DNA methylation-histone modification relationships across the desmin locus in human primary cells

BMC Molecular Biology

Volumn 10, Issue , 2009, Pages

  Allen, Marianne ^a,c   Koch, Christoph M ^b,d   Clelland, Gayle K ^b   Dunham, Ian ^b,e   Antoniou, Michael ^a  

^a GUY S HOSPITAL   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c HARVARD MEDICAL SCHOOL   (United States)

^d QIAGEN GMBH   (Germany)

^e EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DESMIN; HISTONE H3; HISTONE H4; LYSINE; HISTONE;

ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DOWNSTREAM PROCESSING; GENE EXPRESSION; GENE LOCUS; HUMAN; HUMAN CELL; INTRON; MYOBLAST; MYOTUBE; PERIPHERAL BLOOD MONONUCLEAR CELL; PROMOTER REGION; PROTEIN LOCALIZATION; PROTEIN MODIFICATION; TISSUE SPECIFICITY; TRANSCRIPTION INITIATION SITE; ACETYLATION; ANTIBODY SPECIFICITY; CELL CULTURE; CHROMOSOME 2; GENETICS; METABOLISM; MONONUCLEAR CELL; REGULATORY SEQUENCE; SKELETAL MUSCLE;

ACETYLATION; CELLS, CULTURED; CHROMOSOMES, HUMAN, PAIR 2; DESMIN; DNA METHYLATION; HISTONES; HUMANS; LEUKOCYTES, MONONUCLEAR; MUSCLE FIBERS, SKELETAL; MYOBLASTS; ORGAN SPECIFICITY; REGULATORY ELEMENTS, TRANSCRIPTIONAL;

EID: 67649710405     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-10-51     Document Type: Article

References (43)

1. Boguski MS ENCODE and ChIP-chip in the genome era Genomics 2004, 83(3):347-348. 10.1016/S0888-7543(04)00015-1 14962661
2. Bradbury J Human epigenome project - up and running PLoS Biol 2003, 1(3):E82. 300691 14691553 10.1371/journal.pbio.0000082
3. Birney E Stamatoyannopoulos JA Dutta A Guigo R Gingeras TR Margulies EH Weng Z Snyder M Dermitzakis ET Thurman RE et al.: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 2007, 447(7146):799-816. 2212820 17571346 10.1038/ nature05874
4. Koch CM Andrews RM Flicek P Dillon SC Karaoz U Clelland GK Wilcox S Beare DM Fowler JC Couttet P et al.: The landscape of histone modifications across 1% of the human genome in five human cell lines Genome Res 2007, 17(6):691-707. 1891331 17567990 10.1101/gr.5704207
5. Raguz S Hobbs C Yague E Ioannou PA Walsh FS Antoniou M Muscle-Specific Locus Control Region Activity Associated with the Human Desmin Gene Developmental Biology 1998, 201(1):26-42. 10.1006/dbio.1998.8964 9733571
6. Tam JLY Triantaphyllopoulos K Todd H Raguz S de Wit T Morgan JE Partridge TA Makrinou E Grosveld F Antoniou M The human desmin locus: Gene organization and LCR-mediated transcriptional control Genomics 2006, 87(6):733-746. 10.1016/j.ygeno.2006.01.009 16545539
7. Palstra RJ Tolhuis B Splinter E Nijmeijer R Grosveld F de Laat W The beta-globin nuclear compartment in development and erythroid differentiation Nat Genet 2003, 35(2):190-194. 10.1038/ng1244 14517543
8. Anguita E Johnson CA Wood WG Turner BM Higgs DR Identification of a conserved erythroid specific domain of histone acetylation across the alpha-globin gene cluster PNAS 2001, 98(21):12114-12119. 59777 11593024 10.1073/pnas.201413098
9. Dillon N Gene regulation and large-scale chromatin organization in the nucleus Chromosome Res 2006, 14(1):117-126. 10.1007/s10577-006-1027-8 16506101
10. Gardiner-Garden M Frommer M CpG islands in vertebrate genomes J Mol Biol 1987, 196(2):261-282. 10.1016/0022-2836(87)90689-9 3656447
11. Larsen F Gundersen G Lopez R Prydz H CpG islands as gene markers in the human genome Genomics 1992, 13(4):1095-1107. 10.1016/ 0888-7543(92)90024-M 1505946
12. Li B Carey M Workman JL The role of chromatin during transcription Cell 2007, 128(4):707-719. 10.1016/j.cell.2007.01.015 17320508
13. Ho Y Elefant F Cooke N Liebhaber S A Defined Locus Control Region Determinant Links Chromatin Domain Acetylation with Long-Range Gene Activation Molecular Cell 2002, 9(2):291-302. 10.1016/ S1097-2765(02)00447-1 11864603
14. Myers FA Evans DR Clayton AL Thorne AW Crane-Robinson C Targeted and extended acetylation of histones H4 and H3 at active and inactive genes in chicken embryo erythrocytes J Biol Chem 2001, 276(23):20197-20205. 10.1074/jbc.M009472200 11274167
15. Myers FA Chong W Evans DR Thorne AW Crane-Robinson C Acetylation of histone H2B mirrors that of H4 and H3 at the chicken beta-globin locus but not at housekeeping genes J Biol Chem 2003, 278(38):36315-36322. 10.1074/jbc.M305822200 12865423
16. Bird A MOLECULAR BIOLOGY:DNA Methylation de Novo Science 1999, 286(5448):2287-2288. 10.1126/science.286.5448.2287 10636791
17. Vire E Brenner C Deplus R Blanchon L Fraga M Didelot C Morey L Van Eynde A Bernard D Vanderwinden JM et al.: The Polycomb group protein EZH2 directly controls DNA methylation Nature 2006, 439(7078):871-874. 10.1038/nature04431 16357870
18. Schlesinger Y Straussman R Keshet I Farkash S Hecht M Zimmerman J Eden E Yakhini Z Ben-Shushan E Reubinoff BE et al.: Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer Nat Genet 2007, 39(2):232-236. 10.1038/ng1950 17200670
19. Bird A MOLECULAR BIOLOGY: Methylation Talk Between Histones and DNA Science 2001, 294(5549):2113-2115. 10.1126/science.1066726 11739943
20. Cedar H Bergman Y Linking DNA methylation and histone modification: patterns and paradigms Nat Rev Genet 2009, 10(5):295-304. 10.1038/ nrg2540 19308066
21. Barski A Cuddapah S Cui K Roh TY Schones DE Wang Z Wei G Chepelev I Zhao K High-resolution profiling of histone methylations in the human genome Cell 2007, 129(4):823-837. 10.1016/j.cell.2007.05.009 17512414
22. Li ZL Paulin D High level desmin expression depends on a muscle-specific enhancer J Biol Chem 1991, 266(10):6562-6570. 2007603
23. Grunstein M Histone acetylation in chromatin structure and transcription Nature 1997, 389(6649):349-352. 10.1038/38664 9311776
24. Roh T-Y Cuddapah S Zhao K Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping Genes Dev 2005, 19(5):542-552. 551575 15706033 10.1101/gad.1272505
25. Heintzman ND Stuart RK Hon G Fu Y Ching CW Hawkins RD Barrera LO Van Calcar S Qu C Ching KA et al.: Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nat Genet 2007, 39(3):311-318. 10.1038/ng1966 17277777
26. Liang G Lin JCY Wei V Yoo C Cheng JC Nguyen CT Weisenberger DJ Egger G Takai D Gonzales FA et al.: Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome PNAS 2004, 101(19):7357-7362. 409923 15123803 10.1073/ pnas.0401866101
27. Hellman A Chess A Gene body-specific methylation on the active X chromosome Science 2007, 315(5815):1141-1143. 10.1126/science.1136352 17322062
28. Weber M Hellmann I Stadler MB Ramos L Paabo S Rebhan M Schubeler D Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome Nat Genet 2007, 39(4):457-466. 10.1038/ng1990 17334365
29. Zilberman D Gehring M Tran RK Ballinger T Henikoff S Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription Nat Genet 2007, 39(1):61-69. 10.1038/ng1929 17128275
30. Lindahl Allen M Antoniou M Correlation of DNA Methylation with Histone Modifications Across the HNRPA2B1-CBX3 Ubiquitously-Acting Chromatin Open Element (UCOE) Epigenetics 2007, 2(4):227-236. 18032920
31. Li Z Colucci E Babinet C Paulin D The human desmin gene: A specific regulatory programme in skeletal muscle both in vitro and in transgenic mice Neuromuscul Disord 1993, 3(5-6):423-427. 10.1016/ 0960-8966(93)90089-3 8186686
32. Boyer LA Plath K Zeitlinger J Brambrink T Medeiros LA Lee TI Levine SS Wernig M Tajonar A Ray MK et al.: Polycomb complexes repress developmental regulators in murine embryonic stem cells Nature 2006, 441(7091):349-353. 10.1038/nature04733 16625203
33. Brinkman AB Roelofsen T Pennings SW Martens JH Jenuwein T Stunnenberg HG Histone modification patterns associated with the human X chromosome EMBO Rep 2006, 7(6):628-634. 1479594 16648823
34. Lee TI Jenner RG Boyer LA Guenther MG Levine SS Kumar RM Chevalier B Johnstone SE Cole MF Isono K et al.: Control of developmental regulators by Polycomb in human embryonic stem cells Cell 2006, 125(2):301-313. 10.1016/j.cell.2006.02.043 16630818
35. Vakoc CR Sachdeva MM Wang HX Blobel GA Profile of histone lysine methylation across transcribed mammalian chromatin Molecular and Cellular Biology 2006, 26(24):9185-9195. 10.1128/MCB.01529-06
36. Kim A Kiefer CM Dean A Distinctive signatures of histone methylation in transcribed coding and noncoding human beta-globin sequences Molecular and Cellular Biology 2007, 27(4):1271-1279. 10.1128/MCB.01684-06
37. McKinsey TA Zhang CL Olson EN Control of muscle development by dueling HATs and HDACs Current Opinion in Genetics & Development 2001, 11(5):497-504. 10.1016/S0959-437X(00)00224-0 11532390
38. Bernstein BE Kamal M Lindblad-Toh K Bekiranov S Bailey DK Huebert DJ McMahon S Karlsson EK Kulbokas EJ 3rd Gingeras TR et al.: Genomic maps and comparative analysis of histone modifications in human and mouse Cell 2005, 120(2):169-181. 10.1016/j.cell.2005.01.001 15680324
39. Bernstein BE Humphrey EL Erlich RL Schneider R Bouman P Liu JS Kouzarides T Schreiber SL Methylation of histone H3 Lys 4 in coding regions of active genes PNAS 2002, 99(13):8695-8700. 124361 12060701
40. Baguet A Bix M Chromatin landscape dynamics of the Il4-Il13 locus during T helper 1 and 2 development Proc Natl Acad Sci USA 2004, 101(31):11410-11415. 509214 15272080 10.1073/pnas.0403334101
41. Follows GA Dhami P Gottgens B Bruce AW Campbell PJ Dillon SC Smith AM Koch C Donaldson IJ Scott MA et al.: Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites Genome Res 2006, 16(10):1310-1319. 1581440 16963707 10.1101/gr.5373606
42. Jain AN Tokuyasu TA Snijders AM Segraves R Albertson DG Pinkel D Fully automatic quantification of microarray image data Genome Res 2002, 12(2):325-332. 155276 11827952 10.1101/gr.210902
43. Clayton AL Hazzalin CA Mahadevan LC Enhanced Histone Acetylation and Transcription: A Dynamic Perspective Molecular Cell 2006, 23(3):289-296. 10.1016/j.molcel.2006.06.017 16885019