Search tips
Search criteria 


Logo of narLink to Publisher's site
Nucleic Acids Res. 1994 January 25; 22(2): 174–179.
PMCID: PMC307768

Phylogenetic analysis of the core histones H2A, H2B, H3, and H4.


Despite the ubiquity of histones in eukaryotes and their important role in determining the structure and function of chromatin, no detailed studies of the evolution of the histones have been reported. We have constructed phylogenetic trees for the core histones H2A, H2B, H3, and H4. Histones which form dimers (H2A/H2B and H3/H4) have very similar trees and appear to have co-evolved, with the exception of the divergent sea urchin testis H2Bs, for which no corresponding divergent H2As have been identified. The trees for H2A and H2B also support the theory that animals and fungi have a common ancestor. H3 and H4 are 10-fold less divergent than H2A and H2B. Three evolutionary histories are observed for histone variants. H2A.F/Z-type variants arose once early in evolution, while H2A.X variants arose separately, during the evolution of multicellular animals. H3.3-type variants have arisen in multiple independent events.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1014K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Ausio J. Structure and dynamics of transcriptionally active chromatin. J Cell Sci. 1992 May;102(Pt 1):1–5. [PubMed]
  • Wolffe AP. Implications of DNA replication for eukaryotic gene expression. J Cell Sci. 1991 Jun;99(Pt 2):201–206. [PubMed]
  • Felsenfeld G. Chromatin as an essential part of the transcriptional mechanism. Nature. 1992 Jan 16;355(6357):219–224. [PubMed]
  • Svaren J, Hörz W. Histones, nucleosomes and transcription. Curr Opin Genet Dev. 1993 Apr;3(2):219–225. [PubMed]
  • Ferrari N, Pfeffer U, Profumo A, Vidali G. Post-transcriptional control of H3 histone variants synthesis. Biochem Int. 1992 Oct;28(2):239–248. [PubMed]
  • Waterborg JH. Histone synthesis and turnover in alfalfa. Fast loss of highly acetylated replacement histone variant H3.2. J Biol Chem. 1993 Mar 5;268(7):4912–4917. [PubMed]
  • Wunsch AM, Lough J. Histone variant patterns during vertebrate embryogenesis and limb development. Cell Differ Dev. 1990 Apr;30(1):19–25. [PubMed]
  • DeLange RJ, Fambrough DM, Smith EL, Bonner J. Calf and pea histone IV. 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone. J Biol Chem. 1969 Oct 25;244(20):5669–5679. [PubMed]
  • Wells D, McBride C. A comprehensive compilation and alignment of histones and histone genes. Nucleic Acids Res. 1989;17 (Suppl):r311–r346. [PMC free article] [PubMed]
  • Wells D, Brown D. Histone and histone gene compilation and alignment update. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2173–2188. [PMC free article] [PubMed]
  • Benson D, Lipman DJ, Ostell J. GenBank. Nucleic Acids Res. 1993 Jul 1;21(13):2963–2965. [PMC free article] [PubMed]
  • Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. [PMC free article] [PubMed]
  • Feng DF, Doolittle RF. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol. 1987;25(4):351–360. [PubMed]
  • Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987 Jul;4(4):406–425. [PubMed]
  • Woese CR. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. [PMC free article] [PubMed]
  • Wainright PO, Hinkle G, Sogin ML, Stickel SK. Monophyletic origins of the metazoa: an evolutionary link with fungi. Science. 1993 Apr 16;260(5106):340–342. [PubMed]
  • Gaertig J, Thatcher TH, McGrath KE, Callahan RC, Gorovsky MA. Perspectives on tubulin isotype function and evolution based on the observation that Tetrahymena thermophila microtubules contain a single alpha- and beta-tubulin. Cell Motil Cytoskeleton. 1993;25(3):243–253. [PubMed]
  • van Daal A, White EM, Elgin SC, Gorovsky MA. Conservation of intron position indicates separation of major and variant H2As is an early event in the evolution of eukaryotes. J Mol Evol. 1990 May;30(5):449–455. [PubMed]
  • van Daal A, Elgin SC. A histone variant, H2AvD, is essential in Drosophila melanogaster. Mol Biol Cell. 1992 Jun;3(6):593–602. [PMC free article] [PubMed]
  • Mannironi C, Bonner WM, Hatch CL. H2A.X. a histone isoprotein with a conserved C-terminal sequence, is encoded by a novel mRNA with both DNA replication type and polyA 3' processing signals. Nucleic Acids Res. 1989 Nov 25;17(22):9113–9126. [PMC free article] [PubMed]
  • Matsuo Y, Yamazaki T. Nucleotide variation and divergence in the histone multigene family in Drosophila melanogaster. Genetics. 1989 May;122(1):87–97. [PubMed]
  • Hayes JJ, Clark DJ, Wolffe AP. Histone contributions to the structure of DNA in the nucleosome. Proc Natl Acad Sci U S A. 1991 Aug 1;88(15):6829–6833. [PubMed]
  • Baer BW, Rhodes D. Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes. Nature. 1983 Feb 10;301(5900):482–488. [PubMed]
  • Louters L, Chalkley R. Exchange of histones H1, H2A, and H2B in vivo. Biochemistry. 1985 Jun 18;24(13):3080–3085. [PubMed]
  • Waterborg JH. Multiplicity of histone h3 variants in wheat, barley, rice, and maize. Plant Physiol. 1991 Jun;96(2):453–458. [PubMed]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press