Promoter targeting and chromatin remodeling by the SWI/SNF complex

Current Opinion in Genetics and Development

Volumn 10, Issue 2, 2000, Pages 187-192

  Peterson, Craig L ^a   Workman, Jerry L ^b  

^a UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE;

CHROMATIN STRUCTURE; ENZYME SUBUNIT; FERMENTATION; HUMAN; MATING TYPE; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; TRANSCRIPTION REGULATION;

EID: 0034026193     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(00)00068-X     Document Type: Review

References (47)

1. Cairns B.R., Ki Y-J., Sayes M.H., Laurent B.C., Kornberg R.D. A multisubunit complex containing the SWI1/ADR6, SWI2/SNF2, SWI3, SNF5, and SNF6 gene products isolated from yeast. Proc Natl Acad Sci USA. 91:1994;1950-1954.
2. Côté J., Quinn J., Workman J.L., Peterson C.L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF protein complex. Science. 265:1994;53-60.
3. Winston F., Carlson M. Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet. 8:1992;387-391.
4. Kingston R.E., Narlikar G.J. ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev. 13:1999;2252-2339.
5. Kwon H., Imbalzano A.N., Khavari P.A., Kingston R.E., Green M.R. Nucleosome disruption and enhancement of activator binding by a human SWI/SNF complex. Nature. 370:1994;477-481.
6. Muchardt C., Yaniv M.J. ATP-dependent chromatin remodelling: SWI/SNF and Co. are on the job. J Mol Biol. 293:1999;187-198.
7. Cairns B.R., Lorch Y., Li Y., Zhang M., Lacomis L., Erdjument-Bromage H., Tempst P., Du J., Laurent B., Kornberg R.D. RSC, an essential, abundant chromatin-remodeling complex. Cell. 87:1996;1249-1260.
8. Logie C., Tse C., Hansen J., Peterson C.L. The core histone N-terminal domains are required for multiple rounds of catalytic chromatin remodeling by the SWI/SNF and RSC complexes. Biochemistry. 38:1999;2514-2522. A direct comparison of SWI/SNF and RSC ATPase and remodeling activities. The histone amino-terminal domains are found to control the inter-array transfer of SWI/SNF and RSC remodeling activities. This was the first demonstration of a role for the histone amino-terminal tails in modulating the remodeling activity of SWI/SNF or RSC.
9. Quinn J., Fryberg A.M., Ganster R.W., Schmidt M.C., Peterson C.L. DNA-binding properties of the yeast SWI/SNF complex. Nature. 379:1996;844-847.
10. Côté J., Peterson C.L., Workman J.L. Perturbation of nucleosome core structure by the SWI/SNF complex persists following its detachment, enhancing subsequent transcription factor binding. Proc Natl Acad Sci USA. 95:1998;4947-4952. The SWI/SNF-remodeled conformation on mononucleosomes was shown to persist after detachment of the SWI/SNF complex and remained accessible to transcription factor binding.
11. Lorch Y., Cairns B.R., Zhang M., Kornberg R.D. Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell. 94:1998;29-34.
12. Morozov A., Yung E., Kalpana G.V. Structure-function analysis of integrase interactor 1/hSNF5L1 reveals differential properties of two repeat motifs present in the highly conserved region. Proc Natl Acad Sci USA. 95:1998;1120-1125.
13. Wang W., Chi T., Xue Y., Zhou S., Kuo A., Crabtree G.R. Architectural DNA binding by a high-mobility-group/kinesin-like subunit in mammalian SWI/SNF-related complexes. Proc Natl Acad Sci USA. 95:1998;492-498.
14. Bazett-Jones D.P., Côté J., Landel C.C., Peterson C.L., Workman J.L. 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. Electron spectroscopic imaging measurement of the protein to DNA mass ratio in SWI/SNF disrupted nucleosomes reveals ~20% reduction in DNA mass relative to histone mass in these particles. This report provided the first visualization of SWI/SNF and its interactions with DNA and nucleosomal arrays. The results also indicate that remodeling leads to loss of DNA, but not histones from nucleosomes.
