Chromatin marks and machines, the missing nucleosome is a theme: Gene regulation up and downstream

Molecular Cell

Volumn 17, Issue 3, 2005, Pages 323-330

  Carey, Mike ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONE; HISTONE; RNA POLYMERASE II;

BINDING SITE; CATALYSIS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPARATIVE STUDY; DNA MICROARRAY; ENHANCER REGION; EUKARYOTIC CELL; EXPERIMENT; GENE ACTIVATION; GENE EXPRESSION REGULATION; GENE MUTATION; GENETIC ANALYSIS; GENETIC ORGANIZATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HETEROCHROMATIN; HUMAN; IMMUNOPRECIPITATION; MAMMAL; MEDIATOR; MOLECULAR BIOLOGY; MOLECULAR MECHANICS; NONHUMAN; NUCLEOSOME; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; REGULATORY MECHANISM; REVIEW; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TRANSCRIPTION INITIATION; UPREGULATION;

ANIMALS; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION; HETEROCHROMATIN; HISTONES; HUMANS; MOLECULAR CHAPERONES; NUCLEOSOMES; PROMOTER REGIONS (GENETICS); RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE; SILENCER ELEMENTS, TRANSCRIPTIONAL; TRANSCRIPTION, GENETIC;

EUKARYOTA; MAMMALIA;

EID: 13244255361     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2005.01.013     Document Type: Review

References (61)

