Global approaches to chromatin

Chemistry and Biology

Volumn 9, Issue 11, 2002, Pages 1167-1173

  Bernstein, Bradley E ^a,b   Schreiber, Stuart L ^a  

^a HARVARD UNIVERSITY   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

CHEMISTRY; CHROMATIN; DNA MICROARRAY; DRUG SCREENING; GENETIC TRANSCRIPTION; GENETICS; METHODOLOGY; MUTATION; PHYSIOLOGY; POLYMERASE CHAIN REACTION; REVIEW;

CHROMATIN; DRUG EVALUATION, PRECLINICAL; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; TRANSCRIPTION, GENETIC;

EID: 0036849072     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(02)00265-X     Document Type: Review

References (53)

1. Ramaswamy S., Golub T.R. DNA microarrays in clinical oncology. J. Clin. Oncol. 20:2002;1932-1941.
2. Ideker T., Thorsson V., Ranish J.A., Christmas R., Buhler J., Eng J.K., Bumgarner R., Goodlett D.R., Aebersold R., Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science. 292:2001;929-934.
3. Andersen J.S., Lyon C.E., Fox A.H., Leung A.K., Lam Y.W., Steen H., Mann M., Lamond A.I. Directed proteomic analysis of the human nucleolus. Curr. Biol. 12:2002;1-11.
4. Sanders S.L., Jennings J., Canutescu A., Link A.J., Weil P.A. Proteomics of the eukaryotic transcription machinery. identification of proteins associated with components of yeast TFIID by multidimensional mass spectrometry Mol. Cell. Biol. 22:2002;4723-4738.
5. Ho Y., Gruhler A., Heilbut A., Bader G.D., Moore L., Adams S.L., Millar A., Taylor P., Bennett K., Boutilier K.et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature. 415:2002;180-183.
6. Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., Schultz J., Rick J.M., Michon A.M., Cruciat C.M.et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415:2002;141-147.
7. Kuruvilla F.G., Shamji A.F., Sternson S.M., Hergenrother P.J., Schreiber S.L. Dissecting glucose signalling with diversity-oriented synthesis and small-molecule microarrays. Nature. 416:2002;653-657.
8. Jenuwein T., Allis C.D. Translating the histone code. Science. 293:2001;1074-1080.
9. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature. 410:2001;120-124.
10. Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature. 410:2001;116-120.
11. Zeng L., Zhou M.M. Bromodomain. an acetyl-lysine binding domain FEBS Lett. 513:2002;124-128.
12. Imai S., Armstrong C.M., Kaeberlein M., Guarente L. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature. 403:2000;795-800.
13. Aparicio O.M., Billington B.L., Gottschling D.E. Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae. Cell. 66:1991;1279-1287.
14. Braunstein M., Rose A.B., Holmes S.G., Allis C.D., Broach J.R. Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. Genes Dev. 7:1993;592-604.
15. Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J.D., Jacq, C., Johnston, M., et al. (1996). Life with 6000 genes. Science. 274, 546, 563-567.
16. DeRisi J.L., Iyer V.R., Brown P.O. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science. 278:1997;680-686.
17. Wodicka L., Dong H., Mittmann M., Ho M.H., Lockhart D.J. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat. Biotechnol. 15:1997;1359-1367.
18. Wyrick J.J., Holstege F.C., Jennings E.G., Causton H.C., Shore D., Grunstein M., Lander E.S., Young R.A. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature. 402:1999;418-421.
19. Bernstein B.E., Humphrey E.L., Erlich R.L., Schneider R., Bouman P., Liu J.S., Kouzarides T., Schreiber S.L. Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl. Acad. Sci. USA. 99:2002;8695-8700.
20. Bryk M., Briggs S.D., Strahl B.D., Curcio M.J., Allis C.D., Winston F. Evidence that Set1, a factor required for methylation of histone H3, regulates rDNA silencing in S. cerevisiae by a Sir2-independent mechanism. Curr. Biol. 12:2002;165-170.
21. Lee T.I., Causton H.C., Holstege F.C., Shen W.C., Hannett N., Jennings E.G., Winston F., Green M.R., Young R.A. Redundant roles for the TFIID and SAGA complexes in global transcription. Nature. 405:2000;701-704.
22. Bernstein B.E., Tong J.K., Schreiber S.L. Genomewide studies of histone deacetylase function in yeast. Proc. Natl. Acad. Sci. USA. 97:2000;13708-13713.
23. Shamji A.F., Kuruvilla F.G., Schreiber S.L. Partitioning the transcriptional program induced by rapamycin among the effectors of the Tor proteins. Curr. Biol. 10:2000;1574-1581.
24. Iyer V.R., Horak C.E., Scafe C.S., Botstein D., Snyder M., Brown P.O. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature. 409:2001;533-538.
25. Lieb J.D., Liu X., Botstein D., Brown P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28:2001;327-334.
26. Ren B., Robert F., Wyrick J.J., Aparicio O., Jennings E.G., Simon I., Zeitlinger J., Schreiber J., Hannett N., Kanin E.et al. Genome-wide location and function of DNA binding proteins. Science. 290:2000;2306-2309.
27. Roguev A., Schaft D., Shevchenko A., Pijnappel W.W., Wilm M., Aasland R., Stewart A.F. The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4. EMBO J. 20:2001;7137-7148.
28. Briggs S.D., Bryk M., Strahl B.D., Cheung W.L., Davie J.K., Dent S.Y., Winston F., Allis C.D. Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev. 15:2001;3286-3295.
29. Robyr D., Suka Y., Xenarios I., Kurdistani S.K., Wang A., Suka N., Grunstein M. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell. 109:2002;437-446.
30. Kurdistani S.K., Robyr D., Tavazoie S., Grunstein M. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat. Genet. 31:2002;248-254.
31. De Rubertis F., Kadosh D., Henchoz S., Pauli D., Reuter G., Struhl K., Spierer P. The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature. 384:1996;589-591.
32. Rundlett S.E., Carmen A.A., Kobayashi R., Bavykin S., Turner B.M., Grunstein M. HDA1 and RPD3 are members of distinct yeast histone deacetylase complexes that regulate silencing and transcription. Proc. Natl. Acad. Sci. USA. 93:1996;14503-14508.
33. Santos-Rosa H., Schneider R., Zegerman P., Sherriff J., Bernstein B.E., Bannister A.J., Schreiber S.L., Mellor J., Kouzarides T. Active genes are tri-methylated at K4 of histone H3. Nature. 419:2002;407-411.
34. Nishioka K., Chuikov S., Sarma K., Erdjument-Bromage H., Allis C.D., Tempst P., Reinberg D. Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. Genes Dev. 16:2002;479-489.
35. Zegerman P., Canas B., Pappin D., Kouzarides T. Histone H3 Lysine 4 Methylation Disrupts Binding of Nucleosome Remodeling and Deacetylase (NuRD) Repressor Complex. J. Biol. Chem. 277:2002;11621-11624.
36. Tong J.K., Hassig C.A., Schnitzler G.R., Kingston R.E., Schreiber S.L. Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature. 395:1998;917-921.
37. Wade P.A., Jones P.L., Vermaak D., Wolffe A.P. A multiple subunit Mi-2 histone deacetylase from Xenopus laevis cofractionates with an associated Snf2 superfamily ATPase. Curr. Biol. 8:1998;843-846.
38. Xue Y., Wong J., Moreno G.T., Young M.K., Cote J., Wang W. NURD, a novel complex with both ATP-dependent chromatin-remodeling and histone deacetylase activities. Mol. Cell. 2:1998;851-861.
39. Zhang Y., LeRoy G., Seelig H.P., Lane W.S., Reinberg D. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell. 95:1998;279-289.
40. Marks P., Rifkind R.A., Richon V.M., Breslow R., Miller T., Kelly W.K. Histone deacetylases and cancer. causes and therapies Nat. Rev. Cancer. 1:2001;194-202.
41. Sternson S.M., Wong J.C., Grozinger C.M., Schreiber S.L. Synthesis of 7200 small molecules based on a substructural analysis of the histone deacetylase inhibitors trichostatin and trapoxin. Org. Lett. 3:2001;4239-4242.
42. Grozinger C.M., Chao E.D., Blackwell H.E., Moazed D., Schreiber S.L. Identification of a class of small molecule inhibitors of the sirtuin family of NAD-dependent deacetylases by phenotypic screening. J. Biol. Chem. 276:2001;38837-38843.
43. Bedalov A., Gatbonton T., Irvine W.P., Gottschling D.E., Simon J.A. Identification of a small molecule inhibitor of Sir2p. Proc. Natl. Acad. Sci. USA. 98:2001;15113-15118.
44. Sudarsanam P., Iyer V.R., Brown P.O., Winston F. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA. 97:2000;3364-3369.
45. Holstege F.C., Jennings E.G., Wyrick J.J., Lee T.I., Hengartner C.J., Green M.R., Golub T.R., Lander E.S., Young R.A. Dissecting the regulatory circuitry of a eukaryotic genome. Cell. 95:1998;717-728.
46. Ng H.H., Robert F., Young R.A., Struhl K. Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev. 16:2002;806-819.
47. Damelin M., Simon I., Moy T.I., Wilson B., Komili S., Tempst P., Roth F.P., Young R.A., Cairns B.R., Silver P.A. The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Mol. Cell. 9:2002;563-573.
48. Ren B., Cam H., Takahashi Y., Volkert T., Terragni J., Young R.A., Dynlacht B.D. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev. 16:2002;245-256.
49. Weinmann A.S., Yan P.S., Oberley M.J., Huang T.H., Farnham P.J. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 16:2002;235-244.
50. MacBeath G., Schreiber S.L. Printing proteins as microarrays for high-throughput function determination. Science. 289:2000;1760-1763.
51. Haab B.B., Dunham M.J., Brown P.O. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2:2001;4. 1-4.13.
52. Hecht A., Grunstein M. Mapping DNA interaction sites of chromosomal proteins using immunoprecipitation and polymerase chain reaction. Methods Enzymol. 304:1999;399-414.
53. Kuo M.H., Allis C.D. In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods. 19:1999;425-433.