Skip to main content
PMC home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1986 Sep;6(9):3156–3165. doi: 10.1128/mcb.6.9.3156

Structure, organization, and sequence of alpha satellite DNA from human chromosome 17: evidence for evolution by unequal crossing-over and an ancestral pentamer repeat shared with the human X chromosome.

J S Waye, H F Willard
PMCID: PMC367051  PMID: 3785225

Abstract

The centromeric regions of all human chromosomes are characterized by distinct subsets of a diverse tandemly repeated DNA family, alpha satellite. On human chromosome 17, the predominant form of alpha satellite is a 2.7-kilobase-pair higher-order repeat unit consisting of 16 alphoid monomers. We present the complete nucleotide sequence of the 16-monomer repeat, which is present in 500 to 1,000 copies per chromosome 17, as well as that of a less abundant 15-monomer repeat, also from chromosome 17. These repeat units were approximately 98% identical in sequence, differing by the exclusion of precisely 1 monomer from the 15-monomer repeat. Homologous unequal crossing-over is suggested as a probable mechanism by which the different repeat lengths on chromosome 17 were generated, and the putative site of such a recombination event is identified. The monomer organization of the chromosome 17 higher-order repeat unit is based, in part, on tandemly repeated pentamers. A similar pentameric suborganization has been previously demonstrated for alpha satellite of the human X chromosome. Despite the organizational similarities, substantial sequence divergence distinguishes these subsets. Hybridization experiments indicate that the chromosome 17 and X subsets are more similar to each other than to the subsets found on several other human chromosomes. We suggest that the chromosome 17 and X alpha satellite subsets may be related components of a larger alphoid subfamily which have evolved from a common ancestral repeat into the contemporary chromosome-specific subsets.