1. Adkins M.W., Howar S.R., Tyler J.K. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol. Cell. 14:2004;657-666
2. Ahn S.H., Kim M., Buratowski S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing. Mol. Cell. 13:2004;67-76
3. Allen T.A., Von Kaenel S., Goodrich J.A., Kugel J.F. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat. Struct. Mol. Biol. 11:2004;816-821
4. Belotserkovskaya R., Reinberg D. Facts about FACT and transcript elongation through chromatin. Curr. Opin. Genet. Dev. 14:2004;139-146
5. Boeger H., Griesenbeck J., Strattan J.S., Kornberg R.D. Nucleosomes unfold completely at a transcriptionally active promoter. Mol. Cell. 11:2003;1587-1598
6. Boeger H., Griesenbeck J., Strattan J.S., Kornberg R.D. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol. Cell. 14:2004;667-673
7. Bourbon H.M., Aguilera A., Ansari A.Z., Asturias F.J., Berk A.J., Bjorklund S., Blackwell T.K., Borggrefe T., Carey M., Carlson M., et al. A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol. Cell. 14:2004;553-557
8. Cantin G.T., Stevens J.L., Berk A.J. Activation domain-mediator interactions promote transcription preinitiation complex assembly on promoter DNA. Proc. Natl. Acad. Sci. USA. 100:2003;12003-12008
9. Cosgrove M.S., Boeke J.D., Wolberger C. Regulated nucleosome mobility and the histone code. Nat. Struct. Mol. Biol. 11:2004;1037-1043
10. Cosma M.P. Ordered recruitment. gene-specific mechanism of transcription activation Mol. Cell. 10:2002;227-236
11. Cosma M.P., Panizza S., Nasmyth K. Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF. Mol. Cell. 7:2001;1213-1220
12. Cuthbert G.L., Daujat S., Snowden A.W., Erdjument-Bromage H., Hagiwara T., Yamada M., Schneider R., Gregory P.D., Tempst P., Bannister A.J., Kouzarides T. Histone deimination antagonizes arginine methylation. Cell. 118:2004;545-553
13. Dorsett D. Adherin. key to the cohesin ring and cornelia de Lange syndrome Curr. Biol. 14:2004;R834-R836
14. Dover J., Schneider J., Tawiah-Boateng M.A., Wood A., Dean K., Johnston M., Shilatifard A. Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J. Biol. Chem. 277:2002;28368-28371
15. Doyon Y., Selleck W., Lane W.S., Tan S., Cote J. Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Mol. Cell. Biol. 24:2004;1884-1896
16. Drobic B., Espino P.S., Davie J.R. Mitogen- and stress-activated protein kinase 1 activity and histone H3 phosphorylation in oncogene-transformed mouse fibroblasts. Cancer Res. 64:2004;9076-9079
17. Eissenberg J.C., Ma J., Gerber M.A., Christensen A., Kennison J.A., Shilatifard A. dELL is an essential RNA polymerase II elongation factor with a general role in development. Proc. Natl. Acad. Sci. USA. 99:2002;9894-9899
18. Elgin S.C. DNAase I-hypersensitive sites of chromatin. Cell. 27:1981;413-415
19. Espinoza C.A., Allen T.A., Hieb A.R., Kugel J.F., Goodrich J.A. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat. Struct. Mol. Biol. 11:2004;822-829
20. Flaus A., Owen-Hughes T. Mechanisms for ATP-dependent chromatin remodelling. farewell to the tuna-can octamer? Curr. Opin. Genet. Dev. 14:2004;165-173
21. Foulds C.E., Nelson M.L., Blaszczak A.G., Graves B.J. Ras/Mitogen-activated protein kinase signaling activates Ets-1 and Ets-2 by CBP/p300 recruitment. Mol. Cell. Biol. 24:2004;10954-10964
22. Gerber M., Shilatifard A. Transcriptional elongation by RNA polymerase II and histone methylation. J. Biol. Chem. 278:2003;26303-26306
23. Gregory R.I., Yan K.P., Amuthan G., Chendrimada T., Doratotaj B., Cooch N., Shiekhattar R. The Microprocessor complex mediates the genesis of microRNAs. Nature. 432:2004;235-240
24. Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat. Struct. Mol. Biol. 11:2004;394-403
25. Hampsey M., Reinberg D. Tails of intrigue. phosphorylation of RNA polymerase II mediates histone methylation Cell. 113:2003;429-432
26. Han J.S., Szak S.T., Boeke J.D. Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes. Nature. 429:2004;268-274
27. Han M., Grunstein M. Nucleosome loss activates yeast downstream promoters in vivo. Cell. 55:1988;1137-1145
28. Hartzog G.A. Transcription elongation by RNA polymerase II. Curr. Opin. Genet. Dev. 13:2003;119-126
29. Hatzis P., Talianidis I. Dynamics of enhancer-promoter communication during differentiation-induced gene activation. Mol. Cell. 10:2002;1467-1477
30. Haushalter K.A., Kadonaga J.T. Chromatin assembly by DNA-translocating motors. Nat. Rev. Mol. Cell Biol. 4:2003;613-620
31. Hollenhorst P.C., Jones D.A., Graves B.J. Expression profiles frame the promoter specificity dilemma of the ETS family of transcription factors. Nucleic Acids Res. 32:2004;5693-5702
32. Jenuwein T., Allis C.D. Translating the histone code. Science. 293:2001;1074-1080
