Skip to main content
SpringerLink
Log in

Nucleosome Assembly and Remodeling

  • Chapter
Protein Complexes that Modify Chromatin

Part of the book series: Current Topics in Microbiology and Immunology ((CT MICROBIOLOGY,volume 274))

Abstract

Packaging of the eukaryotic genome into chromatin functions not only to constrain the genome within the boundaries of the cell nucleus but also to permit dynamic and broad-ranging changes related to many important biological phenomena. Therefore, chromatin assembly is a process that affects DNA replication, repair, and gene expression. Chromatin structure is linked to transcriptional regulation, and recent studies show how chromatin is altered so as to facilitate transcription. In addition, modification of chromatin structure is an important regulatory mechanism. Here I review the mechanism of chromatin assembly in vitro and the changes of chromatin structure related to transcriptional activation.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Arany Z, Sellers WR, Livingston DM, Eckner R (1994) El Avassociated p300 and CREB-associated CBPbelong to a conserved family of coactivators. Cell 77:799–800

    Article  PubMed  CAS  Google Scholar 

  • Asaharal H, Tartare-Deckertl S, Nakagawa T, Ikehara T, Hirose F, Hunter T, Ito T, Montminy M (2002) Dual roles of p300 in chromatin assembly and transcriptional activation in cooperation with NAP-l in vitro. Mol Cell Biol (in press)

    Google Scholar 

  • Bannister AJ, Kouzarides T (1996) The CBP co-activator is a histone acetyltransferase. Nature 384:641–643

    Article  PubMed  CAS  Google Scholar 

  • Blank TA, Becker PB (1995) Electrostatic mechanism of nucleosome spacing. J Mol Biol 252:305–313

    Article  PubMed  CAS  Google Scholar 

  • Bortvin A, Winston F (1996) Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272:1473–1476

    Article  PubMed  CAS  Google Scholar 

  • Brownell JE, Zhou J, Ranalli T, Kobayashi R, Edmondson DG, Roth SY, Allis CD (1996) Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84:843–851

    Article  PubMed  CAS  Google Scholar 

  • Bulger M, Ito T, Kamakaka RT, Kadonaga JT (1995) Assembly of regularly spaced nucleosome arrays by Drosophila chromatin assembly factor 1 and a 56-kDa histonebinding protein. Proc Natl Acad Sci USA 92:11726–11730

    Article  PubMed  CAS  Google Scholar 

  • Chang L, Loranger SS, Mizzen C, Ernst SG, Allis CD, Annunziato AT (1997) Histones in transit: cytosolic histone complexes and diacetylation of H4 during nucleosome assembly in human cells. Biochemistry 36:469–480

    Article  PubMed  CAS  Google Scholar 

  • Cosma MP, Tanaka T, Nasmyth K (1999) Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle-and developmentally regulated promoter. Cell 97:299–311

    Article  PubMed  CAS  Google Scholar 

  • Eberharter A, Ferrari S, Langst G, Straub T, Imhof A, Varga-Weisz P, Wilm M, Becker PB (2001) Acfl, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. EMBO J 20:3781–3788

    Article  PubMed  CAS  Google Scholar 

  • Eickbush TH, Moudrianakis EN (1978) The histone core complex: an octamer assembled by two sets of protein-protein interactions. Biochemistry 17:4955–4964

    Article  PubMed  CAS  Google Scholar 

  • Elfring LK, Deuring R, Mccallum CM, Peterson CL, Tamkun JW (1994) Identification and characterization of Drosophila relatives of the yeast transcriptional activator SNF2/SWI2. Mol Cell BioI 14:2225–2234

    Article  CAS  Google Scholar 

  • Espinosa JM, Emerson BM (2001) Transcriptional regulation by p53 through intrinsic DNA/chromatin binding and site-directed cofactor recruitment. Mol Cell 8: 57–69

    Article  PubMed  CAS  Google Scholar 

  • Germond JE, Bellard M, Oudet P, Chambon P (1976) Stability of nucleosomes in native and reconstituted chromatins. Nucleic Acids Res 3:3173–3192

    PubMed  CAS  Google Scholar 

  • Glikin GC, Ruberti I, Worcel A (1984) Chromatin assembly in Xenopus oocytes: in vitro studies. Cell 37:33–41

    Article  PubMed  CAS  Google Scholar 

  • Godfreyj JE, Eickbush TH, Moudrianakis EN (1980) Reversible association of calf thymus histones to form the symmetrical octamer (H2AH2BH3H4)2: a case of a mixed-associating system. Biochemistry 19:1339–1346

    Article  Google Scholar 

  • Hassan AH, Neely KE, Workman JL (2001) Histone acetyltransferase complexes stabilize SWIISNF binding to promoter nucleosomes. Cell 104:817–827

    Article  PubMed  CAS  Google Scholar 

  • Hewish DR, Burgoyne LA (1973) Chromatin sub-structure: the digestion of chromatin DNA at regularly spaced sites by a nuclear deoxyribonuclease. Biochem Biophys Res Commun 52:504–510

    Article  PubMed  CAS  Google Scholar 

  • Ikeda K, Steger DJ, Eberharter A, Workman JL (1999) Activation domain-specific and general transcription stimulation by native histone acetyltransferase complexes. Mol Cell BioI 19:855–863

    CAS  Google Scholar 

  • Ishimi Y, Hirosumi I, Sato W, Sugasawa K, Yokota S, Hanaoka F, Yamada M (1984) Purification and initial characterization of a protein which facilitates assembly of nucleosome-like structure from mammalian cells. EurJ Biochem 142:431–439

    Article  CAS  Google Scholar 

  • Ito T, Bulger M, Kobayashi R, Kadonaga JT (1996a) Drosophila NAP-l is a core histone chaperone that functions in ATP-facilitated assembly of regularly spaced nucleosomal arrays. Mol Cell Biol 16:3112–3124

    PubMed  CAS  Google Scholar 

  • Ito T, Tyler JK, Bulger M, Kobayashi R, Kadonaga JT (1996b) ATP-facilitated chromatin assembly with a nucleoplasmin-like protein from Drosophila melanogaster. J BioI Chern 271:25041–25048

    Article  CAS  Google Scholar 

  • Ito T, Bulger M, Pazin MJ, Kobayashi R, Kadonaga JT (1997) ACF, an ISWI-containing and ATP-utilizing chromatin assembly and remodeling factor. Cell 90:145–155

    Article  PubMed  CAS  Google Scholar 

  • Ito T, Levenstein ME, Fyodorov DV, Kutach AK, Kobayashi R, Kadonaga JT (1999) ACFconsists of two subunits, Acfl and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev 13:1529–1539

    Article  PubMed  CAS  Google Scholar 

  • Ito T, Ikehara T, Nakagawa T, Kraus WL, Muramatsu M (2000) p300-mediated acetylation facilitates the transfer of histone H2A-H2Bdimers from nucleosomes to a histone chaperone. Genes Dev 14:1899–1907

    PubMed  CAS  Google Scholar 

  • Jackson V (1990) In vivo studies on the dynamics of histone-DNA interaction: evidence for nucleosome dissolution during replication and transcription and a low level of dissolution independent of both. Biochemistry 29:719–731

    Article  PubMed  CAS  Google Scholar 

  • Kadonaga JT (1998) Eukaryotic transcription: an interlaced network of transcription factors and chromatin-modifying machines. Cell 92:307–313

    Article  PubMed  CAS  Google Scholar 

  • Kamakaka RT, Bulger M, Kaufman PD, Stillman B, Kadonaga JT (1996) Postreplicative chromatin assembly by Drosophila and human chromatin assembly factor 1. Mol Cell BioI 16:810–817

    CAS  Google Scholar 

  • Kingston RE, Narlikar GJ (1999) ATP-dependent remodeling and acetylation as regulators of chromatin fluidity. Genes Dev 13:2339–2352

    Article  PubMed  CAS  Google Scholar 

  • Kingston RE, Bunker CA, Imbalzano AN (1996) Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev 10:905–920

    Article  PubMed  CAS  Google Scholar 

  • Kleinschmidt JA, Franke WW (1982) Soluble acidic complexes containing histones H3 and H4 in nuclei of Xenopus laevis oocytes. Cell 29:799–809

