Boguski MS: ENCODE and ChIP-chip in the genome era. Genomics. 2004, 83 (3): 347-348. 10.1016/S0888-7543(04)00015-1
Article
CAS
PubMed
Google Scholar
Bradbury J: Human epigenome project – up and running. PLoS Biol. 2003, 1 (3): E82- 10.1371/journal.pbio.0000082
Article
PubMed Central
PubMed
Google Scholar
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. 10.1038/nature05874
Article
CAS
PubMed
Google Scholar
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. 10.1101/gr.5704207
Article
PubMed Central
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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. 10.1073/pnas.201413098
Article
PubMed Central
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
Bird A: MOLECULAR BIOLOGY:DNA Methylation de Novo. Science. 1999, 286 (5448): 2287-2288. 10.1126/science.286.5448.2287
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
Bird A: MOLECULAR BIOLOGY: Methylation Talk Between Histones and DNA. Science. 2001, 294 (5549): 2113-2115. 10.1126/science.1066726
Article
CAS
PubMed
Google Scholar
Cedar H, Bergman Y: Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet. 2009, 10 (5): 295-304. 10.1038/nrg2540
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
Li ZL, Paulin D: High level desmin expression depends on a muscle-specific enhancer. J Biol Chem. 1991, 266 (10): 6562-6570.
CAS
PubMed
Google Scholar
Grunstein M: Histone acetylation in chromatin structure and transcription. Nature. 1997, 389 (6649): 349-352. 10.1038/38664
Article
CAS
PubMed
Google Scholar
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. 10.1101/gad.1272505
Article
PubMed Central
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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. 10.1073/pnas.0401866101
Article
PubMed Central
CAS
PubMed
Google Scholar
Hellman A, Chess A: Gene body-specific methylation on the active X chromosome. Science. 2007, 315 (5815): 1141-1143. 10.1126/science.1136352
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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.
Article
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar
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.
PubMed Central
CAS
PubMed
Google Scholar
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
Article
PubMed Central
CAS
PubMed
Google Scholar
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. 10.1128/MCB.01529-06
Article
PubMed Central
CAS
PubMed
Google Scholar
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. 10.1128/MCB.01684-06
Article
PubMed Central
CAS
PubMed
Google Scholar
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
Article
CAS
Google Scholar
Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, 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
Article
CAS
PubMed
Google Scholar
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.
Article
PubMed Central
CAS
PubMed
Google Scholar
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. 10.1073/pnas.0403334101
Article
PubMed Central
CAS
PubMed
Google Scholar
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. 10.1101/gr.5373606
Article
PubMed Central
CAS
PubMed
Google Scholar
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. 10.1101/gr.210902
Article
PubMed Central
CAS
PubMed
Google Scholar
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
Article
CAS
PubMed
Google Scholar