- Open Access
Histone variants: are they functionally heterogeneous?
© BioMed Central Ltd 2001
- Published: 5 July 2001
In most eukaryotes, histones, which are the major structural components of chromatin, are expressed as a family of sequence variants encoded by multiple genes. Because different histone variants can contribute to a distinct or unique nucleosomal architecture, this heterogeneity can be exploited to regulate a wide range of nuclear functions, and evidence is accumulating that histone variants do indeed have distinct functions.
- Core Histone
- Nucleosome Position
- Histone Variant
- Functional Heterogeneity
- Somatic Variant
The basic subunit of eukaryotic chromatin is the nucleosome [1,2]. Two molecules of each of the core histone proteins - H2A, H2B, H3 and H4 - form an octamer, the protein component of the nucleosome core particle, around which 147 basepairs of DNA are wrapped. One histone molecule of the linker or H1 class binds to the octamer near the point where the DNA enters and exits the nucleosome and seals two full turns (approximately 166 basepairs) of DNA around the octamer . Histone H1 also associates with linker DNA between nucleosomes to stabilize higher-order structures. As nucleosomal structure is similar in all metazoans, it is not surprising that histones are among the most highly conserved proteins in terms of both structure and sequence. But in higher organisms each histone subtype, with the possible exception of histone H4, is represented by a family of genes encoding multiple non-allelic primary-sequence variants [1,2,3,4,5]. Why should this be the case?
There are several plausible explanations for the existence of multiple histone-encoding genes [4,5,6]. The first is simply gene dosage. A demand for high gene expression at specific times might require multiple active transcriptional units - for example, in the case of histones large amounts are needed during S phase when DNA is replicated and packaged into nucleosomes. In this case, heterogeneity at the protein-sequence level may be the result of genetic drift and would be of little consequence. An extension of this view might include heterogeneity at the level of regulation: multiple histone genes with distinct expression patterns during differentiation, in specific tissues, or under certain metabolic conditions might be necessary to ensure that adequate amounts of each histone are present in all cells. Evidence for this in higher organisms comes from the presence of replacement variants that, unlike most other histones, are expressed throughout the cell cycle and serve as a source of chromatin components needed during repair or recombination of DNA or to replace histones lost through turnover in quiescent cells. Protein sequence variation would be expected to be limited, but variants with greater stability might be evolutionarily selected. Finally, distinct histone variants might have evolved to confer structural heterogeneity on chromatin. Different histone variants can contribute to distinct or unique nucleosomal architectures, which could potentially be exploited to regulate nuclear functions such as transcription, gene silencing, replication or recombination. In this case, the amino-acid sequence variation among the individual variants within a subtype is presumed to be the driving force for creating and maintaining diversity. I refer to this as 'functional heterogeneity', with the reservation that the extent and mechanisms by which it achieves functional effects are far from clear. Of course, aspects of each of these driving forces may be in operation simultaneously, and experimental demonstration, especially in the case of functional heterogeneity, is difficult.
Core histone variants with potential unique functions
major isotype (%)
64 (in histone
Unclear; altered higher-
CENP-A, a highly conserved histone H3-like variant, is specifically localized to centromeric chromatin in mammals and yeast . The carboxy-terminal two thirds of the CENP-A protein is 62% identical in sequence to histone H3, contains the histone-fold domain, and is required for localizing the protein to centromeric heterochromatin. The amino-terminal 47 amino acids are not related to histone H3. CENP-A synthesis is coordinated with centromeric replication during the mid-S to early G2 phases of the cell cycle. This appears to be important, because expression of CENP-A under control of a histone H3 promoter, which is active early in G1 phase, does not result in centromeric localization of CENP-A . Targeted deletion of the mouse CENP-A homolog results in early embryonic death and disruption of centromeric chromosome organization . The incorporation of this variant in place of histone H3 may serve to episomally mark centromeres for kinetochore assembly, which is required for coordinated separation of sister chromosomes during mitosis.