    Article  PubMed  CAS  Google Scholar 

  • Kleinschmidt JA, Dingwall C, Maier G, Franke WW (1986) Molecular characterization of a karyophilic, histone-binding protein: eDNA cloning, amino acid sequence and expression of nuclear protein Nl/N2 of Xenopus laevis. EMBO J 5:3547–3552

    PubMed  CAS  Google Scholar 

  • Kleinschmidt JA, Seiter A, Zentgraf H (1990) Nucleosome assembly in vitro: separate histone transfer and synergistic interaction of native histone complexes purified from nuclei of Xenopus laevi s oocytes. EMBOJ 9:1309–1318

    CAS  Google Scholar 

  • Kornberg RD (1974) Chromatin structure: a repeating unit of histones and DNA. Science 184:868–871

    Article  PubMed  CAS  Google Scholar 

  • Kornberg RD, Thomas JO (1974) Chromatin structure: oligomers of the histones. Science 184:865–868

    Article  PubMed  CAS  Google Scholar 

  • Kraus WL, Manning ET, Kadonaga JT (1999) Biochemical analysis of distinct activation functions in p300 that enhance transcription initiation with chromatin templates. Mol Cell BioI 19:8123–8135

    CAS  Google Scholar 

  • Krebs IE, Kuo MH, Allis CD, Peterson CL (1999) Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. Genes Dev 13:1412–1421

    Article  PubMed  CAS  Google Scholar 

  • Kundu TK, Palhan VB, Wang Z, An W, Cole PA, Roeder RG (2000) Activator-dependent transcription from chromatin in vitro involving targeted histone acetylation by p300. Mol Cell 6:551–561

    Article  PubMed  CAS  Google Scholar 

  • Laskey RA, Honda BM, Mills AD, Finch JT (1978) Nucleosomes are assembled by an acidic protein which binds histones and transfers them to DNA. Nature 275: 416–420

    Article  PubMed  CAS  Google Scholar 

  • Leroy G, Orphanides G, Lane WS, Reinberg D (1998) Requirement of RSF and FACT for transcription of chromatin templates in vitro. Science 282:1900–1904

    Article  PubMed  CAS  Google Scholar 

  • Leroy G, Loyola A, Lane WS, Reinberg D (2000) Purification and characterization of a human factor that assembles and remodels chromatin. J Biol Chern 275:14787–14790

    Article  CAS  Google Scholar 

  • Leuba SH, Yang G, Robert C, Samori B, Van Holde K, Zlatanova J, Bustamante C (1994) Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. Proc Natl Acad Sci USA 91:11621–11625

    Article  PubMed  CAS  Google Scholar 

  • Lorch Y, Cairns BR, Zhang M, Kornberg RD (1998) Activated RSC-nucleosome complex and persistently altered form of the nucleosome. Cell 94:29–34

    Article  PubMed  CAS  Google Scholar 

  • Lorch Y, Zhang M, Kornberg RD (1999) Histone octamer transfer by a chromatinremodeling complex. Cell 96:389–392

    Article  PubMed  CAS  Google Scholar 

  • Loyola A, Leroy G, Wang YH, Reinberg D (2001) Reconstitution of recombinant chromatin establishes a requirement for histone-tail modifications during chromatin assembly and transcription. Genes Dev 15:2837–2851

    PubMed  CAS  Google Scholar 

  • Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 28 A resolution. Nature 389:251–260

    Article  PubMed  CAS  Google Scholar 

  • Manning ET, Ikehara T, Ito T, Kadonaga JT, Kraus WL (2001) p300 Forms a stable, template-committed complex with chromatin: role for the bromodomain. Mol Cell Biol 21:3876–3887

    Article  PubMed  CAS  Google Scholar 

  • Mcquibban GA, Commisso-Cappelli CN, Lewis PN (1998) Assembly, remodeling, and histone binding capabilities of yeast nucleosome assembly protein 1. J Biol Chern 273:6582–6590

    Article  CAS  Google Scholar 

  • Nakagawa T, Bulger M, Muramatsu M, Ito T (2001) Multistep chromatin assembly on supercoiled plasmid DNAby nucleosome assembly protein-l and ATP-utilizing chromatin assembly and remodeling factor. J Biol Chern 276:27384–27391

