Genomic organization and nucleotide sequences of two histone H3 and two histone H4 genes of Arabidopsis thaliana


Two histone H3 and two histone H4 genes have been cloned from a λgtWESλ·B Arabidopsis thaliana gene library. From their nucleotide sequences and from studies on their genomic organization, the following conclusions can be drawn:

  1. 1)

    The nucleotide sequences of the two H3 coding regions show only 85% homology, but encode the same proteins. The Arabidopsis H3 has the same amino acid sequence as its counterpart in corn, but differs from that of pea and wheat by replacement in position 90 of a serine by an alanine. The two H4 coding regions have 97% sequence homology and encode the same protein, identical to the sequence of their counterpart in pea, corn and one H4 variant in wheat.

  2. 2)

    The 5′-flanking regions of the 4 genes contain the classical histone-gene-specific consensus sequences, except H3A725 which lacks the GATCC-like pentamer. The conserved octanucleotide 5′-CGCGGATC-3′ which was previously found in the 5′-flanking sequences of corn and wheat H3 and H4 genes is also present in all four genes described here approximately 200 to 250 nucleotides upstream from the initiation ATG.

    The 5′-flanking regions of the H4 genes display extensive sequence homology, whereas those of the H3 genes do not.

  3. 3)

    The 3′-flanking regions do not possess the classical histone-gene-specific T hyphenated dyad symmetry motif.

  4. 4)

    Each H3 and H4 gene exists as 5 to 7 copies per haploid genome.

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  1. 1.

    Anderson OD, Litts JC, Gautier MF, Greene FC: Nucleic acid sequence and chromosome assignment of a wheat storage protein gene. Nucleic Acids Res 12: 8129–8144, 1984.

    Google Scholar 

  2. 2.

    Becker A, Gold M: Isolation of the bacteriophage Lambdagene protein. Proc Natl Acad Sci USA 72: 581–585, 1975.

    Google Scholar 

  3. 3.

    Benton WD, Davis RW: Screening λgt recombinant clones by hybridization to single plaques in situ. Science 196: 180–182, 1977.

    Google Scholar 

  4. 4.

    Birnstiel ML, Busslinger M, Strub K: Transcription termination and 3′ processing: the end is in site. Cell 41: 349–359, 1985.

    Google Scholar 

  5. 5.

    Chaubet N, Philipps G, Chaboute ME, Ehling M, Gigot C: Nucleotide sequences of two corn histone H3 genes. Genomic organization of the corn histone H3 and H4 genes. Plant Mol Biol 6: 253–263, 1986.

    Google Scholar 

  6. 6.

    Flavell R: The molecular characterization and organization of plant chromosomal sequences. Annu Rev Plant Physiol 31: 568–596, 1980.

    Google Scholar 

  7. 7.

    Grantham R, Gauthier C, Gouy M, Jacobzone M, Mercier R: Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res 9: r43-r74, 1981.

    Google Scholar 

  8. 8.

    Hentschel C, Birnstiel ML: The organization and expression of histone gene families. Cell 25: 301–313, 1981.

    Google Scholar 

  9. 9.

    Leutwiler LS, Hough-Evans BR, Meyerovitz EM. The DNA of Arabidopsis thaliana. Mol Gen Genet 194: 15–23, 1984.

    Google Scholar 

  10. 10.

    Maxam AM, Gilbert W: Sequencing end-labeled DNA with base-specific chemical cleavage. Methods Enzymol 65: 499–560, 1980.

    Google Scholar 

  11. 11.

    Maxson R, Cohn R, Kedes L, Mohun T: Expression and organization of histone genes. Annu Rev Genet 17: 239–277, 1983.

    Google Scholar 

  12. 12.

    Nussinov R: Some rules in the ordering of nucleotides in the DNA. Nucleic Acids Res 8: 4545–4562, 1980.

    Google Scholar 

  13. 13.

    Patthy L, Smith EL, Johnson J: Histone III: V. The amino acid sequence of pea embryo histone III. J Biol Chem 248: 6834–6840, 1973.

    Google Scholar 

  14. 14.

    Philipps G, Chaubet N, Chaboute ME, Ehling M, Gigot C: Genomic organization and nucleotide sequences of two corn histone H4 genes. Gene 42: 225–229, 1986.

    Google Scholar 

  15. 15.

    Pruitt RE, Meyerovitz EM. Characterization of the genome of Arabidopsis thaliana. J Mol Biol 187: 169–183, 1986.

    Google Scholar 

  16. 16.

    Schaffner W, Kunz G, Daetwyler H, Telford J, Smith HO, Birnstiel ML: Genes and spacers of cloned sea urchin histone DNA analysed by sequencing. Cell 14: 655–671, 1978.

    Google Scholar 

  17. 17.

    Southern EM: Detection of specific sequences among DNA fragments separated by electrophoresis. J Mol Biol 98: 503–517, 1975.

    Google Scholar 

  18. 18.

    Tabata T, Sasaki K, Iwabuchi M: The structural organization and DNA sequence of a wheat histone H4 gene. Nucleic Acids Res 11: 5865–5875, 1983.

    Google Scholar 

  19. 19.

    Tabata T, Iwabuchi M. Molecular cloning and nucleotide sequence of a variant wheat histone H4 gene. Gene 31: 285–289, 1984.

    Google Scholar 

  20. 20.

    Tabata T, Fukasawa M, Iwabuchi M: Nucleotide sequence and genomic organization of a wheat histone H3 gene. Mol Gene Genet 196: 397–400, 1984.

    Google Scholar 

  21. 21.

    Thomas G, Padayatty JD: Organization and bidirectional transcription of H2A, H2B and H4 histone genes in rice embryos. Nature 306: 82–84, 1983.

    Google Scholar 

  22. 22.

    Thomas G, Padayatty JD: Restriction map and partial sequence of a rice DNA fragment carrying histone genes H2A, H2B and H4. Ind J Biochem Biophys 21: 1–6, 1984.

    Google Scholar 

  23. 23.

    Vogelstein B, Gillespie D: Preparative and analytical purification of DNA from agarose. Proc Natl Acad Sci USA 76: 615–619, 1979.

    Google Scholar 

  24. 24.

    Zimmerman JL, Goldberg RB: DNA sequence organization in the genome of Nicotiana tabacum. Chromosoma 59: 227–252, 1977.

    Google Scholar 

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Chaboute, ME., Chaubet, N., Philipps, G. et al. Genomic organization and nucleotide sequences of two histone H3 and two histone H4 genes of Arabidopsis thaliana . Plant Mol Biol 8, 179–191 (1987).

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  • Arabidopsis thaliana
  • codon usage
  • genomic organization
  • histone gene