Histone macroH2A is an extremely divergent variant consisting of an amino-terminal region that has 64% identical amino acids to full-length histone H2A, followed by a large region (57% of the total protein) that is not related to any known histone . The nonhistone region contains a putative leucine-zipper domain and also has similarity to proteins involved in viral RNA replication. Immunofluorescence studies showed that macroH2A is concentrated in the inactive X chromosome of female mammals and remains associated with this chromosome through metaphase . This localization may be mediated through interactions of macroH2A with Xist, a non-coding RNA that is tightly associated with the inactive X chromosome. MacroH2A associates with the inactive X chromosome at or near the time of its inactivation in preimplantation mouse embryos, but in differentiating mouse embryonic stem cells the association occurs well after initiation and propagation of inactivation . Also, conditional deletion of part of the Xist locus from the inactive X chromosome leads to loss of macroH2A association but does not affect maintenance of X inactivation . Thus, the precise role of macroH2A in X inactivation is unclear.
MacroH2A is found at other chromosomal locations as well as the inactive X chromosome, and it may play a more general role in gene silencing. The strong evolutionary conservation of macroH2A among species, including chickens, which do not display X-chromosome inactivation, supports the idea of a conserved function related to the regulation of gene expression . Interestingly, a novel H2A variant has been recently identified and shown to have characteristics distinctly different from those of macroH2A : H2A-Bbd, which is only 42% identical to histone H2A, is markedly excluded from the inactive X chromosome and may be associated with transcriptionally active regions of the genome.
H2A.Z, a minor H2A variant, is found in a wide range of organisms from yeast to mammals . The sequences of H2A.Z variants of different species are more similar to one another than any single H2A.Z is to the major histone H2A in the same organism. This conservation may reflect a unique functional role, an idea that is supported by the demonstration that H2A.Z is essential for viability in both Tetrahymena  and Drosophila . Swapping experiments, in which regions of H2A.Z were replaced with homologous regions from the major histone H2A, identified a distinct domain of H2A.Z required for the rescue of the developmental defect observed in H2A.Z-null flies . This study is particularly relevant as it provides the strongest direct evidence of functional heterogeneity to date. The essential region mapped to a domain important for docking the H2A/H2B dimer to the H3/H4 tetramer to form the histone octamer, and the crystal structure of core particles containing H2A.Z revealed subtle but significant differences from that of particles containing the major H2A proteins . Recent results indicate that H2A.Z can modulate the folding of nucleosomal arrays into higher-order structures and that knockout of the H2A.Z genes in mice results in embryonic death just after implantation (D. Tremethick, personal communication).
I thank Donald Sittman, Susan Wellman, and Asmita Kumar for critical reading of the manuscript and Art Skoultchi and David Tremethick for communicating experimental results prior to publication.
- van Holde KE: Chromatin. New York: Springer,. 1989View ArticleGoogle Scholar
- Wolffe A: Chromatin: structure and function. San Diego: Academic Press,. 1998Google Scholar
- Thomas JO: Histone H1: location and role. Curr Opin Cell Biol. 1999, 11: 312-317. 10.1016/S0955-0674(99)80042-8.View ArticleGoogle Scholar