Full text

PDF
3157

Images in this article

3158Image
on p.3158
3162Image
on p.3162

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Biggin M. D., Gibson T. J., Hong G. F. Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A. 1983 Jul;80(13):3963–3965. doi: 10.1073/pnas.80.13.3963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brutlag D. L. Molecular arrangement and evolution of heterochromatic DNA. Annu Rev Genet. 1980;14:121–144. doi: 10.1146/annurev.ge.14.120180.001005. [DOI] [PubMed] [Google Scholar]
  3. Donehower L., Furlong C., Gillespie D., Kurnit D. DNA sequence of baboon highly repeated DNA: evidence for evolution by nonrandom unequal crossovers. Proc Natl Acad Sci U S A. 1980 Apr;77(4):2129–2133. doi: 10.1073/pnas.77.4.2129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Donehower L., Gillespie D. Restriction site periodicities in highly repetitive DNA of primates. J Mol Biol. 1979 Nov 15;134(4):805–834. doi: 10.1016/0022-2836(79)90487-x. [DOI] [PubMed] [Google Scholar]
  5. Ellison J. W., Hood L. E. Human antibody genes. Evolutionary and molecular genetic perspectives. Adv Hum Genet. 1983;13:113–147. [PubMed] [Google Scholar]
  6. Gillespie D. Newly evolved repeated DNA sequences in primates. Science. 1977 May 20;196(4292):889–891. doi: 10.1126/science.870965. [DOI] [PubMed] [Google Scholar]
  7. Gray K. M., White J. W., Costanzi C., Gillespie D., Schroeder W. T., Calabretta B., Saunders G. F. Recent amplification of an alpha satellite DNA in humans. Nucleic Acids Res. 1985 Jan 25;13(2):521–535. doi: 10.1093/nar/13.2.521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Hagan C. E., Warren G. J. Lethality of palindromic DNA and its use in selection of recombinant plasmids. Gene. 1982 Jul-Aug;19(1):147–151. doi: 10.1016/0378-1119(82)90199-8. [DOI] [PubMed] [Google Scholar]
  9. Henikoff S. Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing. Gene. 1984 Jun;28(3):351–359. doi: 10.1016/0378-1119(84)90153-7. [DOI] [PubMed] [Google Scholar]
  10. Jones R. S., Potter S. S. Characterization of cloned human alphoid satellite with an unusual monomeric construction: evidence for enrichment in HeLa small polydisperse circular DNA. Nucleic Acids Res. 1985 Feb 11;13(3):1027–1042. doi: 10.1093/nar/13.3.1027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Jørgensen A. L., Bostock C. J., Bak A. L. Chromosome-specific subfamilies within human alphoid repetitive DNA. J Mol Biol. 1986 Jan 20;187(2):185–196. doi: 10.1016/0022-2836(86)90227-5. [DOI] [PubMed] [Google Scholar]
  12. Korneluk R. G., Quan F., Gravel R. A. Rapid and reliable dideoxy sequencing of double-stranded DNA. Gene. 1985;40(2-3):317–323. doi: 10.1016/0378-1119(85)90055-1. [DOI] [PubMed] [Google Scholar]
  13. Kurnit D. M. Satellite DNA and heterochromatin variants: the case for unequal mitotic crossing over. Hum Genet. 1979 Mar 12;47(2):169–186. doi: 10.1007/BF00273199. [DOI] [PubMed] [Google Scholar]
  14. Maio J. J., Brown F. L., Musich P. R. Subunit structure of chromatin and the organization of eukaryotic highly repetitive DNA: recurrent periodicities and models for the evolutionary origins of repetitive DNA. J Mol Biol. 1977 Dec 15;117(3):637–655. doi: 10.1016/0022-2836(77)90062-6. [DOI] [PubMed] [Google Scholar]
  15. Maio J. J., Brown F. L., Musich P. R. Toward a molecular paleontology of primate genomes. I. The HindIII and EcoRI dimer families of alphoid DNAs. Chromosoma. 1981;83(1):103–125. doi: 10.1007/BF00286019. [DOI] [PubMed] [Google Scholar]
  16. Manuelidis L., Wu J. C. Homology between human and simian repeated DNA. Nature. 1978 Nov 2;276(5683):92–94. doi: 10.1038/276092a0. [DOI] [PubMed] [Google Scholar]
  17. Melton D. A., Krieg P. A., Rebagliati M. R., Maniatis T., Zinn K., Green M. R. Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 1984 Sep 25;12(18):7035–7056. doi: 10.1093/nar/12.18.7035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Mitchell A. R., Gosden J. R., Miller D. A. A cloned sequence, p82H, of the alphoid repeated DNA family found at the centromeres of all human chromosomes. Chromosoma. 1985;92(5):369–377. doi: 10.1007/BF00327469. [DOI] [PubMed] [Google Scholar]
  19. Rosenberg H., Singer M., Rosenberg M. Highly reiterated sequences of SIMIANSIMIANSIMIANSIMIANSIMIAN. Science. 1978 Apr 28;200(4340):394–402. doi: 10.1126/science.205944. [DOI] [PubMed] [Google Scholar]
  20. Rubin C. M., Deininger P. L., Houck C. M., Schmid C. W. A dimer satellite sequence in bonnet monkey DNA consists of distinct monomer subunits. J Mol Biol. 1980 Jan 15;136(2):151–167. doi: 10.1016/0022-2836(80)90310-1. [DOI] [PubMed] [Google Scholar]
  21. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Shmookler Reis R. J., Srivastava A., Beranek D. T., Goldstein S. Human alphoid family of tandemly repeated DNA. Sequence of cloned tetrameric fragments and analysis of familial divergence. J Mol Biol. 1985 Nov 5;186(1):31–41. doi: 10.1016/0022-2836(85)90254-2. [DOI] [PubMed] [Google Scholar]
  23. Smith G. P. Evolution of repeated DNA sequences by unequal crossover. Science. 1976 Feb 13;191(4227):528–535. doi: 10.1126/science.1251186. [DOI] [PubMed] [Google Scholar]
  24. Solomon M. J., Strauss F., Varshavsky A. A mammalian high mobility group protein recognizes any stretch of six A.T base pairs in duplex DNA. Proc Natl Acad Sci U S A. 1986 Mar;83(5):1276–1280. doi: 10.1073/pnas.83.5.1276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Southern E. M. Application of DNA analysis to mapping the human genome. Cytogenet Cell Genet. 1982;32(1-4):52–57. doi: 10.1159/000131686. [DOI] [PubMed] [Google Scholar]
  26. Strauss F., Varshavsky A. A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome. Cell. 1984 Jul;37(3):889–901. doi: 10.1016/0092-8674(84)90424-0. [DOI] [PubMed] [Google Scholar]
  27. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  28. Waye J. S., Willard H. F. Chromosome-specific alpha satellite DNA: nucleotide sequence analysis of the 2.0 kilobasepair repeat from the human X chromosome. Nucleic Acids Res. 1985 Apr 25;13(8):2731–2743. doi: 10.1093/nar/13.8.2731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Willard H. F. Chromosome-specific organization of human alpha satellite DNA. Am J Hum Genet. 1985 May;37(3):524–532. [PMC free article] [PubMed] [Google Scholar]
  30. Willard H. F., Meakin S. O., Tsui L. C., Breitman M. L. Assignment of human gamma crystallin multigene family to chromosome 2. Somat Cell Mol Genet. 1985 Sep;11(5):511–516. doi: 10.1007/BF01534846. [DOI] [PubMed] [Google Scholar]
  31. Willard H. F., Riordan J. R. Assignment of the gene for myelin proteolipid protein to the X chromosome: implications for X-linked myelin disorders. Science. 1985 Nov 22;230(4728):940–942. doi: 10.1126/science.3840606. [DOI] [PubMed] [Google Scholar]
  32. Willard H. F., Smith K. D., Sutherland J. Isolation and characterization of a major tandem repeat family from the human X chromosome. Nucleic Acids Res. 1983 Apr 11;11(7):2017–2033. doi: 10.1093/nar/11.7.2017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Wolfe J., Darling S. M., Erickson R. P., Craig I. W., Buckle V. J., Rigby P. W., Willard H. F., Goodfellow P. N. Isolation and characterization of an alphoid centromeric repeat family from the human Y chromosome. J Mol Biol. 1985 Apr 20;182(4):477–485. doi: 10.1016/0022-2836(85)90234-7. [DOI] [PubMed] [Google Scholar]
  34. Wu J. C., Manuelidis L. Sequence definition and organization of a human repeated DNA. J Mol Biol. 1980 Sep 25;142(3):363–386. doi: 10.1016/0022-2836(80)90277-6. [DOI] [PubMed] [Google Scholar]
  35. Yang T. P., Hansen S. K., Oishi K. K., Ryder O. A., Hamkalo B. A. Characterization of a cloned repetitive DNA sequence concentrated on the human X chromosome. Proc Natl Acad Sci U S A. 1982 Nov;79(21):6593–6597. doi: 10.1073/pnas.79.21.6593. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES