Multiple roles for ISWI in transcription, chromosome organization and DNA replication

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1677, Issue 1-3, 2004, Pages 113-119

  Corona, Davide F V ^a   Tamkun, John W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

ATP dependent chromatin remodeling; Chromosome structure; ISWI; Replication; Transcription

Indexed keywords

ADENOSINE TRIPHOSPHATASE; DNA; PROTEIN SUBUNIT; REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

AMINO TERMINAL SEQUENCE; CHROMATIN; CHROMATIN STRUCTURE; CHROMOSOME ANALYSIS; CHROMOSOME STRUCTURE; DNA REPLICATION; ENERGY; GENE MUTATION; GENE REPRESSION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; HUMAN; HYDROLYSIS; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; REVIEW; SEQUENCE ANALYSIS; STIMULATION; STRUCTURE ANALYSIS; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; YEAST;

ADENOSINE TRIPHOSPHATASES; ADENOSINE TRIPHOSPHATE; ANIMALS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOMES; DNA REPLICATION; GENE EXPRESSION REGULATION; HUMANS; TRANS-ACTIVATION (GENETICS); TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 1542358189     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbaexp.2003.09.018     Document Type: Review

References (66)

1. Luger K., Mader A.W., Richmond R.K., Sargent D.F., Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 389:1997;251-260.
2. Iizuka M., Smith M.M. Functional consequences of histone modifications. Curr. Opin. Genet. Dev. 13:2003;154-160.
3. Martens J.A., Winston F. Recent advances in understanding chromatin remodeling by Swi/Snf complexes. Curr. Opin. Genet. Dev. 13:2003;136-142.
4. Becker P.B., Horz W. ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71:2002;247-273.
5. Jenuwein T., Allis C.D. Translating the histone code. Science. 293:2001;1074-1080.
6. Turner B.M. Cellular memory and the histone code. Cell. 111:2002;285-291.
7. Langst G., Becker P.B. Nucleosome mobilization and positioning by ISWI-containing chromatin-remodeling factors. J. Cell Sci. 114:2001;2561-2568.
8. Varga-Weisz P. ATP-dependent chromatin remodeling factors: nucleosome shufflers with many missions. Oncogene. 20:2001;3076-3085.
9. Neely K.E., Workman J.L. The complexity of chromatin remodeling and its links to cancer. Biochim. Biophys. Acta. 1603:2002;19-29.
10. Narlikar G.J., Fan H.Y., Kingston R.E. Cooperation between complexes that regulate chromatin structure and transcription. Cell. 108:2002;475-487.
11. Tsukiyama T., Daniel C., Tamkun J., Wu C. ISWI, a member of the SWI2/ SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor. Cell. 83:1995;1021-1026.
12. Tsukiyama T., Wu C. Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell. 83:1995;1011-1020.
13. Varga-Weisz P.D., Wilm M., Bonte E., Dumas K., Mann M., Becker P.B. Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature. 388:1997;598-602.
14. Ito T., Bulger M., Pazin M.J., Kobayashi R., Kadonaga J.T. ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell. 90:1997;145-155.
15. Aasland R., Stewart A.F., Gibson T. The SANT domain: a putative DNA-binding domain in the SWI-SNF and ADA complexes, the transcriptional co-repressor N-CoR and TFIIIB. Trends Biochem. Sci. 21:1996;87-88.
16. Boyer L.A., Langer M.R., Crowley K.A., Tan S., Denu J.M., Peterson C.L. Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes. Mol. Cell. 10:2002;935-942.
17. Grune T., Eberharter B.J.A., Clapier C.R., Corona D.F., Becker P.B., Muller C.W. Crystal structure and functional analysis of the nucleosome recognition module of the remodeling factor ISWI. Mol. Cell. 12:2003;449-460.
18. Corona D.F., Langst G., Clapier C.R., Bonte E.J., Ferrari S., Tamkun J.W., Becker P.B. ISWI is an ATP-dependent nucleosome remodeling factor. Mol. Cell. 3:1999;239-245.
19. Langst G., Bonte E.J., Corona D.F., Becker P.B. Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer. Cell. 97:1999;843-852.
20. Hamiche A., Sandaltzopoulos R., Gdula D.A., Wu C. ATP-dependent histone octamer sliding mediated by the chromatin remodeling complex NURF. Cell. 97:1999;833-842.
