The ins and outs of ATP-dependent chromatin remodeling in budding yeast: Biophysical and proteomic perspectives

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1769, Issue 3, 2007, Pages 153-171

  van Vugt, Joke J F A ^a   Ranes, Michael ^a   Campsteijn, Coen ^b   Logie, Colin ^a  

^a RADBOUD UNIVERSITY NIJMEGEN   (Netherlands)

^b Sars International Centre for Marine Molecular Biology   (Norway)

Author keywords

CHD1; Chromatin; INO80; ISW1; ISW2; Nucleosome; SNF2; STH1; SWR1; YFR038w

Indexed keywords

ADENOSINE TRIPHOSPHATE;

BINDING SITE; BIOINFORMATICS; CHROMATIN ASSEMBLY AND DISASSEMBLY; COMPLEX FORMATION; DNA METHYLATION; DNA REPLICATION; DNA SEQUENCE; GENETIC ANALYSIS; GENOME; HETEROCHROMATIN; MOLECULAR INTERACTION; NONHUMAN; NUCLEOSOME; PHENOTYPE; PRIORITY JOURNAL; PROTEOMICS; REVIEW; SACCHAROMYCES CEREVISIAE; SYSTEMATIC REVIEW; TRANSCRIPTION REGULATION; YEAST;

ADENOSINE TRIPHOSPHATE; CHROMATIN ASSEMBLY AND DISASSEMBLY; GENOME, FUNGAL; NUCLEAR PROTEINS; PROTEOME; SACCHAROMYCETALES;

ANIMALIA; SACCHAROMYCETALES;

EID: 33947684367     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbaexp.2007.01.013     Document Type: Review

References (222)

1. Luger K., Mader A.W., Richmond R.K., Sargent D.F., and Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389 (1997) 251-260
2. Hansen J.C. Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. Annu. Rev. Biophys. Biomol. Struct. 31 (2002) 361-392
3. Rando O.J., Chi T.H., and Crabtree G.R. Second messenger control of chromatin remodeling. Nat. Struct. Biol. 10 (2003) 81-83
4. Strahl B.D., and Allis C.D. The language of covalent histone modifications. Nature 403 (2000) 41-45
5. Millar C.B., and Grunstein M. Genome-wide patterns of histone modifications in yeast. Nat. Rev., Mol. Cell Biol. 7 (2006) 657-666
6. Mohrmann L., and Verrijzer C.P. Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochim. Biophys. Acta 1681 (2005) 59-73
7. Saha A., Wittmeyer J., and Cairns B.R. Chromatin remodeling: the industrial revolution of DNA around histones. Nat. Rev., Mol. Cell Biol. 7 (2006) 437-447
8. Gottesfeld J.M., and Luger K. Energetics and affinity of the histone octamer for defined DNA sequences. Biochemistry 40 (2001) 10927-10933
9. Tomschik M., Zheng H., van Holde K., Zlatanova J., and Leuba S.H. Fast, long-range reversible conformational fluctuations in nucleosomes revealed by single-pair fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. 102 (2005) 3278-3283
10. Eisen J.A., Sweder K.S., and Hanawalt P.C. Evolution of the SF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23 (1995) 2715-2723
11. Singleton M.R., and Wigley D.B. Modularity and specialization in superfamily 1 and 2 helicases. J. Bacteriol. 184 (2002) 1819-1826
12. Winston F., and Allis C.D. The bromodomain: a chromatin-targeting module?. Nat. Struct. Biol. 6 (1999) 601-604
13. Hassan A.H., Prochasson P., Neely K.E., Galasinski S.C., Chandy M., Carrozza M.J., and Workman J.L. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111 (2002) 369-379
14. Grune T., Brzeski J., Eberharter A., Clapier C.R., Corona D.F.V., Becker P.B., and Muller C.W. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol. Cell 12 (2003) 449-460
15. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., and Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410 (2001) 120-124
16. Bakshi R., Prakash T., Dash D., and Brahmachari V. In silico characterization of the INO80 subfamily of SWI2/SNF2 chromatin remodeling proteins. Biochem. Biophys. Res. Commun. 320 (2004) 197-204
17. Dennis K., Fan T., Geiman T., Yan Q., and Muegge K. Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev. 15 (2001) 2940-2944
18. Vongs A., Kakutani T., Martienssen R.A., and Richards E.J. Arabidopsis thaliana DNA methylation mutants. Science 260 (1993) 1926-1928
19. Brzeski J., and Jerzmanowski A. Deficient in DNA methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 278 (2003) 823-826
20. Boyer L.A., Logie C., Bonte E., Becker P.B., Wade P.A., Wolffe A.P., Wu C., Imbalzano A.N., and Peterson C.L. Functional delineation of three groups of the ATP-dependent family of chromatin remodeling enzymes. J. Biol. Chem. 275 (2000) 18864-18870
21. Lia G., Praly E., Ferreira H., Stockdale C., Ching Tse-Dinh Y., Dunlap D., Croquette V., Bensimon D., and Owen-Hughes T. Direct observation of DNA distortion by the RSC complex. Mol. Cell 21 (2006) 417-425
22. Jin J., Cai Y., Yao T., Gottschalk A.J., Florens L., Swanson S.K., Gutierrez J.L., Coleman M.K., Workman J.L., Mushegian A., Washburn M.P., Conaway R.C., and Conaway J.W. A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. J. Biol. Chem. 280 (2005) 41207-41212
23. Tsukiyama T., and Wu C. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 83 (1995) 1011-1020
24. Clapier C.R., Langst G., Corona D.F.V., Becker P.B., and Nightingale K.P. Critical role for the histone H4 N terminus in nucleosome remodeling by ISWI. Mol. Cell. Biol. 21 (2001) 875-883
25. Brehm A., Langst G., Kehle J., Clapier C.R., Imhof A., Eberharter A., Muller J., and Becker P.B. dMi-2 and ISWI chromatin remodeling factors have distinct nucleosome binding and mobilization properties. EMBO J. 19 (2000) 4332-4341
26. Cote J., Quinn J., Workman J.L., and Peterson C.L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science 265 (1994) 53-60
27. Quinn J., Fyrberg A.M., Ganster R.W., Schmidt M.C., and Peterson C.L. DNA-binding properties of the yeast SWI/SNF complex. Nature 379 (1996) 844-847
28. Cote J., Peterson C.L., and Workman J.L. Perturbation of nucleosome core structure by the SWI/SNF complex persists after its detachment, enchancing subsequent transcription factor binding. Proc. Natl. Acad. Sci. 95 (1998) 4947-4952
29. Shen X., Mizuguchi G., Hamiche A., and Wu C. A chromatin remodeling complex involved in transcription and DNA processing. Nature 406 (2000) 541-544
30. Saha A., Wittmeyer J., and Cairns B.R. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 16 (2002) 2120-2134
31. Whitehouse I., Stockdale C., Flause A., Szcezelkun M.D., and Owen-Hughes T. Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme. Mol. Cell. Biol. 23 (2003) 1935-1945
32. Phelan M.L., Sif S., Narlikar G.J., and Kingston R.E. Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol. Cell 3 (1999) 247-253
33. Georgel P.T., Tsukiyama T., and Wu C. Role of histone tails in nucleosome remodeling by Drosophila NURF. EMBO J. 16 (1997) 4717-4726
34. Corona D.F., Längst G., Clapier C.R., Bonte E.J., Ferrari S., Tamkun J.W., and Becker P.B. ISWI is an ATP-dependent nucleosome remodeling factor. Mol. Cell 3 (1999) 239-245
35. Saha A., Wittmeyer J., and Cairns B.R. Chromatin remodeling through directional DNA translocation from an internal nucleosomal site. Nat. Struct. Mol. Biol. 12 (2005) 747-755
36. Neely K.E., and Workman J.L. The complexity of chromatin remodeling and its links to cancer. Biochim. Biophys. Acta 1603 (2002) 19-29
37. Sengupta S.M., VanKanegan M., Persinger J., Logie C., Cairns B.R., Peterson C.L., and Bartholomew B. The interactions of yeast SWI/SNF and RSC with the nucleosome before and after chromatin remodeling. J. Biol. Chem. 276 (2001) 12636-12644
38. Zofall M., Persinger J., Kassabov S.R., and Bartholomew B. Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome. Nat. Struct. Mol. Biol. 13 (2006) 339-346
39. Kassabov S.R., Zhang B., Persinger J., and Bartholomew B. SWI/SNF unwraps, slides and rewraps the nucleosome. Mol. Cell 11 (2003) 391-403
40. Strohner R., Wachsmuth M., Dachauer K., Mazurkiewicz J., Hochstatter J., Rippe K., and Längst G. A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nat. Struct. Mol. Biol. 12 (2005) 683-690
41. Bazett-Jones D.P., Cote J., Landel C.C., Peterson C.L., and Workman J.L. The SWI/SNF complex creates loop domains in DNA and polynucleosome arrays and can disrupt DNA-histone contacts within these domains. Mol. Cell. Biol. 19 (1999) 1470-1478
42. Schwanbeck R., Xiao H., and Wu C. Spatial contacts and nucleosome step movements induced by the NURF chromatin remodeling complex. J. Biol. Chem. 279 (2004) 39933-39941
43. Shundrovsky A., Smith C.L., Lis J.T., Peterson C.L., and Wang M.D. Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nat. Struct. Mol. Biol. 13 (2006) 549-554
44. Zhang Y., Smith C.L., Saha A., Grill S.W., Mihardja S., Smith S.B., Cairns B.R., Peterson C.L., and Bustamante C. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell 24 (2006) 559-568
45. Langst G., and Becker P.B. Nucleosome remodeling: one mechanism, many phenomena?. Biochim. Biophys. Acta 1677 (2004) 58-63
46. Lorch Y., Zhang M., and Kornberg R.D. Histone octamer transfer by a chromatin-remodeling complex. Cell 96 (1999) 389-392
47. Li W., Dou S.-X., Xie P., and Wang P.-Y. Brownian dynamics simulation of directional sliding of histone octamers caused by DNA bending. Phys. Rev., E 73 (2006) 051909
48. Hamiche A., and Richard-Foy H. The switch in the helical handedness of the histone (H3-H4)2 tetramer within a nucleoprotein particle requires a reorientation of the H3-H3 interface. J. Biol. Chem. 273 (1998) 9261-9269
49. Mizuguchi G., Shen X., Landry J., Wu W.H., Sen S., and Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science 303 (2004) 343-348
50. Krogan N.J., Keogh M.-C., Datta N., Sawa C., Ryan O.W., Ding H., Haw R.A., Pootoolal J., Tong A., Canadien V., Richards D.P., Wu X., Emili A., Hughes T.R., Buratowski S., and Greenblatt J.F. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol. Cell 12 (2003) 1565-1576
51. Vicent G.P., Nacht A.S., Smith C.L., Peterson C.L., Dimitrov S., and Beato M. DNA instructed displacement of histones H2A and H2B at an inducible promoter. Mol. Cell 16 (2004) 439-452
52. Bash R., Wang H., Anderson C., Yodh J., Hager G., Lindsay S.M., and Lohr D. AFM imaging of protein movements: histone H2A-H2B release during nucleosome remodeling. FEBS Lett. 580 (2006) 4757-4761
53. Nagaich A.K., Walker D.A., Wolford R., and Hager G.L. Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling. Mol Cell 14 (2004) 163-174
54. Segal E., Fondufe-Mittendorf Y., Chen L., Thastrom A., Field Y., Moore I.K., Wang J.-P.Z., and Widom J. A genomic code for nucleosome positioning. Nature 442 (2006) 772-778
55. Schnitzler G.R., Cheung C.L., Hafner J.H., Saurin A.J., Kingston R.E., and Lieber C.M. Direct imaging of human SWI/SNF-remodeled mono- and polynucleosomes by atomic force microscopy employing carbon nanotube tips. Mol. Cell. Biol. 21 (2001) 8504-8511
56. Blank T.A., and Becker P.B. The effect of nucleosome phasing sequences and DNA topology on nucleosome spacing. J. Mol. Biol. 260 (1996) 1-8
57. Lusser A., Urwin D.L., and Kadonaga J.T. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat. Struct. Mol. Biol. 12 (2005) 160-166
58. Whitehouse I., and Tsukiyama T. Antagonistic forces that position nucleosomes in vivo. Nat. Struct. Mol. Biol. 13 (2006) 633-640
59. Varga-Weisz P.D., Wilm M., Bonte E., Dumas K., Mann M., and Becker P.B. Chromatin-remodeling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388 (1997) 598-602
60. Cairns B.R. Chromatin remodeling complexes: strength in diversity, precision through specialization. Curr. Opin. Genet. Dev. 15 (2005) 185-190
61. Havas K., Flaus A., Phelan M.L., Kinston R., Wade P.A., Lilley D.M.J., and Owen-Hughes T. Generation of superhelical torsion by ATP-dependent chromatin remodeling activities. Cell 103 (2000) 1133-1142
62. Langst G., and Becker P.B. ISWI induces nucleosome sliding on nicked DNA. Mol. Cell 8 (2001) 1085-1092
63. Durr H., Korner C., Muller M., Hickmann V., and Hopfner K.P. X-ray structures of the Sulfolobus solffataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 121 (2005) 363-373
64. Korolev S., Hsieh J., Gauss G.H., Lohman T.M., and Waksman G. Major domain swiveling revealed by the crystal structures of complexes of E. coli Rep helicase bound to single-stranded DNA and ADP. Cell 90 (1997) 635-647
65. Thoma N.H., Czyzewski B.K., Alexeev A.A., Mazin A.V., Kowalczykowski S.C., and Pavletich N.P. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nat. Struct. Mol. Biol. 12 (2005) 350-356
66. Velankar S.S., Soultanas P., Dillingham M.S., Subramanya H.S., and Wigley D.B. Crystal structures of complexes of PcrA DNA helicase with a DNA substrate indicate an inchworm mechanism. Cell 97 (1999) 75-84
67. He X., Fan H.Y., Narlikar G.J., and Kingston R.E. Human ACF1 alters the remodeling strategy of SNF2h. J. Biol. Chem. 281 (2006) 28636-28647
68. Stockdale C., Flaus A., Ferreira H., and Owen-Hughes T. Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. Journal of Biological Chemistry 281 (2006) 16279-16288
69. Lorch Y., Maier-Davis B., and Kornberg R.D. Chromatin remodeling by nucleosome disassembly in vitro. Proc. Natl. Acad. Sci. 103 (2006) 3090-3093
70. Fan H.-Y., Trotter K.W., Archer T.K., and Kingston R.E. Swapping function of two chromatin remodeling complexes. Mol. Cell 17 (2005) 805-815
71. Logie C., and Peterson C.L. Catalytic activity of the yeast SWI/SNF complex on reconstituted nucleosome arrays. EMBO J. 16 (1997) 6772-6782
72. Poirier M., Eroglu S., Chatenay D., and Marko J.F. Reversible and irreversible unfolding of mitotic newt chromosomes by applied force. Mol. Biol. Cell 11 (2000) 269-276
73. Reguly T., Breitkreutz A., Boucher L., Breitkreutz B.J., Hon G.C., Myers C.L., Parsons A., Friesen H., Oughtred R., Tong A., Stark C., Ho Y., Botstein D., Andrews B., Boone C., Troyanskya O.G., Ideker T., Dolinski K., Batada N.N., and Tyers M. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J. Biol. 5 (2006) 11
74. Peri S., Navarro J.D., Amanchy R., Kristiansen T.Z., Jonnalagadda C.K., Surendranath V., Niranjan V., Muthusamy B., Gandhi T.K., Gronborg M., Ibarrola N., Deshpande N., Shanker K., Shivashankar H.N., Rashmi B.P., Ramya M.A., Zhao Z., Chandrika K.N., Padma N., Harsha H.C., Yatish A.J., Kavitha M.P., Menezes M., Choudhury D.R., Suresh S., Ghosh N., Saravana R., Chandran S., Krishna S., Joy M., Anand S.K., Madavan V., Joseph A., Wong G.W., Schiemann W.P., Constantinescu S.N., Huang L., Khosravi-Far R., Steen H., Tewari M., Ghaffari S., Blobe G.C., Dang C.V., Garcia J.G., Pevsner J., Jensen O.N., Roepstorff P., Deshpande K.S., Chinnaiyan A.M., Hamosh A., Chakravarti A., and Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 13 (2003) 2363-2371
75. Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., Li J., Pu S., Datta N., Tikuisis A.P., Punna T., Peregrin-Alvarez J.M., Shales M., Zhang X., Davey M., Robinson M.D., Paccanaro A., Bray J.E., Sheung A., Beattie B., Richards D.P., Canadien V., Lalev A., Mena F., Wong P., Starostine A., Canete M.M., Vlasblom J., Wu S., Orsi C., Collins S.R., Chandran S., Haw R., Rilstone J.J., Gandi K., Thompson N.J., Musso G., St. Onge P., Ghanny S., Lam M.H., Butland G., Altaf-Ul A.M., Kanaya S., Shilatifard A., O'Shea E., Weissman J.S., Ingles C.J., Hughes T.R., Parkinson J., Gerstein M., Wodak S.J., Emili A., and Greenblatt J.F. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440 (2006) 637-643
76. Gavin A.-C., Aloy P., Grandi P., Krause R., Boesche M., Marzioch M., Rau C., Jensen L.J., Bastuck S., Dumpelfeld B., Edelmann A., Heurtier M.-A., Hoffman V., Hoefert C., Klein K., Hudak M., Michon A.-M., Schelder M., Schirle M., Remor M., Rudi T., Hooper S., Bauer A., Bouwmeester T., Casari G., Drewes G., Neubauer G., Rick J.M., Kuster B., Bork P., Russell R.B., and Superti-Furga G. Proteome survey reveals modularity of the yeast cell machinery. Nature 440 (2006) 631-636
77. Breitkreutz B.J., Stark C., and Tyers M. Osprey: a network visualization system. Genome Biol. 4 (2003) R22
78. Gendrel A.V., Lippman Z., Yordan C., Colot V., and Martienssen R.A. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297 (2002) 1871-1873
79. Yan Q., Huang J., Fan T., Zhu H., and Muegge K. Lsh, a modulator of CpG methylation, is crucial for normal histone methylation. EMBO 22 (2003) 5154-5162
80. May B.P., Lippman Z.B., Fang Y., Spector D.L., and Martienssen R.A. Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet. 1 (2005) e79
81. 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., Conaway J.W., Conaway R.C., Emmons S.W., Fondell J.D., Freedman L.P., Fukasawa T., Gustafsson C.M., Han M., He X., Herman P.K., Hinnebusch A.G., Holmberg S., Holstege F.C., Jaehning J.A., Kim Y.J., Kuras L., Leutz A., Lis J.T., Meisterernest M., Naar A.M., Nasmyth K., Parvin J.D., Ptashne M., Reinberg D., Ronne H., Sadowski I., Sakurai H., Sipiczki M., Sternberg P.W., Stillman D.J., Strich R., Struhl K., Svejstrup J.Q., Tuck S., Winston F., Roeder R.G., and Kornberg R.D. A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol. Cell 14 (2004) 553-557
82. Fan T., Hagan J.P., Kozlov S.V., Stewart C.L., and Muegge K. Lsh controls silencing of the imprinted Cdkn1c gene. Development 132 (2005) 635-644
83. Zhu H., Geiman T.M., Xi S., Jiang Q., Schmidtmann A., Chen T., Li E., and Muegge K. Lsh is involved in de novo methylation of DNA. EMBO J. 25 (2006) 335-345
84. De La Fuente R., Baumann C., Fan T., Schmidtmann A., Dobrinski I., and Muegge K. Lsh is required for meiotic chromosome synapsis and retrotransposon silencing in female germ cells. Nat. Cell Biol. 8 (2006) 1448-1454
85. Peterson C.L., and Herskowitz I. Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription. Cell 68 (1992) 573-583
86. Peterson C.L., Dingwall A., and Scott M.P. Five SWI/SNF gene products are components of a large multisubunit complex required for transcriptional enhancement. Proc. Natl. Acad. Sci. 91 (1994) 2905-2908
87. Hirschhorn J.N., Brown S.A., Clark C.D., and Winston F. Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev. 6 (1992) 2288-2298
88. Cairns B.R., Lorch Y., Li Y., Zhang M., Lacomis L., Erdjument-Bromage H., Tempst P., Du J., Laurent B., and Kornberg R.D. RSC, an essential, abundant chromatin-remodeling complex. Cell 87 (1996) 1249-1260
89. Ghaemmaghami S., Huh W.K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., and Weissman J.S. Global analysis of protein expression in yeast. Nature 425 (2003) 737-741
90. Holstege F.C., Jennings E.G., Wyrick J.J., Lee T.I., Hengartner C.J., Green M.R., Golub T.R., Landers E.S., and Young R.A. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95 (1998) 717-728
91. Sudarsanam P., Lyer V.R., Brown P.O., and Winston F. Whole-genome expression analysis of snf/swi mutants of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 97 (2000) 3364-3369
92. Roberts S.M., and Winston F. Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. Genetics 147 (1997) 451-465
93. Gaillard H., Fitzgerald D.J., Smith C.L., Peterson C.L., Richmond T.J., and Thoma F. Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase. J. Biol. Chem. 278 (2003) 17655-17663
94. Chai B., Huang J., Cairns B.R., and Laurent B.C. Distinct roles for the RSC and Swi/Snf ATP-dependent chromatin remodelers in DNA double-strand break repair. Genes Dev. 19 (2005) 1656-1661
95. Yu Y., and Waters R. Histone acetylation, chromatin remodeling and nucleotide excision repair: hint from the study on MFA2 in Saccharomyces cerevisiae. Cell Cycle 4 (2005) 1043-1045
96. Gong F., Fahy D., and Smerdon M.J. Rad4-Rad23 interaction with SWI/SNF links ATP-dependent chromatin remodeling with nucleotide excision repair. Nat. Struct. Mol. Biol. 13 (2006) 902-907
97. Cairns B.R., Schlichter A., Erdjument-Bromage H., Tempst P., Kornberg R.D., and Winston F. Two functionally distinct forms of the RSC nucleosome-remodeling complex, containing essential AT hook, BAH, and bromodomains. Mol. Cell 4 (1999) 715-723
98. Angus-Hill M.L., Schlichter A., Roberts D., Erdjument-Bromage H., Tempst P., and Cairns B.R. A Rsc3/Rsc30 zinc cluster dimer reveals novel roles for the chromatin remodeler RSC in gene expression and cell cycle control. Mol. Cell 7 (2001) 741-751
99. Huang J., and Laurent B.C. A role for the RSC chromatin remodeler in regulating cohesion of sister chromatid arms. Cell Cycle 3 (2004) 973-975
100. Baetz K.K., Krogan N.J., Emili A., Greenblatt J., and Hieter P. The ctf13-30/CTF13 genomic haploinsufficiency modifier screen identifies the yeast chromatin remodeling complex RSC, which is required for the establishment of sister chromatid cohesion. Mol. Cell. Biol. 24 (2004) 1232-1244
101. Hsu J.M., Huang J., Meluh P.B., and Laurent B.C. The yeast RSC chromatin-remodeling complex is required for kinetochore function in chromosome segregation. Mol. Cell. Biol. 23 (2003) 3202-3215
102. Du J., Nasir I., Benton B.K., Kladde M.P., and Laurent B.C. Sth1p, a Saccharomyces cerevisiae Snf2p/Swi2p homolog, is an essential ATPase in RSC and differs from Snf/Swi in its interaction with histones and chromatin-associated proteins. Genetics 150 (1998) 987-1005
103. Wechser M.A., Kladde M.P., Alfieri J.A., and Peterson C.L. Effects of Sin-versions of histone H4 on yeast chromatin structure and function. EMBO J. 16 (1997) 2086-2095
104. Bortvin A., and Winston F. Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272 (1996) 1473-1476
105. Kaplan C.D., Laprade L., and Winston F. Transcription elongation factors repress transcription initiation from cryptic sites. Science 301 (2003) 1096-1099
106. Carey M., Li B., and Workman J.L. RSC exploits histone acetylation to abrogate the nucleosomal block to RNA polymerase II elongation. Mol. Cell 24 (2006) 481-487
107. Martin D.G., Baetz K., Shi X., Walter K.L., Macdonald V.E., Wlodarski M.J., Gozani O., Hieter P., and Howe L. The yng1p plant homeodomain finger is a methyl-histone binding module that recognizes lysine 4-methylated histone h3. Mol. Cell Biol. 26 (2006) 7871-7879
108. Zeisig D.T., Bittner C.B., Zeisig B.B., Garcia-Cuellar M.-P., Hess J.L., and Slany R.K. The eleven-nineteen-leukemia protein ENL connects nuclear MLL fusion partners with chromatin. Oncogene 24 (2005) 5525-5532