    Article  CAS  Google Scholar 

  • Nelson T, Wiegand R, Brutlag D (1981) Ribonucleic acid and other polyanions facilitate chromatin assembly in vitro. Biochemistry 20:2594–2601

    Article  PubMed  CAS  Google Scholar 

  • Noll M (1974) Internal structure of the chromatin subunit. Nucleic Acids Res 1:1573–1578

    Article  PubMed  CAS  Google Scholar 

  • Noll M, Kornberg RD (1977) Action of micrococcal nuclease on chromatin and the location of histone HI. J Mol BioI 109:393–404

    Article  CAS  Google Scholar 

  • Ogryzko VV, Schiltz RL, Russanova V, Howard BH, Nakatani Y (1996) The transcriptional coactivators p300 and CBP are histone acetyltransferases. Cell 87:953–959

    Article  PubMed  CAS  Google Scholar 

  • Olins AL, Olins DE (1974) Spheroid chromatin units (v bodies). Science 183:330–332

    Article  PubMed  CAS  Google Scholar 

  • Owen-Hughes T, Workman JL (1996) Remodeling the chromatin structure of a nucleosome array by transcription factor-targeted trans-displacement of histones. EMBO J 15:4702–4712

    PubMed  CAS  Google Scholar 

  • Pfaffle P, Jackson V (1990) Studies on rates of nucleosome formation with DNA under stress. J Biol Chern 265:16821–16829

    CAS  Google Scholar 

  • Richmond TJ, Finch JT, Rushton B, Rhodes D, Klug A (1984) Structure of the nucleosome core particle at 7 A resolution. Nature 311:532–537

    Article  PubMed  CAS  Google Scholar 

  • Sahasrabuddhe CG, Van Holde KE (1974) The effect of trypsin on nuclease-resistant chromatin fragments. J BioI Chern 249:152–156

    CAS  Google Scholar 

  • Schnitzler G, Sif S, Kingston RE (1998) Human SWIISNF interconverts a nucleosome between its base state and a stable remodeled state. Cell 94:17–27

    Article  PubMed  CAS  Google Scholar 

  • Seo SB, McNamara P, Heo S, Turner A, Lane WS, Chakravarti D (2001) Regulation of histone acetylation and transcription by INHAT, a human cellular complex containing the set oncoprotein. Cell 104:119–130

    Article  PubMed  CAS  Google Scholar 

  • Shikama N, Chan HM, Krstic-Demonacos M, Smith L, Lee CW, Cairns W, La Thangue NB (2000) Functional interaction between nucleosome assembly proteins and p300/CREB-binding protein family coactivators. Mol Cell BioI 20:8933–8943

    Article  CAS  Google Scholar 

  • Simpson RT (1978) Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNAand all the histones. Biochemistry 17:5524–5531

    Article  PubMed  CAS  Google Scholar 

  • Smith S, Stillman B (1989) Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro. Cell 58:15–25

    Article  PubMed  CAS  Google Scholar 

  • Stein A, Whitlock Jr JP, Bina M (1979) Acidic polypeptides can assemble both histones and chromatin in vitro at physiological ionic strength. Proc Natl Acad Sci USA 76:5000–5004

    Article  PubMed  CAS  Google Scholar 

  • Stillman B (1986) Chromatin assembly during SV40 DNA replication in vitro. Cell 45:555–565

    Article  PubMed  CAS  Google Scholar 

  • Stillman BW, Gluzman Y (1985) Replication and supercoiling of simian virus 40 DNAin cell extracts from human cells. Mol Cell Biol 5:2051–2060

    PubMed  CAS  Google Scholar 

  • Tsukiyama T, Wu C (1995) Purification and properties of an ATP-dependent nucleosome remodeling factor. Cell 83:1011–1020

    Article  PubMed  CAS  Google Scholar 

  • Tsukiyama T, Wu C (1997) Chromatin remodeling and transcription. Curr Opin Genet Dev 7:182–191

    Article  PubMed  CAS  Google Scholar 

  • Tsukiyama T, Palmer J, Landel CC, Shiloach J, Wu C (1999) Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev 13:686–697

