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. 1987 Sep 25;15(18):7549–7569. doi: 10.1093/nar/15.18.7549

Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes.

J S Waye 1, H F Willard 1
PMCID: PMC306267  PMID: 3658703

Abstract

The human alpha satellite DNA family is composed of diverse, tandemly reiterated monomer units of approximately 171 basepairs localized to the centromeric region of each chromosome. These sequences are organized in a highly chromosome-specific manner with many, if not all human chromosomes being characterized by individually distinct alphoid subsets. Here, we compare the nucleotide sequences of 153 monomer units, representing alphoid components of at least 12 different human chromosomes. Based on the analysis of sequence variation at each position within the 171 basepair monomer, we have derived a consensus sequence for the monomer unit of human alpha satellite DNA which we suggest may reflect the monomer sequence from which different chromosomal subsets have evolved. Sequence heterogeneity is evident at each position within the consensus monomer unit and there are no positions of strict nucleotide sequence conservation, although some regions are more variable than others. A substantial proportion of the overall sequence variation may be accounted for by nucleotide changes which are characteristic of monomer components of individual chromosomal subsets or groups of subsets which have a common evolutionary history.

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Selected References

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

  1. Clarke L., Amstutz H., Fishel B., Carbon J. Analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe. Proc Natl Acad Sci U S A. 1986 Nov;83(21):8253–8257. doi: 10.1073/pnas.83.21.8253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Darling S. M., Crampton J. M., Williamson R. Organization of a family of highly repetitive sequences within the human genome. J Mol Biol. 1982 Jan 5;154(1):51–63. doi: 10.1016/0022-2836(82)90416-8. [DOI] [PubMed] [Google Scholar]
  3. Devilee P., Slagboom P., Cornelisse C. J., Pearson P. L. Sequence heterogeneity within the human alphoid repetitive DNA family. Nucleic Acids Res. 1986 Mar 11;14(5):2059–2073. doi: 10.1093/nar/14.5.2059. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. 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]
  5. 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]
  6. Fitzgerald-Hayes M., Clarke L., Carbon J. Nucleotide sequence comparisons and functional analysis of yeast centromere DNAs. Cell. 1982 May;29(1):235–244. doi: 10.1016/0092-8674(82)90108-8. [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. Hieter P., Pridmore D., Hegemann J. H., Thomas M., Davis R. W., Philippsen P. Functional selection and analysis of yeast centromeric DNA. Cell. 1985 Oct;42(3):913–921. doi: 10.1016/0092-8674(85)90287-9. [DOI] [PubMed] [Google Scholar]
  9. Jabs E. W., Wolf S. F., Migeon B. R. Characterization of a cloned DNA sequence that is present at centromeres of all human autosomes and the X chromosome and shows polymorphic variation. Proc Natl Acad Sci U S A. 1984 Aug;81(15):4884–4888. doi: 10.1073/pnas.81.15.4884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. John B., Miklos G. L. Functional aspects of satellite DNA and heterochromatin. Int Rev Cytol. 1979;58:1–114. doi: 10.1016/s0074-7696(08)61473-4. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. 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]
  13. Jørgensen A. L., Bostock C. J., Bak A. L. Homologous subfamilies of human alphoid repetitive DNA on different nucleolus organizing chromosomes. Proc Natl Acad Sci U S A. 1987 Feb;84(4):1075–1079. doi: 10.1073/pnas.84.4.1075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kiyama R., Matsui H., Oishi M. A repetitive DNA family (Sau3A family) in human chromosomes: extrachromosomal DNA and DNA polymorphism. Proc Natl Acad Sci U S A. 1986 Jul;83(13):4665–4669. doi: 10.1073/pnas.83.13.4665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lee T. N., Singer M. F. Structural organization of alpha-satellite DNA in a single monkey chromosome. J Mol Biol. 1982 Oct 25;161(2):323–342. doi: 10.1016/0022-2836(82)90156-5. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Maio J. J. DNA strand reassociation and polyribonucleotide binding in the African green monkey, Cercopithecus aethiops. J Mol Biol. 1971 Mar 28;56(3):579–595. doi: 10.1016/0022-2836(71)90403-7. [DOI] [PubMed] [Google Scholar]
  18. Mann C., Davis R. W. Structure and sequence of the centromeric DNA of chromosome 4 in Saccharomyces cerevisiae. Mol Cell Biol. 1986 Jan;6(1):241–245. doi: 10.1128/mcb.6.1.241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Manuelidis L. Chromosomal localization of complex and simple repeated human DNAs. Chromosoma. 1978 Mar 22;66(1):23–32. doi: 10.1007/BF00285813. [DOI] [PubMed] [Google Scholar]
  20. Manuelidis L. Complex and simple sequences in human repeated DNAs. Chromosoma. 1978 Mar 22;66(1):1–21. doi: 10.1007/BF00285812. [DOI] [PubMed] [Google Scholar]
  21. 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]
  22. McDermid H. E., Duncan A. M., Higgins M. J., Hamerton J. L., Rector E., Brasch K. R., White B. N. Isolation and characterization of an alpha-satellite repeated sequence from human chromosome 22. Chromosoma. 1986;94(3):228–234. doi: 10.1007/BF00288497. [DOI] [PubMed] [Google Scholar]
  23. Miklos G. L., John B. Heterochromatin and satellite DNA in man: properties and prospects. Am J Hum Genet. 1979 May;31(3):264–280. [PMC free article] [PubMed] [Google Scholar]
  24. 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]
  25. Musich P. R., Brown F. L., Maio J. J. Highly repetitive component alpha and related alphoid DNAs in man and monkeys. Chromosoma. 1980;80(3):331–348. doi: 10.1007/BF00292688. [DOI] [PubMed] [Google Scholar]
  26. Nakaseko Y., Adachi Y., Funahashi S., Niwa O., Yanagida M. Chromosome walking shows a highly homologous repetitive sequence present in all the centromere regions of fission yeast. EMBO J. 1986 May;5(5):1011–1021. doi: 10.1002/j.1460-2075.1986.tb04316.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Neitz M., Carbon J. Identification and characterization of the centromere from chromosome XIV in Saccharomyces cerevisiae. Mol Cell Biol. 1985 Nov;5(11):2887–2893. doi: 10.1128/mcb.5.11.2887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Panzeri L., Philippsen P. Centromeric DNA from chromosome VI in Saccharomyces cerevisiae strains. EMBO J. 1982;1(12):1605–1611. doi: 10.1002/j.1460-2075.1982.tb01362.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Pech M., Streeck R. E., Zachau H. G. Patchwork structure of a bovine satellite DNA. Cell. 1979 Nov;18(3):883–893. doi: 10.1016/0092-8674(79)90140-5. [DOI] [PubMed] [Google Scholar]
  30. Pike L. M., Carlisle A., Newell C., Hong S. B., Musich P. R. Sequence and evolution of rhesus monkey alphoid DNA. J Mol Evol. 1986;23(2):127–137. doi: 10.1007/BF02099907. [DOI] [PubMed] [Google Scholar]
  31. Prassolov V. S., Kuchino Y., Nemoto K., Nishimura S. Nucleotide sequence of the BamHI repetitive sequence, including the HindIII fundamental unit, as a possible mobile element from the Japanese monkey Macaca fuscata. J Mol Evol. 1986;23(3):200–204. doi: 10.1007/BF02115576. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. 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]
  34. 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]
  35. Singer M. F. Highly repeated sequences in mammalian genomes. Int Rev Cytol. 1982;76:67–112. doi: 10.1016/s0074-7696(08)61789-1. [DOI] [PubMed] [Google Scholar]
  36. 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]
  37. Southern E. M. Long range periodicities in mouse satellite DNA. J Mol Biol. 1975 May 5;94(1):51–69. doi: 10.1016/0022-2836(75)90404-0. [DOI] [PubMed] [Google Scholar]
  38. 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]
  39. Waye J. S., Creeper L. A., Willard H. F. Organization and evolution of alpha satellite DNA from human chromosome 11. Chromosoma. 1987;95(3):182–188. doi: 10.1007/BF00330349. [DOI] [PubMed] [Google Scholar]
  40. Waye J. S., England S. B., Willard H. F. Genomic organization of alpha satellite DNA on human chromosome 7: evidence for two distinct alphoid domains on a single chromosome. Mol Cell Biol. 1987 Jan;7(1):349–356. doi: 10.1128/mcb.7.1.349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. 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]
  42. Waye J. S., Willard H. F. 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. Mol Cell Biol. 1986 Sep;6(9):3156–3165. doi: 10.1128/mcb.6.9.3156. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. 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]
  44. 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]
  45. 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]
  46. 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]
  47. 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]

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