Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 14, 2011, Pages 5626-5631

  Tao, Yongguang ^a   Xi, Sichuan ^a   Shan, Jigui ^b   Maunakea, Alika ^c   Che, Anney ^b   Briones, Victorino ^a   Lee, Eunice Y ^a   Geiman, Theresa ^a   Huang, Jiaqiang ^a   Stephens, Robert ^b   Leighty, Robert M ^b   Zhao, Keji ^c   Muegge, Kathrin ^a  

^a Laboratory of Cancer Prevention   (United States)

^b SAIC FREDERICK INC   (United States)

^c NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

Author keywords

ChIP sequencing; Epigenetics; Methylated DNA immunoprecipitation

Indexed keywords

CYTOSINE; LSH PROTEIN; NUCLEAR PROTEIN; REPETITIVE DNA; UNCLASSIFIED DRUG;

ANIMAL CELL; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME; CONFERENCE PAPER; CONTROLLED STUDY; DNA METHYLATION; EMBRYO; GENE CONTROL; GENE DELETION; GENE EXPRESSION; MOUSE; NONHUMAN; PRIORITY JOURNAL;

MURINAE;

EID: 79954993753     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1017000108     Document Type: Article

References (37)

1. Cedar H, Bergman Y (2009) Linking DNA methylation and histone modification: Patterns and paradigms. Nat Rev Genet 10:295-304.
2. Ooi SK, O'Donnell AH, Bestor TH (2009) Mammalian cytosine methylation at a glance. J Cell Sci 122:2787-2791.
3. Reik W (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447:425-432. (Pubitemid 46816749)
4. Jones PA, Baylin SB (2007) The epigenomics of cancer. Cell 128:683-692. (Pubitemid 46273572)
5. Ball MP, et al. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27:361-368.
6. Cokus SJ, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215-219. (Pubitemid 351380251)
7. Feng S, et al. (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 107:8689-8694.
8. Lister R, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536.
9. Lister R, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315-322.
10. Meissner A, et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454:766-770.
11. Rauch TA, et al. (2008) High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc Natl Acad Sci USA 105:252-257.
12. Weber M, et al. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853-862. (Pubitemid 41077111)
13. Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916-919.
14. Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39:61-69. (Pubitemid 46026502)
15. Li E, Bestor TH, Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69:915-926.
16. Okano M, Bell DW, Haber DA, Li E (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99: 247-257. (Pubitemid 29519904)
17. Dennis K, Fan T, Geiman T, Yan Q, Muegge K (2001) Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev 15:2940-2944. (Pubitemid 33078944)
18. Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22:94-97. (Pubitemid 29214813)
19. Sun LQ, et al. (2004) Growth retardation and premature aging phenotypes in mice with disruption of the SNF2-like gene, PASG. Genes Dev 18:1035-1046.
20. Gendrel AV, Lippman Z, Yordan C, Colot V, Martienssen RA (2002) Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297:1871-1873. (Pubitemid 35024346)
21. Yan Q, Huang J, Fan T, Zhu H, Muegge K (2003) Lsh, a modulator of CpG methylation, is crucial for normal histone methylation. EMBO J 22:5154-5162. (Pubitemid 37222035)
22. Geiman TM, et al. (2001) Lsh, a SNF2 family member, is required for normal murine development. Biochim Biophys Acta 1526:211-220. (Pubitemid 32452257)
23. De La Fuente R, et al. (2006) Lsh is required for meiotic chromosome synapsis and retrotransposon silencing in female germ cells. Nat Cell Biol 8:1448-1454. (Pubitemid 44835121)
24. Huang J, et al. (2004) Lsh, an epigenetic guardian of repetitive elements. Nucleic Acids Res 32:5019-5028. (Pubitemid 39445488)
25. Lippman Z, et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471-476. (Pubitemid 38987911)
26. Xi S, et al. (2009) Lsh participates in DNA methylation and silencing of stem cell genes. Stem Cells 27:2691-2702.
27. Tao Y, Xi S, Briones V, Muegge K (2010) Lsh mediated RNA polymerase II stalling at HoxC6 and HoxC8 involves DNA methylation. PLoS ONE 5:e9163.
28. Xi S, et al. (2007) Lsh controls Hox gene silencing during development. Proc Natl Acad Sci USA 104:14366-14371. (Pubitemid 350003267)
29. Fan T, Hagan JP, Kozlov SV, Stewart CL, Muegge K (2005) Lsh controls silencing of the imprinted Cdkn1c gene. Development 132:635-644. (Pubitemid 40352824)
30. Yan Q, Cho E, Lockett S, Muegge K (2003) Association of Lsh, a regulator of DNA methylation, with pericentromeric heterochromatin is dependent on intact heterochromatin. Mol Cell Biol 23:8416-8428. (Pubitemid 37433350)
31. Zhu H, et al. (2006) Lsh is involved in de novo methylation of DNA. EMBO J 25: 335-345. (Pubitemid 43152854)
32. Fan T, et al. (2003) Lsh-deficient murine embryonal fibroblasts show reduced proliferation with signs of abnormal mitosis. Cancer Res 63:4677-4683. (Pubitemid 36951047)
33. Schones DE, et al. (2008) Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887-898.
34. Wu H, et al. (2010) Dnmt3a-dependent nonpromoter DNA methylation facilitates transcription of neurogenic genes. Science 329:444-448.
35. Myant K, et al. (2011) LSH and G9a/GLP complex are required for developmentally programmed DNA methylation. Genome Res 21:83-94.
36. Harris RA, et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28:1097-1105.
37. Saze H, Kakutani T (2007) Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J 26: 3641-3652. (Pubitemid 47236873)