15. Schnitzler G., Sif S., Kingston R.E. Human SWI/SNF interconverts a nucleosome between its base state and a stable remodeled state. Cell. 94:1998;17-27. The human SWI/SNF complex is shown to catalyze the interconversion of nucleosomes from the standard conformation and the remodeled conformation. Fractionation of the remodeled nucleosomes reveals a particle with the molecular weight of a di-nucleosome with an increased affinity for transcription factors.
16. Imbalzano A.N., Schnitzler G.R., Kingston R.E. Nucleosome disruption by human SWI/SNF is maintained in the absence of continued ATP hydrolysis. J Biol Chem. 271:1996;20726-20733.
17. Logie C., Peterson C.L. Catalytic nucleosome remodeling by the yeast SWI/SNF complex on nucleosome arrays. EMBO J. 16:1997;6772-6782.
18. Owen-Hughes T.A., Utley R.T., Côté J., Peterson C.L., Workman J.L. Persistent site-specific remodeling of a nucleosome array by transient action of the SWI/SNF complex. Science. 273:1996;513-516.
19. Gavin I.M., Simpson R.T. Interplay of yeast global transcriptional regulators Ssn6p-Tup1p and Swi-Snf and their effect on chromatin structure. EMBO J. 16:1997;6263-6271.
20. Gregory P.D., Schmid A., Zavari M., Munsterkotter M., Horz W. Chromatin remodelling at the PHO8 promoter requires SWI-SNF and SAGA at a step subsequent to activator binding. EMBO J. 18:1999;6407-6414.
21. Wu L., Winston F. Evidence that Snf-Swi controls chromatin structure over both the TATA and UAS regions of the SUC2 promoter in Saccharomyces cerevisiae. Nucleic Acids Res. 25:1997;4230-4234.
22. Lorch Y., Zhang M., Kornberg R.D. Histone octamer transfer by a chromatin-remodeling complex. Cell. 96:1999;389-392. The RSC complex catalyzes the transfer of histone octamers from donor chromatin onto acceptor naked DNA illustrating a function of RSC in trans-displacement of histone octamers from chromatin.
23. 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.
24. 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.
25. Whitehouse I., Flaus A., Cairns B.R., White M.F., Workman J.L., Owen-Hughes T. Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature. 400:1999;784-787. The SWI/SNF complex is shown to catalyze the movement of histone octamers along DNA in cis. This movement is stopped by a block along the DNA path, indicating that sliding occurred by a spooling or twisting mechanism.
26. 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.
27. Cho H.G., Orphanides X., Sun X.J., Yang V., Ogryzko E., Lees Y., Nakatani Y., Reinberg D. A human RNA polymerase II complex containing factors that modify chromatin structure. Mol Cell Biol. 18:1998;5355-5363.
28. Neish A.S., Anderson S.F., Schlegel B.P., Wei W., Parvin J.D. Factors associated with the mammalian RNA polymerase II holoenzyme. Nucleic Acids Res. 26:1998;847-853.
29. Wilson C.J., Chao D.M., Imbalzano A.N., Schnitzler G.R., Kingston R.E., Young R.A. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodelling. Cell. 84:1996;235-244.
30. Myers L.C., Gustafsson C.M., Bushnell D.A., Lui M., Erdjument-Bromage H., Tempst P., Kornberg R.D. The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. Genes Dev. 12:1998;45-54.
31. Natarajan K., Jackson B.M., Zhou H., Winston F., Hinnebusch A.G. Transcriptional activation by Gcn4p involves independent interactions with SWI/SNF complex and SRB/Mediator. Mol Cell. 4:1999;657-664. The SWI/SNF complex is shown to play a role in GCN4-mediated transcription activation in vivo. GCN4 is shown to recruit SWI/SNF independently from the RNA polymerase II mediator complex in vitro.
32. Yudkovky N., Logie C., Hahn S., Peterson C.L. Recruitment of the SWI/SNF chromatin remodeling complex by transcriptional activators. Genes Dev. 13:1999;2369-2374. An immoblized template assay is used to demonstrate that SWI/SNF can be recruited to promoters by a DNA-bound activation domain. Recruitment is independent of an intact RNA PolII holoenzyme. Acidic activators are also shown to recruit SWI/SNF remodeling activity to nucleosomal arrays in a purified system.