21. Whitehouse I., Stockdale C., Flaus A., Szczelkun M.D., Owen-Hughes T. Evidence for DNA translocation by the ISWI chromatin-remodeling enzyme. Mol. Cell. Biol. 23:2003;1935-1945.
22. Di Croce L., Koop R., Venditti P., Westphal H.M., Nightingale K.P., Corona D.F., Becker P.B., Beato M. Two-step synergism between the progesterone receptor and the DNA-binding domain of nuclear factor 1 on MMTV minichromosomes. Mol. Cell. 4:1999;45-54.
23. Tsukiyama T., Becker P.B., Wu C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature. 367:1994;525-532.
24. Mizuguchi G., Tsukiyama T., Wisniewski J., Wu C. Role of nucleosome remodeling factor NURF in transcriptional activation of chromatin. Mol. Cell. 1:1997;141-150.
25. Okada M., Hirose S. Chromatin remodeling mediated by Drosophila GAGA factor and ISWI activates fushi tarazu gene transcription in vitro. Mol. Cell. Biol. 18:1998;2455-2461.
26. Xiao H., Sandaltzopoulos R., Wang H.M., Hamiche A., Ranallo R., Lee K.M., Fu D., Wu C. Dual functions of largest NURF subunit NURF301 in nucleosome sliding and transcription factor interactions. Mol. Cell. 8:2001;531-543.
27. Mizuguchi G., Vassilev A., Tsukiyama T., Nakatani Y., Wu C. ATP-dependent nucleosome remodeling and histone hyperacetylation synergistically facilitate transcription of chromatin. J. Biol. Chem. 276:2001;14773-14783.
28. Levenstein M.E., Kadonaga J.T. Biochemical analysis of chromatin containing recombinant Drosophila core histones. J. Biol. Chem. 277:2002;8749-8754.
29. LeRoy G., Orphanides G., Lane W.S., Reinberg D. Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science. 282:1998;1900-1904.
30. Deuring R., Fanti L., Armstrong J.A., Sarte M., Papoulas O., Prestel M., Daubresse G., Verardo M., Moseley S.L., Berloco M., Tsukiyama T., Wu C., Pimpinelli S., Tamkun J.W. The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo. Mol. Cell. 5:2000;355-365.
31. Badenhorst P., Voas M., Rebay I., Wu C. Biological functions of the ISWI chromatin remodeling complex NURF. Genes Dev. 16:2002;3186-3198.
32. Armstrong J.A., Papoulas O., Daubresse G., Sperling A.S., Lis J.T., Scott M.P., Tamkun J.W. The Drosophila BRM complex facilitates global transcription by RNA polymerase II. EMBO J. 21:2002;5245-5254.
33. Goldmark J.P., Fazzio T.G., Estep P.W., Church G.M., Tsukiyama T. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell. 103:2000;423-433.
34. Tsukiyama T., Palmer J., Landel C.C., Shiloach J., Wu C. Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev. 13:1999;686-697.
35. Kent N.A., Karabetsou N., Politis P.K., Mellor J. In vivo chromatin remodeling by yeast ISWI homologs Isw1p and Isw2p. Genes Dev. 15:2001;619-626.
36. Trachtulcova P., Janatova I., Kohlwein S.D., Hasek J. Saccharomyces cerevisiae gene ISW2 encodes a microtubule-interacting protein required for premeiotic DNA replication. Yeast. 16:2000;35-47.
37. Fazzio T.G., Kooperberg C., Goldmark J.P., Neal C., Basom R., Delrow J., Tsukiyama T. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell. Biol. 21:2001;6450-6460.
38. Vary J.C. Jr., Gangaraju V.K., Qin J., Landel C.C., Kooperberg C., Bartholomew B., Tsukiyama T. Yeast Isw1p forms two separable complexes in vivo. Mol. Cell. Biol. 23:2003;80-91.
39. Hughes T.R., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., Bennett H.A., Coffey E., Dai H., He Y.D., Kidd M.J., King A.M., Meyer M.R., Slade D., Lum P.Y., Stepaniants S.B., Shoemaker D.D., Gachotte D., Chakraburtty K., Simon J., Bard M., Friend S.H. Functional discovery via a compendium of expression profiles. Cell. 102:2000;109-126.
40. Cuperus G., Shore D. Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8. Genetics. 162:2002;633-645.
41. Kassabov S.R., Henry N.M., Zofall M., Tsukiyama T., Bartholomew B. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Mol. Cell. Biol. 22:2002;7524-7534.
42. Kikyo N., Wade P.A., Guschin D., Ge H., Wolffe A.P. Active remodeling of somatic nuclei in egg cytoplasm by the nucleosomal ATPase ISWI. Science. 289:2000;2360-2362.
43. Alen C., Kent N.A., Jones H.S., O'Sullivan J., Aranda A., Proudfoot N.J. A role for chromatin remodeling in transcriptional termination by RNA polymerase II. Mol. Cell. 10:2002;1441-1452.