33. Kirmizis A., Bartley S.M., Kuzmichev A., Margueron R., Reinberg D., Green R., Farnham P.J. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev. 18:2004;1592-1605
34. Kobor, M.S., Venkatasubrahmanyam, S., Meneghini, M.D., Gin, J.W., Jennings, J.L., Link, A.J., Madhani, H.D., and Rine, J. (2004). A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol 2(5).
35. Korber P., Horz W. SWRred not shaken; mixing the histones. Cell. 117:2004;5-7
36. Krogan N.J., Dover J., Wood A., Schneider J., Heidt J., Boateng M.A., Dean K., Ryan O.W., Golshani A., Johnston M., et al. The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p. linking transcriptional elongation to histone methylation Mol. Cell. 11:2003;721-729. a
37. Krogan N.J., Keogh M.C., Datta N., Sawa C., Ryan O.W., Ding H., Haw R.A., Pootoolal J., Tong A., Canadien V., et al. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell. 12:2003;1565-1576. b
38. Kusch T., Florens L., Macdonald W.H., Swanson S.K., Glaser R.L., Yates Iii J.R., Abmayr S.M., Washburn M.P., Workman J.L. Acetylation by Tip60 Is Required for Selective Histone Variant Exchange at DNA Lesions. Science. 306:2004;2084-2087
39. Lee C.K., Shibata Y., Rao B., Strahl B.D., Lieb J.D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36:2004;900-905
40. Lindstrom D.L., Squazzo S.L., Muster N., Burckin T.A., Wachter K.C., Emigh C.A., McCleery J.A., Yates J.R. 3rd, Hartzog G.A. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol. Cell. Biol. 23:2003;1368-1378
41. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 389:1997;251-260
42. Miller O.L. Jr. The nucleolus, chromosomes, and visualization of genetic activity. J. Cell Biol. 91:1981;15s-27s
43. Mizuguchi G., Shen X., Landry J., Wu W.H., Sen S., Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science. 303:2004;343-348
44. Ng H.H., Robert F., Young R.A., Struhl K. 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
45. Nourani A., Utley R.T., Allard S., Cote J. Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation. EMBO J. 23:2004;2597-2607
46. Nowak S.J., Corces V.G. Phosphorylation of histone H3. a balancing act between chromosome condensation and transcriptional activation Trends Genet. 20:2004;214-220
47. Oki M., Valenzuela L., Chiba T., Ito T., Kamakaka R.T. Barrier proteins remodel and modify chromatin to restrict silenced domains. Mol. Cell. Biol. 24:2004;1956-1967
48. Prochasson P., Neely K.E., Hassan A.H., Li B., Workman J.L. Targeting activity is required for SWI/SNF function in vivo and is accomplished through two partially redundant activator-interaction domains. Mol. Cell. 12:2003;983-990
49. Reinke H., Horz W. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol. Cell. 11:2003;1599-1607
50. Rodriguez C.R., Cho E.J., Keogh M.C., Moore C.L., Greenleaf A.L., Buratowski S. Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II. Mol. Cell. Biol. 20:2000;104-112
51. Sato S., Tomomori-Sato C., Parmely T.J., Florens L., Zybailov B., Swanson S.K., Banks C.A., Jin J., Cai Y., Washburn M.P., et al. A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. Mol. Cell. 14:2004;685-691
52. Schwabish M.A., Struhl K. Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA Polymerase II. Mol. Cell. Biol. 24:2004;10111-10117
53. Shang Y., Myers M., Brown M. Formation of the androgen receptor transcription complex. Mol. Cell. 9:2002;601-610
54. Shilatifard A. Transcriptional elongation control by RNA polymerase II. a new frontier Biochim. Biophys. Acta. 1677:2004;79-86
55. Simic R., Lindstrom D.L., Tran H.G., Roinick K.L., Costa P.J., Johnson A.D., Hartzog G.A., Arndt K.M. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 22:2003;1846-1856
56. Simone C., Forcales S.V., Hill D.A., Imbalzano A.N., Latella L., Puri P.L. p38 pathway targets SWI-SNF chromatin-remodeling complex to muscle-specific loci. Nat. Genet. 36:2004;738-743
57. Smith C.L., Horowitz-Scherer R., Flanagan J.F., Woodcock C.L., Peterson C.L. Structural analysis of the yeast SWI/SNF chromatin remodeling complex. Nat. Struct. Biol. 10:2003;141-145
58. Wood A., Krogan N.J., Dover J., Schneider J., Heidt J., Boateng M.A., Dean K., Golshani A., Zhang Y., Greenblatt J.F., et al. Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol. Cell. 11:2003;267-274
59. Xu W., Cho H., Kadam S., Banayo E.M., Anderson S., Yates J.R. 3rd, Emerson B.M., Evans R.M. A methylation-mediator complex in hormone signaling. Genes Dev. 18:2004;144-156
60. Zhang L., Eugeni E.E., Parthun M.R., Freitas M.A. Identification of novel histone post-translational modifications by peptide mass fingerprinting. Chromosoma. 112:2003;77-86
61. Zhao H., Dean A. An insulator blocks spreading of histone acetylation and interferes with RNA polymerase II transfer between an enhancer and gene. Nucleic Acids Res. 32:2004;4903-4919