- Cole RD: Microheterogeneity in H1 histones and its consequences. Int J Pept Protein Res. 1987, 30: 433-449.View ArticleGoogle Scholar
- Wang ZF, Sirotkin AM, Buchold GM, Skoultchi AI, Marzluff WF: The mouse histone H1 genes: gene organization and differential regulation. J Mol Biol. 1997, 271: 124-138. 10.1006/jmbi.1997.1166.View ArticleGoogle Scholar
- Jackson JD, Gorovsky MA: Histone H2A.Z has a conserved function that is distinct from that of the major H2A sequence variants. Nucleic Acids Res. 2000, 28: 3811-3816. 10.1093/nar/28.19.3811.View ArticleGoogle Scholar
- Choo KHA: Centromerization. Trends Cell Biol. 2000, 10: 182-188. 10.1016/S0962-8924(00)01739-6.View ArticleGoogle Scholar
- Shelby RD, Vafa O, Sullivan KF: Assembly of CENP-A into centromeric chromatin requires a cooperative array of nucleosomal DNA contact sites. J Cell Biol. 1997, 136: 501-513. 10.1083/jcb.136.3.501.View ArticleGoogle Scholar
- Howman EV, Fowler KJ, Newsom AJ, Redward S, MacDonald AC, Kalitsis P, Choo KHA: Early disruption of centromeric chromatin organization in centromere protein A (Cenpa) null mice. Proc Natl Acad Sci USA. 2000, 97: 1148-1153. 10.1073/pnas.97.3.1148.View ArticleGoogle Scholar
- Pehrson JR, Fuji RN: Evolutionary conservation of histone macroH2A subtypes and domains. Nucleic Acids Res. 1998, 26: 2837-2842. 10.1093/nar/26.12.2837.View ArticleGoogle Scholar
- Costanzi C, Pehrson JR: Histone macroH2A1 is concentrated in the inactive X chromosome of female mammals. Nature. 1998, 393: 599-601. 10.1038/31275.View ArticleGoogle Scholar
- Mermoud JE, Costanzi C, Pehrson JR, Brockdorff N: Histone macroH2A relocates to the inactive X chromosome after initiation and propogation of X-inactivation. J Cell Biol. 1999, 147: 1399-1408. 10.1083/jcb.147.7.1399.View ArticleGoogle Scholar
- Csankovski G, Panning B, Bates B, Pehrson JR, Jaenisch R: Conditional deletion of Xist disrupts histone macroH2A localization but not maintenance of X inactivation. Nat Genet. 1999, 22: 323-324. 10.1038/11887.View ArticleGoogle Scholar
- Chadwick BP, Willard HF: A novel chromatin protein, distantly related to histone H2A, is largely excluded from the inactive Xchromosome. J Cell Biol. 2001, 152: 375-384. 10.1083/jcb.152.2.375.View ArticleGoogle Scholar
- Liu X, Li B, Gorovsky MA: Essential and nonessential histone H2A variants in Tetrahymena thermophila. Mol Cell Biol. 1996, 16: 4305-4311.View ArticleGoogle Scholar
- van Daal A, Elgin SC: A histone variant, H2AvD, is essential in Drosophila melanogaster. Mol Biol Cell. 1992, 3: 593-602.View ArticleGoogle Scholar
- Clarkson MJ, Wells JRE, Gibson F, Saint R, Tremethick DJ: Regions of variant histone His2AvD required for Drosophila development. Nature. 1999, 399: 694-697. 10.1038/21436.View ArticleGoogle Scholar
- Suto RK, Clarkson MJ, Tremethick DJ, Luger K: Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nat Struct Biol. 2000, 7: 1121-1124. 10.1038/81971.View ArticleGoogle Scholar
- Parseghian MH, Henschen AH, Krieglstein KG, Hamkalo BA: A proposal for a coherent mammalian histone H1 nomenclature correlated with amino acid sequences. Protein Sci. 1994, 3: 575-587.View ArticleGoogle Scholar
- Ponte I, Vidal-Taboada JM, Suau P: Evolution of the vertebrate H1 histone class: evidence for the functional differentiation of the subtypes. Mol Biol Evol. 1998, 15: 702-708.View ArticleGoogle Scholar
- Zlatanova J, Caiafa P, van Holde K: Linker histone binding and displacement: versatile mechanisms for transcriptional regulation. FASEB J. 2000, 14: 1697-1704. 10.1096/fj.99-0869rev.View ArticleGoogle Scholar
