Changing the DNA landscape: Putting a SPN on chromatin

Current Topics in Microbiology and Immunology

Volumn 274, Issue , 2003, Pages 171-201

  Formosa, Tim ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CASEIN KINASE II; DNA; DNA DIRECTED DNA POLYMERASE ALPHA; DNA POLYMERASE; ELONGATION FACTOR; HISTONE; PROTEASOME; PROTEIN; PROTEIN CP; PROTEIN DUF; PROTEIN FACT; PROTEIN SPN; RNA POLYMERASE; RNA POLYMERASE II; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

CHROMATIN; CHROMATIN STRUCTURE; COMPLEX FORMATION; DNA REPLICATION; DNA SEQUENCE; DNA TEMPLATE; DNA TRANSCRIPTION; ENZYME ACTIVITY; ENZYME SPECIFICITY; GENE DUPLICATION; GENE INTERACTION; HUMAN; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN MODIFICATION; REVIEW; RNA TRANSLATION; TRANSCRIPTION REGULATION; XENOPUS LAEVIS; YEAST;

ANURA; EUKARYOTA; XENOPUS LAEVIS;

EID: 0037241069     PISSN: 0070217X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-55747-7_7     Document Type: Review

References (68)

1. ARAVIND L, KOONIN EV (1998) Eukaryotic transcription regulators derive from ancient enzymatic domains. Curr Biol 8:R111-R113
2. BORTVIN A, WINSTON F (1996) Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272:1473-1476
3. BREWSTER NK, JOHNSTON GC, SINGER RA (1998) Characterization of the CP complex, an abundant dimer of Cdc68 and Pob3 proteins that regulates yeast transcriptional activation and chromatin repression. J Biol Chem 273:21972-21979
4. BREWSTER NK, JOHNSTON GC, SINGER RA (2001) A bipartite yeast SSRP1 analog comprised of Pob3 and Nhp6 proteins modulates transcription. Mol Cell Biol 21: 3491-3502
5. BURLEY SK, ROEDER RG (1996) Biochemistry and structural biology of transcription factor IID (TFIID). Annu Rev Biochem 65:769-799
6. BUSTIN M (1999) Regulation of DNA-dependent activities by the functional motifs of the high-mobility-group chromosomal proteins. Mol Cell Biol 19:5237-5246
7. CHANG CH, LUSE DS (1997) The H3/H4 tetramer blocks transcript elongation by RNA polymerase II in vitro. J Biol Chem 272:23427-23434
8. CHANG M, FRENCH-CORNAY D, FAN HY, KLEIN H, DENIS CL, JAEHNING JA (1999) A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol Cell Biol 19:1056-1067
9. CLARK-ADAMS CD, NORRIS D, OSLEY MA, FASSLER JS, WINSTON F (1988) Changes in histone gene dosage alter transcription in yeast. Genes Dev 2:150-159
10. COSTA PJ, ARNDT KM (2000) Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae rtf1 protein in transcription elongation. Genetics 156: 535-547
11. COSTIGAN C, KOLODRUBETZ D, SNYDER M (1994) NHP6a and NHP6b, which encode HMG1-like proteins, are candidates for downstream components of the yeast SLT2 mitogen-activated protein kinase pathway. Mol Cell Biol 14:2391-2403
12. COTE J (2002) The MYST family of histone acetyltransferases. Springer-Verlag, Heidelberg
13. EISENMANN DM, DOLLARD C,WINSTON F (1989) SPT15, the gene encoding the yeast TATA binding factor TFIID, is required for normal transcription initiation in vivo. Cell 58:1183-1191
14. EVANS DR, BREWSTER NK, XU Q, ROWLEY A, ALTHEIM BA, JOHNSTON GC, SINGER RA (1998) The yeast protein complex containing cdc68 and pob3 mediates core-promoter repression through the cdc68 N-terminal domain. Genetics 150:1393-1405