33. Yoshinaga S.K., Peterson C.L., Herskowitz I., Yamamoto K. Roles of SWI1, SWI2, and SWI3 proteins for transcriptional enhancement by steroid receptors. Science. 258:1992;1598-1604.
34. Ostlund Farrants A.K., Blomquist P., Kwon H., Wrange O. Glucocorticoid receptor-glucocorticoid response element binding stimulates nucleosome disruption by the SWI/SNF complex. Mol Cell Biol. 17:1997;895-905.
35. Neely K.E., Hassan A.H., Wallberg A.E., Steger D.J., Cairns B.R., Wright A.P.H., 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. The SWI/SNF complex is shown to stimulate transcription from nucleosomal arrays in an activation domain dependent manner. SWI/SNF is shown to interact directly with acidic activation domains of transcription activators, GCN4, SWI5, VP16.
36. Cosma M.P., Tanaka T., Nasmyth K. Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle-and developmentally regulated promoter. Cell. 97:1999;299-311. Recruitment of SWI/SNF to the HO locus is shown to require the SWI5 activator. SWI/SNF was then required for recruitment of the ADA2 subunit of SAGA. SWI/SNF and SAGA were required for subsequent recruitment of the SBF activator.
37. 1 by a GCN5-dependent acetyltransferase. Acetylation preceeded and was independent of HO transcription. Recruitment of acetyltransferase activity required the SWI5 activator and SWI/SNF. Inactivation of the SIN3/RPD3 deacetylase led to acetylation of the entire HO locus throughout the cell cycle.
38. Dimova D., Zeena N., Furgeson S., Eguchi S., Osley M.A. A role for transcriptional repressors in targeting the yeast Swi/Snf complex. Mol Cell. 4:1999;75-83. Swi/Snf is required for expression of the yeast histone HTA1-HTB1 locus to counteract the Hir1p and Hir2p corepressors. However, the corepressors appear to play a role in the recruitment of SWI/SNF to the locus.
39. Fryer C.J., Archer T.K. Chromatin remodelling by the glucocorticoid receptor requires the BRG1 complex. Nature. 393:1998;88-91.
40. Kowenz-Leutz E., Leutz A. A C/EBP isoform recruits the SWI/SNF complex to activate myeloid genes. Mol Cell. 4:1999;735-743.
41. Lee C.H., Murphy M.R., Lee J.S., Chung J.H. Targeting a SWI/SNF related chromatin remodeling complex to the beta-globin promoter in erythroid cells. Proc Natl Acad Sci USA. 96:1999;12311-12315. A novel assay called PIN*POINT is used to map the interactions of a human SWI/SNF complex with the β-globin promoter region in vivo. The results indicate that recruitment of human SWI/SNF requires both the β-globin LCR and EKLF transcription factor binding site.
42. Utley R.T., Côté J., Owen-Hughes T., Workman J.L. SWI/SNF stimulates the formation of disparate activator-nucleosome complexes but is partially redundant with cooperative binding. J Biol Chem. 272:1997;12642-12649.
43. Burns L., Peterson C.L. Yeast SWI/SNF complex facilitates the binding of a transcriptional activator to nucleosomal sites in vivo. Mol Cell Biol. 17:1997;4811-4819.
44. Phelan M.L., Sif S., Narlikar G.J., Kingston R.E. Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits. Mol Cell. 3:1999;247-253.
45. Lee K.M., Sif S., Kingston R.E., Hayes J.J. hSWI/SNF disrupts interactions between the H2A N-terminal tail and nucleosomal DNA. Biochemistry. 38:1999;8423-8429. Human SWI/SNF is shown to disrupt histone-DNA interactions for a nucleosome containing an H2A amino-terminal tail crosslinked to nucleosomal DNA. This result indicates that nucleosome disruption can occur in the absence of histone octamer mobilization.
46. Jaskelioff M., Gavin I., Peterson C.L., Logie C. SWI/SNF-mediated nucleosome remodeling: role of histone octamer mobility in the persistence of the remodeled state. Mol Cell Biol. 2000;. in press.
47. Boyer L.A., Shao X., Ebright R.H., Peterson C.L. Roles of the histone H2A/H2B dimers and (H3/H4)2 tetramer in nucleosome remodeling by SWI/SNF complex. J Biol Chem. 2000;. in press.