    Article  PubMed  CAS  Google Scholar 

  • Tyler JK, Adams CR, Chen SR, Kobayashi R, Kamakaka RT, Kadonaga JT (1999) The RCAF complex mediates chromatin assembly during DNA replication and repair. Nature 402:555–560

    Article  PubMed  CAS  Google Scholar 

  • Ura K, Araki M, Saeki H, Masutani C, Ito T, Iwai S, Mizukoshi T, Kaneda Y, Hanaoka F (2001) ATP-dependent chromatin remodeling facilitates nucleotide excision repair of UV-induced DNA lesions in synthetic dinucleosomes. EMBO J 20:2004–2014

    Article  PubMed  CAS  Google Scholar 

  • Utley RT, Ikeda K, Grant PA, Cote J, Steger DJ, Eberharter A, John S, Workman JL (1998) Transcriptional activators direct histone acetyltransferase complexes to nucleosomes. Nature 394:498–502

    Article  PubMed  CAS  Google Scholar 

  • Van Holde KE, Sahasrabuddhe CG, Shaw BR (1974) A model for particulate structure in chromatin. Nucleic Acids Res 1:1579–1586

    Article  PubMed  Google Scholar 

  • Van Holde KE, Lohr DE, Robert C (1992) What happens to nucleosomes during transcription? J BioI Chern 267:2837–2840

    Google Scholar 

  • Varga-Weisz PD, Becker PB (1998) Chromatin-remodeling factors: machines that regulate? Curr Opin Cell BioI 10:346–353

    Article  CAS  Google Scholar 

  • Varga-Weisz PD, Wilm M, Bonte E, Dumas K, Mann M, Becker PB (1997) Chromatin-remodelling factor CHRAC contains the ATPases ISWI and topoisomerase II. Nature 388:598–602

    Article  PubMed  CAS  Google Scholar 

  • Varshavsky AJ, Bakayev VV, Georgiev GP (1976) Heterogeneity of chromatin subunits in vitro and location of histone HI. Nucleic Acids Res 3:477–492

    PubMed  CAS  Google Scholar 

  • Verreault A, Kaufman PD, Kobayashi R, Stillman B (1996) Nucleosome assembly by a complex of CAF-l and acetylated histones H3/H4. Cell 87:95–104

    Article  PubMed  CAS  Google Scholar 

  • Walter PP, Owen-Hughes TA, Cote J, Workman JL (1995) Stimulation of transcription factor binding and histone displacement by nucleosome assembly protein 1 and nucleoplasmin requires disruption of the histone octamer. Mol Cell Biol 15:6178–6187

    PubMed  CAS  Google Scholar 

  • Whitehouse I, Flaus A, Cairns BR, White MF, Workman JL, Owen-Hughes T (1999) Nucleosome mobilization catalysed by the yeast SWIISNF complex. Nature 400:784–787

    Article  PubMed  CAS  Google Scholar 

  • Woodcock CL, Safer JP, Stanchfield JE (1976) Structural repeating units in chromatin I: evidence for their general occurrence. Exp Cell Res 97:101–110

    Article  PubMed  CAS  Google Scholar 

  • Worcel A, Han S, Wong ML (1978) Assembly of newly replicated chromatin. Cell 15: 969–977

    Article  PubMed  CAS  Google Scholar 

  • Yang XJ, Ogryzko VV, Nishikawa J, Howard BH, Nakatani Y (1996) A p300/CBPassociated factor that competes with the adenoviral oncoprotein EIA. Nature 382: 319–324

    Article  PubMed  CAS  Google Scholar 

  • Zhang Q, Vo N, Goodman RH (2000) Histone binding protein RbAp48 interacts with a complex of CREB binding protein and phosphorylated CREB. Mol Cell Biol 20: 4970–4978

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan

    T. Ito

Authors
  1. T. Ito
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Howard Hughes Medical Institute Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 306 Althouse Lab, University Park, PA, 16802, USA

    J. L. Workman Ph. D

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Ito, T. (2003). Nucleosome Assembly and Remodeling. In: Workman, J.L. (eds) Protein Complexes that Modify Chromatin. Current Topics in Microbiology and Immunology, vol 274. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-55747-7_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-55747-7_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-62909-9

  • Online ISBN: 978-3-642-55747-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation