Twenty-Five Years of the Nucleosome, Fundamental Particle of the Eukaryote Chromosome

Abstract

The chromatin field needs much more information about structure beyond the nucleosome. Even the trajectory of the DNA entering and exiting the nucleosome, immediately beyond the core particle, is unclear (reviewed by Prunell 1998xA topological approach to nucleosome structure and dynamics (the linking number paradox and other issues) . Prunell, A. Biophys. J. 1998; 74: 2531–2544Abstract | Full Text | Full Text PDF | PubMedSee all ReferencesPrunell 1998). The pattern of coiling a chain of nucleosomes in a thicker fiber remains uncertain (reviewed by Ramakrishnan 1997xHistone H1 and chromatin higher-order structure. Ramakrishnan, V. Crit. Rev. Eukaryot. Gene Expr. 1997; 7: 215–230Crossref | PubMedSee all ReferencesRamakrishnan 1997). Whereas additional coiling in a succession of higher helices would be a most plausible mechanism of further condensation, alternative hypotheses have been advanced. Many of the difficulties of analyzing chromatin problems stem from the variability inherent in higher order chromatin structures. Existing methods of structure determination require averaging and thus are of limited use in the face of variability.Solution of the higher order structure problem is crucial for understanding chromatin function. Histone tail modifications and interactions with other proteins, important for regulation, seem likely to influence higher order structure more than core particle structure. There is, however, insufficient evidence that acetylation actually causes chromatin unfolding, and only a suggestion of the interplay between acetylation and the chromatin remodeling events that affect core particle structure (14xOrdered recruitment of transcription and chromatin-remodeling factors to a cell cycle– and developmentally regulated promoter. Cosma, M.P, Tanaka, T, and Nasmyth, K. Cell. 1999; 97: 299–311Abstract | Full Text | Full Text PDF | PubMed | Scopus (545)See all References, 81xThe nucleosome remodeling complex, Snf/Swi, is required for the maintenance of transcription in vivo and is partially redundant with the histone acetyltransferase, gcn5. Sudarsanam, P, Cao, Y, Wu, L, Laurent, B.C, and Winston, F. EMBO J. 1999; 18: 3101–3106Crossref | PubMed | Scopus (86)See all References). Histone phosphorylation, long correlated with chromosome condensation, has recently been linked to transcriptional activity (reviewed by Bjorklund et al. 1999xGlobal transcription regulators of eukaryotes. Bjorklund, S, Almouzni, G, Davidson, I, Nightingale, K.P, and Weiss, K. Cell. 1999; 96: 759–767Abstract | Full Text | Full Text PDF | PubMedSee all ReferencesBjorklund et al. 1999). There is no information as to the structural or functional consequences of other modifications, such as ubiquitination and glycosylation. Histone H1 is thought to promote condensation, but an understanding of its structural role and the connection with gene activity is lacking. Elucidation of gene silencing by heterochromatin similarly depends on determination of its structure.Finally, functional analysis in cell-free systems must be extended beyond the nucleosome to the chromosomal context. Histone–DNA complexes assembled in vitro reveal effects of HAT and chromatin-remodeling complexes on transcription (56xRole of nucleosome remodeling factor NURF in transcriptional activation of chromatin. Mizuguchi, G, Tsukiyama, T, Wisniewski, J, and Wu, C. Mol. Cell. 1997; 1: 141–150Abstract | Full Text | Full Text PDF | PubMedSee all References, 49xRequirement of RSF and FACT for transcription of chromatin templates in vitro. LeRoy, G, Orphanides, G, Lane, W.S, and Reinberg, D. Science. 1998; 282: 1900–1904Crossref | PubMedSee all References, 88xTranscriptional activators direct histone acetyltransferase complexes to nucleosomes. Utley, R.T, Ikeda, K, Grant, P.A, Cote, J, Steger, D.J, Eberharter, A, John, S, and Workman, J.L. Nature. 1998; 394: 498–502Crossref | PubMed | Scopus (406)See all References), but in vivo, promoters are associated with additional, nonhistone proteins, which influence the locations of nucleosomes and undoubtedly the higher order configuration of chromatin as well. These associations extend, in the broadest sense, to such DNA elements as locus control regions, which regulate the structure and activity of entire chromosomal domains. Only when transcription, replication, recombination, and other DNA transactions have been reconstituted in vitro with naturally assembled chromatin templates will a full understanding of the nucleosome be achieved.*To whom correspondence should be addressed (e-mail: kornberg@ stanford.edu).