity. EMBO J. 2008, 27:2691-2701.
10. Tamaru H., Selker E.U. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 2001, 414:277-283.
11. Jackson J.P., et al. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 2002, 416:556-560.
12. Lehnertz B., et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 2003, 13:1192-1200.
13. Bushman F.D. Targeting survival: integration site selection by retroviruses and LTR-retrotransposons. Cell 2003, 115:135-138.
14. Tachibana M., et al. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev. 2002, 16:1779-1791.
15. Rice J.C., et al. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell 2003, 12:1591-1598.
16. Mikkelsen T.S., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
17. Leung D.C., et al. Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:5718-5723.
18. Schultz D.C., et al. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 2002, 16:919-932.
19. Rowe H.M., et al. KAP1 controls endogenous retroviruses in embryonic stem cells. Nature 2010, 463:237-240.
20. Wolf D., et al. Primer binding site-dependent restriction of murine leukemia virus requires HP1 binding by TRIM28. J. Virol. 2008, 82:4675-4679.
21. Karimi M.M., et al. DNA Methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements, and chimeric transcripts in mESCs. Cell Stem Cell 2011, 8:676-687.
22. Komashko V.M., Farnham P.J. 5-Azacytidine treatment reorganizes genomic histone modification patterns. Epigenetics 2010, 5:229-240.
23. Macfarlan T.S., et al. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A. Genes Dev. 2011, 25:594-607.
24. Leeb M., et al. Polycomb complexes act redundantly to repress genomic repeats and genes. Genes Dev. 2010, 24:265-276.
25. Hake S.B., et al. Expression patterns and post-translational modifications associated with mammalian histone H3 variants. J. Biol. Chem. 2006, 281:559-568.
26. Daujat S., et al. H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming. Nat. Struct. Mol. Biol. 2009, 16:777-781.
27. Wu S.C., Zhang Y. Active DNA demethylation: many roads lead to Rome. Nat. Rev. Mol. Cell Biol. 2010, 11:607-620.
28. Tahiliani M., et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009, 324:930-935.
29. Iqbal K., et al. Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:3642-3647.
30. He Y.F., et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 2011, 333:1303-1307.
31. Ito S., et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 2011, 333:1300-1303.
32. Ito S., et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 2010, 466:1129-1133.
33. Koh K.P., et al. Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells. Cell Stem Cell 2011, 8:200-213.
34. Ruzov A., et al. Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development. Cell Res. 2011, 21:1332-1342.
35. Wossidlo M., et al. 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat. Commun. 2011, 2:241.
36. Bogdanović O., Veenstra G.J. DNA methylation and methyl-CpG binding proteins: developmental requirements and function. Chromosoma 2009, 118:549-565.
37. Frauer C., et al. Recognition of 5-hydroxymethylcytosine by the Uhrf1 SRA domain. PLoS ONE 2011, 6:e21306.
38. Valinluck V., et al. Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of methyl-CpG binding protein 2 (MeCP2). Nucleic Acids Res. 2004, 32:4100-4108.
39. Xu Y., et al. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Mol. Cell 2011, 42:451-464.
40. Ficz G., et al. Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 2011, 473:398-402.
41. Gu T.P., et al. The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes. Nature 2011, 477:606-610.
42. Nestor C., et al. Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA. Biotechniques 2010, 48:317-319.
43. Williams K., et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity. Nature 2011, 473:343-348.
44. Hajkova P., et al. Epigenetic reprogramming in mouse primordial germ cells. Mech. Dev. 2002, 117:15-23.
45. Hajkova P., et al. Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science 2010, 329:78-82.
46. Lane N., et al. Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 2003, 35:88-93.
47. Kuramochi-Miyagawa S., et al. MVH in piRNA processing and gene silencing of retrotransposons. Genes Dev. 2010, 24:887-892.
48. Globisch D., et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE 2010, 5:e15367.
49. Song C.X., et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 2010, 29:68-72.
50. Kriaucionis S., Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 2009, 324:929-930.
51. Szwagierczak A., et al. Sensitive enzymatic quantification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res. 2010, 38:e181.
52. Szulwach K.E., et al. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat. Neurosci. 2011, 10.1038/nn.2959.
53. Jurka J., et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 2005, 110:462-467.