15. EXINGER F, LACROUTE F (1992) 6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae. Curr Genet 22:9-11
16. FERDOUS A, GONZALEZ F, SUN L, KODADEK T, JOHNSTON SA (2001) The 19S regulatory particle of the proteasome is required for efficient transcription elongation by RNA polymerase II. Mol Cell 7:981-991
17. FORMOSA T, ERIKSSON P, WITTMEYER J, GINN J, YU Y, STILLMAN DJ (2001) Spt16-Pob3 and the HMG protein Nhp6 combine to form the nucleosome-binding factor SPN. Embo J 20:3506-3517
18. FORMOSA T, NITTIS T (1969) Dna2 Mutants Reveal Interaction s with DNA Polymerase α and Ctf4, α Pol α Accessory Factor, and Show That Full Dna2 Helicase Activity Is Not Essential for Growth. Genetics 151:1459-1470
19. GAVIN AC, BOSCHE M, KRAUSE R, GRANDI P, MARZIOCH M, BAUER A, SCHULTZ J, RICK JM, MICHON AM, CRUCIAT C M, REMOR M, HOFERT C, SCHELDER M, BRAJENOVIC M, RUFFNER H, MERINO A, KLEIN K, HUDAK M, DICKSON D, RUDI T, GNAU V, BAUCH A, BASTUCK S, HUHSE B, LEUTWEIN C, HEURTIER MA, COPLEY RR, EDELMANN A, QUERFURTH E, RYBIN V, DREWES G, RAIDA M, BOUWMEESTER T, BORK P, SERAPHIN B, KUSTER B, NEUBAUER G, SUPERTI-FURGA G (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147
20. HARTZOG GA, WADA T, HANDA H, WINSTON F (1998) Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev 12:357-369
21. HIRSCHHORN JN, BROWN SA, CLARK CD, WINSTON F (1992) Evidence that SNF2/SWI2 and SNF5 activate transcription in yeast by altering chromatin structure. Genes Dev 6:2288-2298
22. HO Y, GRUHLER A, HEILBUT A, BADER GD, MOORE L, ADAMS SL, MILLAR A, TAYLOR P, BENNETT K, BOUTILIER K, YANG L, WOLTING C, DONALDSON I, SCHANDORFF S, SHEWNARANE J, VO M, TAGGART J, GOUDREAULT M, MUSKAT B, ALFARANO C, DEWAR D, LIN Z, MICHALICKOVA K, WILLEMS AR, SASSI H, NIELSEN PA, RASMUSSEN KJ, ANDERSEN JR, JOHANSEN LE, HANSEN LH, JESPERSEN H, PODTELEINIKOV A, NIELSEN E, CRAWFORD J, POULSEN V, SORENSEN BD, MATTHIESEN J, HENDRICKSON RC, GLEESON F, PAWSON T, MORAN MF, DUROCHER D, MANN M, HOGUE CW, FIGEYS D, TYERS M (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415:180-183
23. IZBAN MG, LUSE DS (1991) Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev 5:683-696
24. JOHN S, HOWE L, TAFROV ST, GRANT PA, STERNGLANZ R, WORKMAN JL (2000) The something about silencing protein, Sas3, is the catalytic subunit of NuA3, a yTAF(II)30-containing HAT complex that interacts with the Spt16 subunit of the yeast CP (Cdc68/Pob3)-FACT complex. Genes Dev 14:1196-1208
25. KANG SW, KUZUHARA T, HORIKOSHI M (2000) Functional interaction of general transcription initiation factor TFIIE with general chromatin factor SPT16/CDC68. Genes Cells 5:251-263
26. KELLER DM, ZENG X, WANG Y, ZHANG QH, KAPOOR M, SHU H, GOODMAN R, LOZANO G, ZHAO Y, LU H (2001) A DNA damage-induced p53 serine 392 kinase complex contains CK2, hSpt16, and SSRP1. Mol Cell 7:283-292
27. LIPFORD JR, BELL SP (2001) Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol Cell 17:21-30
28. LYCAN D, MIKESELL G, BUNGER M, BREEDEN L (1994) Differential effects of Cdc68 on cell cycle-regulated promoters in Saccharomyces cerevisiae. Mol Cell Biol 14: 7455-7465
29. MALONE EA, CLARK CD, CHIANG A,WINSTON F (1991) Mutation in SPT16/CDC68 suppress cis- and trans-acting mutations that affect promoter function in Saccharomyces cerevisiae. Mol Cell Biol 11:5710-5717
30. MILES J, FORMOSA T (1992 a) Evidence that POB1, a Saccharomyces cerevisiae protein that binds to DNA polymerase a, acts in DNA metabolism in vivo. Mol Cell Biol 12:5724-5735
31. MILES J, FORMOSA T (1992 b) Protein affinity chromatography with purified yeast DNA polymerase a detects proteins that bind to DNA polymerase. Proc Natl Acad Sci USA 89:1276-1280
32. NEWPORT J (1987) Nuclear reconstitution in vitro: stages of assembly around protein-free DNA. Cell 48:205-217
33. OKUHARA K, OHTA K, SEO H, SHIODA M, YAMADA T, TANAKA Y, DOHMAE N, SEYAMA Y, SHIBATA T, MUROFUSHI H (1999) A DNA unwinding factor involved in DNA replication in cell-free extracts of xenopus eggs. Curr Biol 9:341-350
34. ORPHANIDES G, LEROY G, CHANG C-H, LUSE DS, REINBERG D (1998) FACT, a factor that facilitates transcript elongation through nucleosomes. Cell 92:105-116
35. ORPHANIDES G, REINBERG D (2000) RNA polymerase II elongation through chromatin. Nature 407:471-475
36. ORPHANIDES G, WU WH, LANE WS, HAMPSEY M, REINBERG D (1999) The chromatin-specific transcription elongation factor FACT comprises the human SPT16/CDC68 and SSRP1 proteins. Nature 400:284-288
37. PAULL TT, CAREY M, JOHNSON RC (1996) Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional activation in vivo and assembly of preinitiation complexes in vitro. Genes Dev 10:2769-2781
38. POWELL W, REINES D (1996) Mutations in the second largest subunit of RNA polymerase II cause 6-azauracil sensitivity in yeast and increased transcriptional arrest in vitro. J Biol Chem 271:6866-6873
39. PRENDERGAST JA, MURRAY LE, ROWLEY A, CARRUTHERS DR, SINGER RA, JOHNSTON GC (1990) Size selection identifies new genes that regulate Saccharomyces cerevisiae cell proliferation. Genetics 124:81-90
40. ROTH SY, DENU JM, ALLIS CD (2001) Histone acetyltransferases. Annu Rev Biochem 70:81-120
41. ROWLEY A, SINGER RA, JOHNSTON G (1991) CDC68, a yeast gene that affects regulation of cell proliferation and transcription, encodes a protein with a highly acidic carboxyl terminus. Mol Cell Biol 11:5718-5726
42. RUBIN DM, COUX O, WEFES I, HENGARTNER C, YOUNG RA, GOLDBERG AL, FINLEY D (1996) Identification of the gal4 suppressor Sug1 as a subunit of the yeast 26S proteasome. Nature 379:655-657
43. SCHLESINGER MB, FORMOSA T (2000) POB3 is required for both transcription and replication in the yeast Saccharomyces cerevisiae. Genetics 155:1593-1606
44. SCHNELL R, D'ARI L, FOSS M, GOODMAN D, RINE J (1989) Genetic and molecular characterization of suppressors of SIR4 mutations in Saccharomyces cerevisiae. Genetics 122:29-46
45. SHAW RJ, REINES D (2000) Saccharomyces cerevisiae transcription elongation mutants are defective in PUR5 induction in response to nucleotide depletion. Mol Cell Biol 20:7427-7437
46. SHI X, CHANG M, WOLF AJ, CHANG CH, FRAZER-ABEL AA, WADE PA, BURTON ZF, JAEHNING JA (1997) Cac73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. Mol Cell Biol 17:1160-1169
47. SIDOROVA J, BREEDEN L (1999) The MSN1 and NHP6A genes suppress SWI6 defects in Saccharomyces cerevisiae. Genetics 151:45-55
48. SQUAZZO SL, COSTA PJ, LINDSTROM D, KUMER KE, SIMIC R, JENNINGS JL, LINK AJ, ARNDT KM, HARTZOG G (2002) The Paf1 complex physically and functionally associates with transcriptioh elongation factors in vivo. EMBO J. In Press
49. STRAHL BD, ALLIS CD (2000) The language of covalent histone modifications. Nature 403:41-45
50. STRAHL-BOLSINGER S, HECHT A, LUO K, GRUNSTEIN M (1997) SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. Genes Dev 11:83-93
51. VERMA R, CHEN S, FELDMAN R, SCHIELTZ D, YATES J, DOHMEN J, DESHAIES RJ (2000) Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes. Mol Biol Cell 11:3425-3439
52. VERRIJZER CP (2002) Gene Regulation by SWI/SNF Related Chromatin Remodeling Factors. Springer-Verlag, Heidelberg
53. VOGES D, ZWICKL P, BAUMEISTER W (1999) The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu Rev Biochem 68:1015-1068
54. WADA T, ORPHANIDES G, HASEGAWA J, KIM DK, SHIMA D, YAMAGUCHI Y, FUKUDA A, HISATAKE K, OH S, REINBERG D, HANDA H (2000) FACT relieves DSIF/NELF-mediated inhibition of transcriptional elongation and reveals functional differences between P-TEFb and TFIIH. Mol Cell 5:1067-1072
55. WADA T, TAKAGI T, YAMAGUCHI Y, FERDOUS A, IMAI T, HIROSE S, SUGIMOTO S, YANO K, HARTZOG GA, WINSTON F, BURATOWSKI S, HANDA H (1998) DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev 12:343-356
56. WANG W (2002) The SWI/SNF family of ATP-dependent chromatin remodelers: similar mechanisms but diverse functions. Springer-Verlag, Heidelberg
57. WEINERT T (1998) DNA damage and checkpoint pathways: molecular anatomy and interactions with repair. Cell 94:555-558
58. WHITE CL, SUTO RK, LUGER K (2001) Structure of the yeast nucleosome core particle reveals fundamental changes in internucleosome interactions. Embo J 20:5207-5218
59. WINSTON F (1992) Analysis of SPT genes: A genetic approach towards analysis of TFIID, histones, and other transcription factors of yeast. In McKnight SL and Yamamoto KR (eds.), Transcriptional Regulation. Cold Spring Harbor Laboratory Press, Plainview, NY, pp. 1271-1293
60. WINSTON F, CARLSON M (1992) Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin, connection. Trends Genet 8:387-391
61. WINSTON F, CHALEFF DT, VALENT B, FINK GR (1984) Mutations affecting Ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae. Genetics 107:179-197
62. WITTMEYER J, FORMOSA T (1997) 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 17:4178-4190
63. WITTMEYER J, JOSS L, FORMOSA T (1999) Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha. Biochemistry 38:8961-8971
64. WORKMAN JL, KINGSTON RE (1998) Alteration of nucleosome structure as a mechanism of transcriptional regulation. Annu Rev Biochem 67:545-579
65. XU Q, JOHNSTON GC, SINGER RA (1993) The Saccharomyces cerevisiae Cdc68 transcription activator is antagonized by San1, a protein implicated in transcriptional silencing. Mol Cell Biol 13:7553-7565
66. XU Q, SINGER RA, JOHNSTON GC (1995) Sug1 modulates yeast transcription activation by Cdc68. Mol and Cell Biol 15:6025-6035
67. YARNELL AT, OH S, REINBERG D, LIPPARD SJ (2001) Interaction of FACT, SSRP1, and the high mobility group (HMG) domain of SSRP1 with DNA damaged by the anti-cancer drug cisplatin. J Biol Chem 276:25736-25741
68. Yu Y, ERIKSSON P, STILLMAN DJ (2000) Architectural transcription factors and the SAGA complex function in parallel pathways to activate transcription. Mol Cell Biol 20:2350-2357