Dynamic nucleosomes and gene transcription

Trends in Genetics

Volumn 22, Issue 6, 2006, Pages 320-329

  Mellor, Jane ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; HISTONE H3; HISTONE H4; REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

ACETYLATION; CHROMATIN; DEACETYLATION; DNA MODIFICATION; ENZYME ACTIVITY; EPIGENETICS; GENETIC CODE; GENETIC REGULATION; GENETIC TRANSCRIPTION; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN MODIFICATION; REGULATOR GENE; REVIEW; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

ACETYLATION; AMINO ACID SEQUENCE; ANIMALS; CHROMATIN; DIMERIZATION; HISTONE DEACETYLASES; HISTONES; HUMANS; METHYLATION; MOLECULAR SEQUENCE DATA; NUCLEOSOMES; TRANSCRIPTION, GENETIC;

EID: 33646926758     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2006.03.008     Document Type: Review

References (75)

1. Clarke D.J., et al. Selective use of H4 acetylation sites in the yeast Saccharomyces cerevisiae. Biochem. J. 294 (1993) 557-561
2. Peterson C.L., and Laniel M.-A. Histones and histone modifications. Curr. Biol. 14 (2004) R546-R551
3. Cosgrove M.S., et al. Regulated nucleosome mobility and the histone code. Nat. Struct. Mol. Biol. 11 (2004) 1037-1043
4. Strahl B.D., and Allis C.D. The language of covalent histone modifications. Nature 403 (2000) 41-45
5. da Cunha J.P., et al. Trypanosoma cruzi histone H1 is phosphorylated in a typical cyclin dependent kinase site accordingly to the cell cycle. Mol. Biochem. Parasitol. 140 (2005) 75-86
6. Jenuwein T., and Allis C.D. Translating the histone code. Science 293 (2001) 1074-1080
7. Chen D., et al. Condensed mitotic chromatin is accessible to transcription factors and chromatin structural proteins. J. Cell Biol. 168 (2005) 41-54
8. Bustin M., et al. The Dynamics of Histone H1 Function in Chromatin. Mol. Cell 17 (2005) 617-620
9. Phair R.D., et al. Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol. Cell. Biol. 24 (2004) 6393-6402
10. Th'ng J.P., et al. H1 family histones in the nucleus. Control of binding and localization by the C-terminal domain. J. Biol. Chem. 280 (2005) 27809-27814
11. Lever M.A., et al. Rapid exchange of histone H1.1 on chromatin in living human cells. Nature 408 (2000) 873-876
12. Catez F., et al. Network of dynamic interactions between histone H1 and high-mobility-group proteins in chromatin. Mol. Cell. Biol. 24 (2004) 4321-4328
13. Zlatanova J., et al. Linker histone binding and displacement: versatile mechanism for transcriptional regulation. FASEB J. 14 (2000) 1697-1704
14. Karpova T.S., et al. Dynamic interactions of a transcription factor with DNA are accelerated by a chromatin remodeller. EMBO Rep. 5 (2004) 1064-1070
15. Muratani M., et al. The F Box protein Dsg1/Mdm30 is a transcriptional coactivator that stimulates Gal4 turnover and cotranscriptional mRNA processing. Cell 120 (2005) 887-899
16. Phair R.D., et al. Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy. Methods Enzymol. 375 (2004) 393-414
17. Vicent G.P., et al. Complex role of histone H1 in transactivation of MMTV promoter chromatin by progesterone receptor. J Steroid Biochem Mol Biol. 83 (2002) 15-23
18. Kimura H. Histone dynamics in living cells revealed by photobleaching. DNA Repair (Amst.) 4 (2005) 939-950
19. Kimura H., and Cook P.R. Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J. Cell Biol. 153 (2001) 1341-1353
20. Thiriet C., and Hayes J.J. Replication-independent core histone dynamics at transcriptionally active loci in vivo. Genes Dev. 19 (2005) 677-682
21. Henikoff S., et al. Histone variants, nucleosome assembly and epigenetic inheritance. Trends Genet. 20 (2004) 320-326
22. Tagami H., et al. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116 (2004) 51-61
23. Daury L., et al. Histone H3.3 deposition at E2F-regulated genes is linked to transcription. EMBO Rep. 7 (2005) 66-71
24. Chow C.-M., et al. Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division. EMBO Rep. 6 (2005) 354-360
25. Shi Y., et al. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119 (2004) 941-953
26. Sims III R.J., et al. Histone lysine methylation: a signature for chromatin function. Trends Genet. 19 (2003) 629-639
27. Cuthbert G.L., et al. Histone deimination antagonizes arginine methylation. Cell 118 (2004) 545-553
28. Wang Y., et al. Human PAD4 regulates histone arginine methylation levels via demethylimination. Science 306 (2004) 279-283
29. Tsukada Y., et al. Histone demethylation by a family of JmjC domain-containing proteins. Nature 439 (2006) 811-816
30. Metivier R., et al. Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115 (2003) 751-763
31. Metivier R., et al. Transcriptional complexes engaged by apo-estrogen receptor-αisoforms have divergent outcomes. EMBO J. 23 (2004) 3653-3666
32. Reid G., et al. Multiple mechanisms induce transcriptional silencing of a subset of genes, including oestrogen receptor alpha, in response to deacetylase inhibition by valproic acid and trichostatin A. Oncogene 24 (2005) 4894-4907
33. Morillon A., et al. Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Mol. Cell 18 (2005) 723-734
34. Ng H.H., et al. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell 11 (2003) 709-719
35. Joshi A.A., and Struhl K. Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol. Cell 20 (2005) 971-978
36. Keogh M.C., et al. Cotranscriptional Set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 123 (2005) 593-605
37. Carrozza M.J., et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123 (2005) 581-592
38. Santos-Rosa H., et al. Active genes are tri-methylated at K4 of histone H3. Nature 419 (2002) 407-411
39. Bernstein B.E., et al. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 8695-8700
40. Schneider R., et al. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat. Cell Biol. 6 (2004) 73-77
41. Lefevre P., et al. Differentiation dependent alterations in histone methylation and chromatin architecture at chicken lysozyme gene. J. Biol. Chem. 280 (2005) 27552-27560
42. Bannister A.J., et al. Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes. J. Biol. Chem. 280 (2005) 17732-17736
43. Morris S.A., et al. Histone H3 K36 methylation is associated with transcription elongation in Schizosaccharomyces pombe. Eukaryot. Cell 4 (2005) 1446-1454
44. Kristjuhan A., and Svejstrup J.Q. Evidence for distinct mechanisms facilitating transcript elongation through chromatin in vivo. EMBO J. 23 (2004) 4243-4252
45. Kristjuhan A., et al. Transcriptional inhibition of genes with severe histone H3 hypoacetylation in the coding region. Mol. Cell 10 (2002) 925-933
46. Kaplan C.D., et al. Transcription elongation factors repress transcription initiation from cryptic sites. Science 301 (2003) 1096-1099
47. Shi Y.J., et al. Regulation of LSD1 histone demethylase activity by its associated factors. Mol. Cell 19 (2005) 857-864
48. Lee M.G., et al. An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation. Nature 437 (2005) 432-435
49. Studitsky V.M., et al. Chromatin remodeling by RNA polymerases. Trends Biochem. Sci. 29 (2004) 127-135
50. Bruno M., et al. Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Mol. Cell 12 (2003) 1599-1606
51. Park Y.J., et al. Nucleosome assembly protein 1 exchanges histone H2A-H2B dimers and assists nucleosome sliding. J. Biol. Chem. 280 (2005) 1817-1825
52. Nagaich A.K., et al. Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling. Mol. Cell 14 (2004) 163-174
53. Reid G., et al. Cyclic, proteasome-mediated turnover of unliganded and liganded ERα on responsive promoters is an integral feature of estrogen signaling. Mol. Cell 11 (2003) 695-707
54. Vicent G.P., et al. DNA instructed displacement of histones H2A and H2B at an inducible promoter. Mol. Cell 16 (2004) 439-452
55. Rayasam G.V., et al. Ligand-specific dynamics of the progesterone receptor in living cells and during chromatin remodeling in vitro. Mol. Cell. Biol. 25 (2005) 2406-2418
56. Metivier R., et al. Transcriptional complexes engaged by apo-estrogen receptor-α isoforms have divergent outcomes. EMBO J. 23 (2004) 3653-3666
57. Tansey W.P. Transcriptional activation: risky business. Genes Dev. 15 (2001) 1045-1050
58. Muratani M., and Tansey W.P. How the ubiquitin proteasome system controls transcription. Nat. Rev. Mol. Cell Biol. 4 (2003) 192-201
59. Aiyar S.E., et al. Attenuation of estrogen receptor α-mediated transcription through estrogen-stimulated recruitment of a negative elongation factor. Genes Dev. 18 (2004) 2134-2146
60. Sims III R.J., et al. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18 (2004) 2437-2468
61. Fischle W., et al. Binary switches and modification cassettes in histone biology and beyond. Nature 425 (2003) 475-479
62. Hatzis P., and Talianidis I. Dynamics of enhancer-promoter communication during differentiation-induced gene activation. Mol. Cell 10 (2002) 1467-1477
63. Martens J.A., and Winston F. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13 (2003) 136-142
64. Agalioti T., et al. Ordered recruitment of chromatin modifying and general transcription factors to the IFN-B promoter. Cell 103 (2000) 667-678
65. Geng F., and Laurent B.C. Roles of SWI/SNF and HATs throughout the dynamic transcription of a yeast glucose-repressible gene. EMBO J. 23 (2004) 127-137
66. Thomson S., et al. Distinct stimulus-specific histone modifications at Hsp70 chromatin targeted by the transcription factor heat shock factor-1. Mol. Cell 15 (2004) 585-594
67. McMahon S.J., et al. Polyglutamine-expanded spinocerebellar ataxia-7 protein disrupts normal SAGA and SLIK histone acetyltransferase activity. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 8478-8482
68. Macdonald N., et al. Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3. Mol. Cell 20 (2005) 199-211
69. Dhalluin C., et al. Structure and ligand of a histone acetyltransferase bromodomain. Nature 399 (1999) 491-496
70. Zegerman P., et al. Histone H3 lysine 4 methylation disrupts binding of nucleosome remodeling and deacetylase (NuRD) repressor complex. J. Biol. Chem. 277 (2002) 11621-11624
71. Langst G., and Becker P.B. Nucleosome remodeling: one mechanism, many phenomena?. Biochim. Biophys. Acta 1677 (2004) 58-63
72. Bannister A.J., et al. Histone methylation: dynamic or static?. Cell 109 (2002) 801-806
73. Okada Y., et al. hDOT1L links histone methylation to leukemogenesis. Cell 121 (2005) 167-178
74. Chiang P.W., et al. Isolation, sequencing, and mapping of the human homologue of the yeast transcription factor, SPT5. Genomics 38 (1996) 421-424
75. Stoler S., et al. A mutation in CSE4, an essential gene encoding a novel chromatin-associated protein in yeast, causes chromosome nondisjunction and cell cycle arrest at mitosis. Genes Dev. 9 (1995) 573-586