109. Shia W.J., Osada S., Florens L., Swanson S.K., Washburn M.P., and Workman J.L. Characterization of the yeast trimeric-SAS acetyltransferase complex. J. Biol. Chem. 280 (2005) 11987-11994
110. Zhang H., Richardson D.O., Roberts D.N., Utley R., Erdjument-Bromage H., Tempst P., Cote J., and Cairns B.R. The Yaf9 component of the SWR1 and NuA4 complexes is required for proper gene expression, histone H4 acetylation, and Htz1 replacement near telomeres. Mol. Cell. Biol. 24 (2004) 9424-9436
111. Neely K.E., Hassan A.H., Wallberg A.E., Steger D.J., Cairns B.R., Wright A.P., and Workman J.L. Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. Mol. Cell 4 (1999) 649-655
112. Soutourina J., Bordas-Le Floch V., Gendrel G., Flores A., Ducrot C., Dumay-Odelot H., Soularue P., Navarro R., Cairns B.R., Lefebvre O., and Werner M. Rsc4 connects the chromatin remodeler RSC to RNA polymerases. Mol. Cell. Biol. 26 (2006) 4920-4933
113. Kos W., Kal A.J., van Wilpe S., and Tabak H.F. Expression of genes encoding peroxisomal proteins in Saccharomyces cerevisiae is regulated by different circuits of transcriptional control. Biochim. Biophys. Acta 1264 (1995) 79-86
114. Rothermel B.A., Shyjan A.W., Etheredge J.L., and Butow R.A. Transactivation by the Rtg1p, a basic helix-loop-helix protein that functions in communication between mitochondria and the nucleus in yeast. J. Biol. Chem. 270 (1995) 29476-29482
115. Huang M., Zhou Z., and Elledge S.J. The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor. Cell 94 (1998) 595-605
116. Huang J., Hsu J.M., and Laurent B.C. The RSC nucleosome-remodeling complex is required for cohesin's association with chromosome arms. Mol. Cell 13 (2004) 739-750
117. Losada A., and Hirano T. Dynamic molecular linkers of the genome: the first decade of SMC proteins. Genes Dev. 19 (2005) 1269-1287
118. Boyer L.A., and Peterson C.L. Actin-related proteins (Arps): conformational switches for chromatin-remodeling machines?. BioEssays 22 (2000) 666-672
119. Shen X., Ranallo R., Choi E., and Wu C. Involvement of Actin-Related Proteins in ATP-dependent chromatin remodeling. Mol. Cell 12 (2003) 147-155
120. Downs J.A., Allard S., Jobin-Robitaille O., Javaheri A., Auger A., Bouchard N., Kron S.J., Jackson S.P., and Cote J. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites. Mol. Cell 16 (2004) 979-990
121. Mellor J., and Morillon A. ISWI complexes in Saccharomyces cerevisiae. Biochim. Biophys. Acta 1677 (2004) 100-112
122. Vary Jr. J.C., Gangaraju V.K., Qin J., Landel C.C., Kooperberg C., Bartholomew B., and Tsukiyama T. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. 23 (2003) 80-91
123. Morillon A., Karabetsou N., O'Sullivan J., Kent N., Proudfoot N., and Mellor J. Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell 115 (2003) 425-435
124. Lindstrom K.C., Vary J.C., Parthun M.R., Delrow J., and Tsukiyama T. Isw1 functions in parallel with the NuA4 and SWR1 complexes in stress-induced gene repression. Mol. Cell. Biol. 26 (2006) 6117-6129
125. Carrozza M.J., Li B., Florens L., Suganuma T., Swanson S.K., Lee K.K., Shia W.J., Anderson S., Yates J., Washburn M.P., and Workman J.L. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123 (2005) 581-592
126. Morillon A., Karabetsou N., Nair A., and Mellor J. Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Mol. Cell 18 (2005) 723-734
127. Cuperus G., and Shore D. Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8. Genetics 162 (2002) 633-645
128. Rehman M.A., Fourel G., Mathews A., Ramdin D., Espinosa M., Gilson E., and Yankulov K. Differential requirement of DNA replication factors for subtelomeric ARS consensus sequence protosilencers in Saccharomyces cerevisiae. Genetics 174 (2006) 1801-1810
129. Kagalwala M.N., Glaus B.J., Dang W., Zofall M., and Bartholomew B. Topography of the ISW2-nucleosome complex: insights into nucleosome spacing and chromatin remodeling. EMBO J. 23 (2004) 2092-2104
130. Goldmark J.P., Fazzio T.G., Estep P.W., Church G.M., and Tsukiyama T. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell 103 (2000) 423-433
131. Fazzio T.G., Kooperberg C., Goldmark J.P., Neal C., Basom R., Delrow J., and Tsukiyama T. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell. Biol. 21 (2001) 6450-6460
132. Iida T., and Araki H. Noncompetitive counteractions of DNA polymerase e and ISW2/yCHRAC for epigenetic inheritance of telomere position effect in Saccharomyces cerevisiae. Mol. Cell. Biol. 24 (2004) 217-227
133. Tsubota T., Tajima R., Ode K., Kubota H., Fukuhara N., Kawabata T., Maki S., and Maki H. Double-stranded DNA binding, an unusual property of DNA polymerase epsilon, promotes epigenetic silencing in Saccharomyces cerevisiae. J. Biol. Chem. 281 (2006) 32898-32908
134. Hartlepp K.F., Fernandez-Tornero C., Eberharter A., Grune T., Muller C.W., and Becker P.B. The histone fold subunits of Drosophila CHRAC facilitate nucleosome sliding through dynamic DNA interactions. Mol. Cell. Biol. 25 (2005) 9886-9896
135. Diffley J.F., and Stillman B. Similarity between the transcriptional silencer binding proteins ABF1 and RAP1. Science 246 (1989) 1034-1038
136. Ehrenhofer-Murray A.E. Chromatin dynamics at DNA replication, transcription and repair. Eur. J. Biochem. 271 (2004) 2335-2349
137. Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., Hannett N.M., Harbison C.T., Thompson C.M., Simon I., Zeitlinger J., Jennings E.G., Murray H.L., Gordon D.B., Ren B., Wyrick J.J., Tagne J.B., Volkert T.L., Fraenkel E., Gifford D.K., and Young R.A. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
138. Donato J.J., Chung S.C., and Tye B.K. Genome-wide hierarchy of replication origin usage in Saccharomyces cerevisiae. PLoS Genet 2 (2006) e141
139. Pina B., Fernandez-Larrea J., Garcia-Reyero N., and Idrissi F.Z. The different (sur)faces of Rap1p. Mol. Genet. Genomics 268 (2003) 791-798
140. Zhang Y., Yu Z., Fu X., and Liang C. Noc3p, a bHLH protein, plays an integral role in the initiation of DNA replication in budding yeast. Cell 109 (2002) 849-860
141. Snyder M., Sapolsky R.J., and Davis R.W. Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol. Cell. Biol. 8 (1988) 2184-2194
142. Flaus A., Martin D.M.A., Barton G.J., and Owen-Hughes T. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res. 34 (2006) 2887-2905
143. Tran H.G., Steger D.J., Lyer V.R., and Johnson A.D. The chromo domain protein Chd1p from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J. 19 (2000) 2323-2331
144. Krogan N.J., Kim M., Ahn S.H., Zhong G., Kobor M.S., Cagney G., Emili A., Shilatifard A., Buratowski S., and Greenblatt J.F. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22 (2002) 6979-6992
145. Bouazoune K., and Brehm A. dMi-2 chromatin binding and remodeling activities are regulated by dCK2 phosphorylation. J. Biol. Chem. 280 (2005) 41912-41920
146. Reinberg D., and Sims III R.J. de FACTo nucleosome dynamics. J. Biol. Chem. 281 (2006) 23297-23301
147. Simic R., Lindstrom D.L., Tran H.G., Roinick K.L., Costa P.J., Johnson A.D., Hartzog G.A., and Arndt K.M. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 22 (2003) 1846-1856
148. Pavri R., Zhu B., Li G., Trojer P., Mandal S., Shilatifard A., and Reinberg D. Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell 125 (2006) 703-717
149. Dover J., Schneider J., Tawiah-Boateng M.A., Wood A., Dean K., Johnston M., and Shilatifard A. Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J. Biol. Chem. 277 (2002) 28368-28371
150. Sun Z.W., and Allis C.D. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418 (2002) 104-108
151. Sims III R.J., Chen C.F., Santos-Rosa H., Kouzarides T., Patel S.S., and Reinberg D. Human but not yeast CHD1 binds directly and selectively to histone H3 methylated lysine 4 via its tandem chromodomains. J. Biol. Chem. 280 (2005) 41789-41792
152. Pray-Grant M.G., Daniel J.A., Schieltz D., Yates III J.R., and Grant P.A. Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433 (2005) 434-438
153. Pray-Grant M.G., Schieltz D., Mc.MAhon S.J., Wood J.M., Kennedy E.L., Cook R.G., Workman J.L., Yates III J.R., and Grant P.A. The novel SLIK histone acetyltransferase complex functions in the yeast retrograde response pathway. Mol. Cell. Biol. 22 (2002) 8774-8786
154. Kohler A., Pascual-Garcia P., Llopis A., Zapater M., Posas F., Hurt E., and Rodriguez-Navarro S. The mRNA export factor Sus1 is involved in Spt/Ada/Gcn5 acetyltransferase-mediated H2B deubiquitinylation through its interaction with Ubp8 and Sgf11. Mol. Biol. Cell 17 (2006) 4228-4236
155. Henry K.W., Wyce A., Lo W.S., Duggan L.J., Emre N.C., Kao C.F., Pillus L., Shilatifard A., Osley M.A., and Berger S.L. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 17 (2003) 2648-2663
156. Motegi A., Kuntz K., Majeed A., Smith S., and Myung K. Regulation of gross chromosomal rearrangements by ubiquitin and SUMO ligases in Saccharomyces cerevisiae. Mol. Cell. Biol. 26 (2006) 1424-1433
157. VanDenmark A.P., Blanksma M., Ferris E., Heroux A., Hill C.P., and Formosa T. The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition. Mol. Cell 22 (2006) 363-374
158. Wittmeyer J., and Formosa T. The Saccharomyces cerevisiae DNA polymerase alpha catalytic subunit interacts with Cdc68/Spt16 and with Pob3, a protein similar to an HMG1-like protein. Mol. Cell. Biol. 17 (1997) 4178-4190
159. Ebbert R., Birkmann A., and Schuller H.J. The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. Mol. Microbiol. 32 (1999) 741-751
160. Matangkasombut O., and Buratowski S. Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation. Mol. Cell 11 (2003) 353-363
161. Jónsson Z., Jha S., Wohlschlegel J.A., and Dutta A. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol. Cell 16 (2004) 465-477
162. Bauer A., Chauvet S., Usseglio F., Rothbacher U., Aragnol D., Kemler R., and Pradel J. Pontin52 and Reptin52 function as antagonistic regulators of beta-catenin signalling activity. EMBO 19 (2000) 6121-6130
163. Tora L. A unified nomenclature for TATA box binding protein (TBP)-associated factors (TAFs) involved in RNA polymerase II transcription. Genes Dev. 16 (2002) 673-675
164. Dikstein R., Ruppert S., and Tjian R. TAFII250 is a bipartite protein kinase that phosphorylates the base transcription factor RAP74. Cell 84 (1996) 781-790
165. Durant M., and Pugh B.F. Genome-wide relationships between TAF1 and histone acetyltransferases in Saccharomyces cerevisiae. Mol. Cell. Biol. 26 (2006) 2791-2802
166. Komarnitsky P., Cho E.J., and Buratowski S. Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14 (2000) 2452-2460
167. Kobor M.S., Venkatasubrahmanyam S., Meneghini M.D., Gin J.W., Jennings J.L., Link A.J., Madhani H.D., and Rine J. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A, Z into euchromatin. PLoS Biol. 2 (2004)
168. Zhang H., Roberts D.N., and Cairns B.R. Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. Cell 123 (2005) 219-231
169. Raisner R.M., Hartley P.D., Meneghini M.D., Bao M.Z., Liu C.L., Schreiber S.L., Rando O.J., and Madhani H.D. Histone variant H2A.Z marks the 5′ends of both active and inactive genes in euchromatin. Cell 123 (2005) 233-248
170. Keogh M.C., Mennella T.A., Sawa C., Berthelet S., Krogan N.J., Wolek A., Podolny V., Carpenter L.R., Greenblatt J.F., Baetz K., and Buratowski S. The Saccharomyces cerevisiae histone H2A variant Htz1 is acetylated by NuA4. Genes Dev. 20 (2006) 660-665
171. Matangkasombut O., Buratowski R.M., Swilling N.W., and Buratowski S. Bromodomain factor 1 corresponds to a missing piece of yeast TFIID. Genes Dev. 14 (2000) 951-962
172. Jacobson R.H., Ladurner A.G., King D.S., and Tjian R. Structure and function of a human TAFII250 double bromodomain module. Science 288 (2000) 1422-1425
173. Papamichos-Chronakis M., Krebs J.E., and Peterson C.L. Interplay between Ino80 and Swr1 chromatin remodeling enzymes regulates cell cycle checkpoint adaptation in response to DNA damage. Genes Dev. 20 (2006) 2437-2449
174. Tsukuda T., Fleming A.B., Nickoloff J.A., and Osley M.A. Chromatin remodeling at a DNA double-strand break site in Saccharomyces cerevisiae. Nature 438 (2005) 379-383
175. Murr R., Loizou J.I., Yang Y.G., Cuenin C., Li H., Wang Z.Q., and Herceg Z. Histone acetylation by Trrap-Tip60 modulates loading of repair proteins and repair of DNA double-strand breaks. Nat. Cell Biol. 8 (2006) 91-99
176. Kusch T., Florens L., Macdonald W.H., Swanson S.K., Glaser R.L., Yates III J.R., Abmayr S.M., Washburn M.P., and Workman J.L. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 306 (2004) 2084-2087
177. Shim E.Y., Hong S.J., Oum J.H., Yanez Y., Zhang Y., and Lee S.E. RSC mobilizes nucleosomes to improve accessibility of repair machinery to the damaged chromatin. Mol. Cell. Biol. 27 (2007) 1602-16013
178. Scott K.L., and Plon S.E. Loss of Sin3/Rpd3 histone deacetylase restores the DNA damage response in checkpoint-deficient strains of Saccharomyces cerevisiae. Mol. Cell. Biol. 23 (2003) 4522-4531
179. Tamburini B.A., and Tyler J.K. Localized histone acetylation and deacetylation triggered by the homologous recombination pathway of double-strand DNA repair. Mol. Cell. Biol. 25 (2005) 4903-4913
180. Bianchi M.E., and Agresti A. HMG proteins: dynamic players in gene regulation and differentiation. Curr. Opin. Genet. Dev. 15 (2005) 496-506
181. Goodwin G.H., Sanders C., and Johns E.W. A new group of chromatin-associated proteins with a high content of acidic and basic amino acids. Eur. J. Biochem. 38 (1973) 14-19
182. Moreira J.M., and Holmberg S. Chromatin-mediated transcriptional regulation by the yeast architectural factors NHP6A and NHP6B. EMBO J. 19 (2000) 6804-6813
183. Rhoades A.R., Ruone S., and Formosa T. Structural features of nucleosomes reorganized by yeast FACT and its HMB box component Nhp6. Mol. Cell. Biol. 24 (2004) 3907-3917
184. Formosa T., Eriksson P., Wittmeyer J., Ginn J., Yu Y., and Stillman D.J. Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. EMBO J. 20 (2001) 3506-3517
185. Morrison A.J., Highland J., Krogan N.J., Arbel-Eden A., Greenblatt J.F., Haber J.E., and Shen X. INO80 and γ-H2AX interaction links ATP-dependent chromatin remodeling to DNA repair. Cell 119 (2004) 767-775
186. Van Attikum H., and Gasser S.M. The histone code at DNA breaks: a guide to repair?. Nat. Rev., Mol. Cell Biol. 6 (2005) 757-765
187. Diffley J.F., and Stillman B. A close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. Proc. Natl. Acad. Sci. U. S. A. 88 (1991) 7864-7868
188. Friddle R.W., Klare J.E., Martin S.S., Corzett M., Balhorn R., Baldwin E.P., Baskin R.J., and Noy A. Mechanism of DNA compaction by yeast mitochondrial protein Abf2p. Biophys. J. 86 (2004) 1632-1639
189. Szerlong H., Saha A., and Cairns B.R. The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J. 22 (2003) 3175-3187
190. Brewster N.K., Johnston G.C., and Singer R.A. A bipartite yeast SSRP1 analog comprised of Pob3 and Nhp6 proteins modulates transcription. Mol. Cell. Biol. 21 (2001) 3491-3502
191. Lindstrom D.L., Squazzo S.L., Muster N., Burckin T.A., Wachter K.C., Emigh C.A., McCleery J.A., Yates III J.R., and 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
192. Hall D.B., Wade J.T., and Struhl K. An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol. Cell. Biol. 26 (2006) 3672-3679
193. Kim H., and Livingston D.M. A high mobility group protein binds to long CAG repeat tracts and establishes their chromatin organization in Saccharomyces cerevisiae. J. Biol. Chem. 281 (2006) 15735-15740
194. Zhou W., Ryan J.J., and Zhou H. Global analyses of sumoylated proteins in Saccharomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J. Biol. Chem. 279 (2004) 32262-32268
195. Wohlschlegel J.A., Johnson E.S., Reed S.I., and Yates III J.R. Global analysis of protein sumoylation in Saccharomyces cerevisiae. J. Biol. Chem. 279 (2004) 45662-45668
196. Panse V.G., Hardeland U., Werner T., Kuster B., and Hurt E. A proteome-wide approach identifies sumoylated substrate proteins in yeast. J. Biol. Chem. 279 (2004) 41346-41351
197. Hannich J.T., Lewis A., Kroetz M.B., Li S.J., Heide H., Emili A., and Hochstrasser M. Defining the SUMO-modified proteome by multiple approaches in Saccharomyces cerevisiae. J. Biol. Chem. 280 (2005) 4102-4110
198. Kim J.H., Choi H.J., Kim B., Kim M.H., Lee J.M., Kim I.S., Lee M.H., Choi S.J., Kim K.I., Kim S.I., Chung C.H., and Baek S.H. Roles of sumoylation of a reptin chromatin-remodeling complex in cancer metastasis. Nat. Cell Biol. 8 (2006) 631-639
199. Sterner D.E., Nathan D., Reindle A., Johnson E.S., and Berger S.L. Sumoylation of the yeast Gcn5 protein. Biochemistry 45 (2006) 1035-1042
200. Nathan D., Ingvarsdottir K., Sterner D.E., Bylebyl G.R., Dokmanovic M., Dorsey J.A., Whelan K.A., Krsmanovic M., Lane W.S., Meluh P.B., Johnson E.S., and Berger S.L. Histone sumoylation is a negative regulator in Saccharomyces cerevisiae and shows dynamic interplay with positive-acting histone modifications. Genes Dev. 20 (2006) 966-976
201. Pan X., Yuan D.S., Xiang D., Wang X., Sookhai-Mahadeo S., Bader J.S., Hieter P., Spencer F., and Boeke J.D. A robust toolkit for functional profiling of the yeast genome. Mol. Cell 16 (2004) 487-496
202. Krogan N.J., Baetz K., Keogh M.C., Datta N., Sawa C., Kwok T.C., Thompson N.J., Davey M.G., Pootoolal J., Hughes T.R., Emili A., Buratowski S., Hieter P., and Greenblatt J.F. Regulation of chromosome stability by the histone H2A variant Htz1, the Swr1 chromatin remodeling complex, and the histone acetyltransferase NuA4. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 13513-13518
203. Tong A.H., Lesage G., Bader G.D., Ding H., Xu H., Xin X., Young J., Berriz G.F., Brost R.L., Chang M., Chen Y., Cheng X., Chua G., Friesen H., Goldberg D.S., Haynes J., Humphries C., He G., Hussein S., Ke L., Krogan N., Li Z., Levinson J.N., Lu H., Menard P., Munyana C., Parsons A.B., Ryan O., Tonikian R., Roberts T., Sdicu A.M., Shapiro J., Sheikh B., Suter B., Wong S.L., Zhang L.V., Zhu H., Burd C.G., Munro S., Sander C., Rine J., Greenblatt J., Peter M., Bretscher A., Bell G., Roth F.P., Brown G.W., Andrews B., Bussey H., and Boone C. Global mapping of the yeast genetic interaction network. Science 303 (2004) 808-813
204. Dhillon N., Oki M., Szyjka S.J., Aparicio O.M., and Kamakaka R.T. H2A.Z functions to regulate progression through the cell cycle. Mol. Cell. Biol. 26 (2006) 489-501
205. Hakimi M.A., Bochar D.A., Schmiesing J.A., Dong Y., Barak O.G., Speicher D.W., Yokomori K., and Shiekhattar R. A chromatin remodeling complex that loads cohesin onto human chromosomes. Nature 418 (2002) 994-998
206. Auble D.T., Wang D., Post K.W., and Hahn S. Molecular analysis of the SNF2/SWI2 protein family member MOT1, an ATP-driven enzyme that dissociates TATA-binding protein from DNA. Mol. Cell. Biol. 17 (1997) 4842-4851
207. Sawa C., Nedea E., Krogan N., Wada T., Handa H., Greenblatt J., and Buratowski S. Bromodomain factor 1 (Bdf1) is phosphorylated by protein kinase CK2. Mol. Cell. Biol. 24 (2004) 4734-4742
208. Vidan S., and Mitchell A.P. Stimulation of yeast meiotic gene expression by the glucose-repressible protein kinase Rim15p. Mol. Cell. Biol. 17 (1997) 2688-2697
209. Swinnen E., Wanke V., Roosen J., Smets B., Dubouloz F., Pedruzzi I., Cameroni E., De Virgilio C., and Winderickx J. Rim15 and the crossroads of nutrient signalling pathways in Saccharomyces cerevisiae. Cell Div. 1 (2006) 3
210. Damelin M., Simon I., Moy T.I., Wilson B., Komili S., Tempst P., Roth F.P., Young R.A., Cairns B.R., and 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
211. Neigeborn L., and Mitchell A.P. The yeast MCK1 gene encodes a protein kinase homolog that activates early meiotic gene expression. Genes Dev. 5 (1991) 533-548
212. Shero J.H., Koval M., Spencer F., Palmer R.E., Hieter P., and Koshland D. Analysis of chromosome segregation in Saccharomyces cerevisiae. Methods Enzymol. 194 (1991) 749-773
213. Geerlings T.H., Faber A.W., Bister M.D., Vos J.C., and Raue H.A. Rio2p, an evolutionarily conserved, low abundant protein kinase essential for processing of 20 S Pre-rRNA in Saccharomyces cerevisiae. J. Biol. Chem. 278 (2003) 22537-22545
214. Posas F., Bollen M., Stalmans W., and Arino J. Biochemical characterization of recombinant yeast PPZ1, a protein phosphatase involved in salt tolerance. FEBS Lett. 168 (1995) 39-44
215. Yenush L., Mulet J.M., Arino J., and Serrano R. The Ppz protein phosphatases are key regulators of K+ and pH homeostasis: implications for salt tolerance, cell wall integrity and cell cycle progression. EMBO J. 21 (2002) 920-929
216. Santisteban M.S., Kalashnikova T., and Smith M.M. Histone H2A.Z regulates transcription and is partially redundant with nucleosome remodeling complexes. Cell 103 (2000) 411-422
217. Robzyk K., Recht J., and Osley M.A. Rad6-dependent ubiquitination of histone H2B in yeast. Science 287 (2000) 501-504
218. Wood A., Krogan N.J., Dover J., Schneider J., Heidt J., Boateng M.A., Dean K., Golshani A., Zhang Y., Greenblatt J.F., Johnston M., and Shilatifard A. Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol. Cell 11 (2003) 267-274
219. Collins S.R., Schuldiner M., Krogan N.J., and Weissman J.S. A strategy for extracting and analyzing large-scale quantitative epistatic interaction data. Genome Biol. 7 (2006) R63
220. Schuldiner M., Collins S.R., Thompson N.J., Denic V., Bhamidipati A., Punna T., Ihmels J., Andrews B., Boone C., Greenblatt J.F., Weissman J.S., and Krogan N.J. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123 (2005) 507-519
221. Workman C.T., Mak H.C., McCuine S., Tagne J.B., Agarwal M., Ozier O., Begley T.J., Samson L.D., and Ideker T. A systems approach to mapping DNA damage response pathways. Science 312 (2006) 1054-1059
222. Huh W.K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., and O'Shea E.K. Global analysis of protein localization in budding yeast. Nature 425 (2003) 686-691