- Kochbin S, Wolffe AP: Developmentally regulated expression of linker histone variants in vertebrates. Eur J Biochem. 1994, 225: 501-510.View ArticleGoogle Scholar
- Talasz H, Helliger W, Puschendorf B, Lindner H: In vivo phosphorylation of histone H1 variants during the cell cycle. Biochemistry. 1996, 35: 1761-1767. 10.1021/bi951914e.View ArticleGoogle Scholar
- Talasz H, Sapojnikova N, Helliger W, Lindner H, Puschendorf B: In vitro binding of H1 histone subtypes to nucleosomal organized mouse mammary tumor virus long terminal repeat. J Biol Chem. 1998, 273: 32236-32243. 10.1074/jbc.273.48.32236.View ArticleGoogle Scholar
- Parseghian MH, Newcomb RL, Winokur ST, Hamkalo BA: The distribution of somatic H1 subtypes is non-random on active vs. inactive chromatin: distribution in human fetal fibroblasts. Chromosome Res. 2000, 8: 405-424. 10.1023/A:1009262819961.View ArticleGoogle Scholar
- Bouvet P, Dimitrov S, Wolffe AP: Specific regulation of Xenopus chromosomal 5S rRNA gene transcription in vivo by histone H1. Genes Dev. 1994, 8: 1147-1159.View ArticleGoogle Scholar
- Kandolf H: The H1A histone variant is an in vivo repressor of oocyte-type 5S gene transcription in Xenopus laevis embryos. Proc Natl Acad Sci USA. 1994, 91: 7257-7261.View ArticleGoogle Scholar
- Sera T, Wolffe AP: Role of histone H1 as an architectural determinant of chromatin structure and as a specific repressor of transcription on Xenopus oocyte 5S rRNA genes. Mol Cell Biol. 1998, 18: 3668-3680.View ArticleGoogle Scholar
- Panetta G, Buttinelli M, Flaus A, Richmond TJ, Rhodes D: Differential nucleosome positioning on Xenopus oocyte and somatic 5S RNA genes determines both TFIIIA and H1 binding: a mechanism for selective H1 repression. J Mol Biol. 1998, 282: 683-697. 10.1006/jmbi.1998.2087.View ArticleGoogle Scholar
- Lin Q, Sirotkin A, Skoultchi AI: Normal spermatogenesis in mice lacking the testis-specific linker histone H1t. Mol Cell Biol. 2000, 20: 2122-2128. 10.1128/MCB.20.6.2122-2128.2000.View ArticleGoogle Scholar
- Fantz DA, Hatfield WR, Horvath G, Kistler MK, Kistler WS: Mice with a targeted disruption of the H1t gene are fertile and undergo normal changes in structural chromosomal proteins during spermiogenesis. Biol Reprod. 2001, 64: 425-431.View ArticleGoogle Scholar
- Drabent B, Saftig P, Bode C, Doenecke D: Spermatogenesis proceeds normally in mice without linker H1t. Histochem Cell Biol. 2000, 113: 433-442.Google Scholar
- Tanaka M, Hennebold JD, Macfarlane J, Adashi EY: A mammalian oocyte-specific linker histone H1oo: homology with the genes for the oocyte-specific cleavage stage histone (cs-H1) of sea urchin and the B4/H1M histone of the frog. Development. 2001, 128: 655-664.Google Scholar
- Brown DT, Alexander BT, Sittman DB: Differential effect of H1 variant overexpression on cell cycle progression and gene expression. Nucleic Acids Res. 1996, 24: 486-493. 10.1093/nar/24.3.486.View ArticleGoogle Scholar
- Brown DT, Gunjan A, Alexander BT, Sittman DB: Differential effect of H1 variant overproduction on gene expression is due to differences in the central globular domain. Nucleic Acids Res. 1997, 25: 5003-5009. 10.1093/nar/25.24.5003.View ArticleGoogle Scholar
- Sirotkin AM, Edelmen W, Cheng G, Klein-Szanto A, Kucherlapati R, Skoultchi AI: Mice develop normally without the H1(0) linker histone. Proc Natl Acad Sci USA. 1995, 92: 6434-6438.View ArticleGoogle Scholar
- Lever MA, Th'ng JPH, Sun X, Hendzel MJ: Rapid exchange of histone H1.1 on chromatin in living human cells. Nature. 2000, 408: 873-876. 10.1038/35048603.View ArticleGoogle Scholar
- Misteli T, Gunjan A, Hock R, Bustin M, Brown DT: Dynamic binding of histone H1 to chromatin in living cells. Nature. 2000, 408: 877-881. 10.1038/35048610.View ArticleGoogle Scholar