44. Strohner R., Nemeth A., Jansa P., Hofmann-Rohrer U., Santoro R., Langst G., Grummt I. NoRC - a novel member of mammalian ISWI-containing chromatin remodeling machines. EMBO J. 20:2001;4892-4900.
45. Zhou Y., Santoro R., Grummt I. The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription. EMBO J. 21:2002;4632-4640.
46. Hilfiker A., Hilfiker-Kleiner D., Pannuti A., Lucchesi J.C. Mof, a putative acetyl transferase gene related to the Tip60 and MOZ human genes and to the SAS genes of yeast, is required for dosage compensation in Drosophila. EMBO J. 16:1997;2054-2060.
47. Park Y., Kuroda M.I. Epigenetic aspects of X-chromosome dosage compensation. Science. 293:2001;1083-1085.
48. Smith E.R., Allis C.D., Lucchesi J.C. Linking global histone acetylation to the transcription enhancement of X-chromosomal genes in Drosophila males. J. Biol. Chem. 276:2001;31483-31486.
49. Corona D.F., Clapier C.R., Becker P.B., Tamkun J.W. Modulation of ISWI function by site-specific histone acetylation. EMBO Rep. 3:2002;242-247.
50. Clapier C.R., Nightingale K.P., Becker P.B. A critical epitope for substrate recognition by the nucleosome remodeling ATPase ISWI. Nucleic Acids Res. 30:2002;649-655.
51. Hamiche A., Kang J.G., Dennis C., Xiao H., Wu C. Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF. Proc. Natl. Acad. Sci. U. S. A. 98:2001;14316-14321.
52. Yasui D., Miyano M., Cai S., Varga-Weisz P., Kohwi-Shigematsu T. SATB1 targets chromatin remodelling to regulate genes over long distances. Nature. 419:2002;641-645.
53. Hakimi M.A., Bochar D.A., Schmiesing J.A., Dong Y., Barak O.G., Speicher D.W., Yokomori K., Shiekhattar R. A chromatin remodelling complex that loads cohesin onto human chromosomes. Nature. 418:2002;994-998.
54. Campbell J.L., Cohen-Fix O. Chromosome cohesion: ring around the sisters? Trends Biochem. Sci. 27:2002;492-495.
55. MacCallum D.E., Losada A., Kobayashi R., Hirano T. ISWI remodeling complexes in Xenopus egg extracts: identification as major chromosomal components that are regulated by INCENP-aurora B. Mol. Biol. Cell. 13:2002;25-39.
56. Demeret C., Bocquet S., Lemaitre J.M., Francon P., Mechali M. Expression of ISWI and its binding to chromatin during the cell cycle and early development. J. Struct. Biol. 140:2002;57-66.
57. de la Serna I.L., Imbalzano A.N. Unfolding heterochromatin for replication. Nat. Genet. 32:2002;560-562.
58. Alexiadis V., Varga-Weisz P.D., Bonte E., Becker P.B., Gruss C. In vitro chromatin remodelling by chromatin accessibility complex (CHRAC) at the SV40 origin of DNA replication. EMBO J. 17:1998;3428-3438.
59. Collins N., Poot R.A., Kukimoto I., Garcia-Jimenez C., Dellaire G., Varga-Weisz P.D. An ACF1-ISWI chromatin-remodeling complex is required for DNA replication through heterochromatin. Nat. Genet. 32:2002;627-632.
60. Bozhenok L., Wade P.A., Varga-Weisz P. WSTF-ISWI chromatin remodeling complex targets heterochromatic replication foci. EMBO J. 21:2002;2231-2241.
61. Corona D.F., Eberharter A., Budde A., Deuring R., Ferrari S., Varga-Weisz P., Wilm M., Tamkun J., Becker P.B. Two histone fold proteins, CHRAC-14 and CHRAC-16, are developmentally regulated subunits of chromatin accessibility complex (CHRAC). EMBO J. 19:2000;3049-3059.
62. Poot R.A., Dellaire G., Hulsmann B.B., Grimaldi M.A., Corona D.F., Becker P.B., Bickmore W.A., Varga-Weisz P.D. HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. EMBO J. 19:2000;3377-3387.
63. Fuss J., Linn S. Human DNA polymerase epsilon colocalizes with proliferating cell nuclear antigen and DNA replication late, but not early, in S phase. J. Biol. Chem. 277:2002;8658-8666.
64. Wolffe A.P. Transcriptional regulation in the context of chromatin structure. Essays Biochem. 37:2001;45-57.
65. Caretti G., Motta M.C., Mantovani R. NF-Y associates with H3-H4 tetramers and octamers by multiple mechanisms. Mol. Cell. Biol. 19:1999;8591-8603.
66. Bolognese F., Imbriano C., Caretti G., Mantovani R. Cloning and characterization of the histone-fold proteins YBL1 and YCL1. Nucleic Acids Res. 28:2000;3830-3838.