Abstract
The human alpha satellite DNA family, like many highly repeated satellite DNAs in eukaryotic genomes, is organized in distinct chromosome-specific subsets. As part of investigations into the molecular and evolutionary basis for the chromosome-specific nature of such subsets, we report the isolation and characterization of alpha satellite sequences specific for human chromosome 3. This subset is characterized by a predominant tandemly arranged ∼2.9 kb higher-order repeat unit which, in turn, consists of 17 tandem diverged monomer repeat units of ∼171 bp. Nucleotide sequence analysis reveals that the chromosome 3 higher-order repeat units are comprised, at least in part, of diverged dimeric (∼ 340 bp) sub-repeats and that this divergence accounts for the chromosome-specific behavior of this subset. Pulsed-field gel electrophoresis demonstrates that the chromosome 3 higher-order repeat units are localized in large domains, at least 1000 kb in length. Familial restriction fragment length polymorphisms associated with the satellite subset can be detected by pulsed field gel electrophoresis and may facilitate molecular analysis of interchromosomal variation.
Similar content being viewed by others
References
Beauchamp RS, Mitchell AR, Buckland RA, Bostock CJ (1979) Specific arrangement of human satellite III DNA sequences in human chromosomes. Chromosoma 71:153–166
Carle GF, Olson MV (1984) Separation of chromosomal DNA molecules from yeast by orthogonal-field-alteration gel electrophoresis. Nucleic Acids Res 12:5647–5664
Cooke HJ, Hindley J (1979) Cloning of human satellite III DNA: different components are on different chromosomes. Nucleic Acids Res 6:3177–3197
Delattre O, Bernard A, Malfoy B, Marlhens F, Viegas-Pequignot E, Brossard C, Haguenauer O, Creau-Goldberg N, Van Cong N, Dutrillaux B, Thomas G (1988) Studies on the human chromosome 3 centromere with a cloned alphoid DNA probe. Hum Hered 38:156–167
Devilee P, Kievits T, Waye JS, Pearson PL, Willard HF (1988) Chromosome-specific alpha satellite DNA: isolation and mapping of a polymorphic alphoid repeat from human chromosome 10. Genomics 3:1–7
Gosden JR, Mitchell AR, Buckland RA, Clayton RP, Evans HJ (1975) The location of four satellite DNAs on human chromosomes. Exp Cell Res 92:148–158
Jorgensen AL, Bostock CJ, Bak AL (1986) Chromosome-specific subfamilies within human alphoid repetitive DNA. J Mol Biol 187:185–196
Kenwrick S, Patterson M, Speer A, Fischbeck K, Davies K (1987) Molecular analysis of the Duchenne muscular dystrophy region using pulsed field gel electrophoresis. Cell 48:351–357
Kit S (1961) Equilibrium sedimentation in density gradients of DNA preparations from animal tissues. J Mol Biol 3:711–716
Lee TNH, Singer MF (1982) Structural organization of alpha satellite DNA in a single monkey chromosome. J Mol Biol 161:323–342
Manuelidis L (1978) Chromosomal location of complex and single repeated human DNAs. Chromosoma 66:23–32
Manuelidis L, Wu JC (1978) Homology between human and simian repeated DNA. Nature 276:92–94
Melton DA, Krieg PA, Rebagliati MR, Maniatis T, Zinn K, Green R (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing the SP6 promoter. Nucleic Acids Res 12:7035–7056
Miklos GLG, John B (1979) Heterochromatin and satellite DNA in man: properties and prospects. Am J Hum Genet 31:264–280
Moyzis RK, Albright K, Bartholdi M, Cram L, Deaven L, Hindebrand C, Joste N, Longmire JL, Meyne L, Schwarzachen-Robinson T (1987) Human chromosome-specific repetitive DNA sequences. Chromosoma 95:375–386
Murray V, Martin RF (1987) Nucleotide sequences of human alpha-DNA repeats. Gene 57:255–259
Pardue ML, Gall JG (1970) Chromosome location of mouse satellite DNA. Science 168:1356–1358
Pike LM, Carlisle A, Newell C, Hong S, Musich PR (1986) Sequence and evolution of rhesus monkey alphoid DNA. J Mol Evol 23:127–137
Schwartz D, Cantor C (1984) Separation of yeast chromosomesized DNAs by pulsed field gradient gel electrophoresis. Cell 37:67–75
Shmookler Reis RJ, Srivastava A, Beranek DT, Goldstein S (1985) Human alphoid family of tandemly repeated DNA: sequence of cloned tetrameric fragments and analysis of familial divergence. J Mol Biol 186:31–41
Singer MF (1982) Highly repeated sequences in mammalian genomes. Int Rev Cytol 76:67–112
Southern EM (1975) Long range periodicities in mouse satellite DNA. J Mol Biol 94:51–69
Sueoka N (1961) Variation and heterogeneity of base composition of DNAs: a compilation of old and new data. J Mol Biol 3:31–40
Tyler-Smith C, Brown WRA (1987) Structure of the major block of alphoid satellite DNA on the human Y chromosome. J Mol Biol 195:457–470
Waye JS, Willard HF (1986) 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 X chromosome. Mol Cell Biol 6:3156–3165
Waye JS, Willard HF (1987) Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes. Nucleic Acids Res 15:7549–7569
Waye JS, Durfy SJ, Pinkel D, Kenwrick S, Patterson M, Davies KE, Willard HF (1987a) Chromosome-specific alpha satellite DNA from human chromosome 1: hierarchical structure and genomic organization of a polymorphic domain spanning several hundred kilobase pairs of centromeric DNA. Genomics 1:43–51
Waye JS, England SB, Willard HF (1987b) Genomic organization of alpha satellite DNA from human chromosome 7: evidence for two distinct alphoid domains on a single chromosome. Mol Cell Biol 7:349–356
Willard HF (1985) Chromosome-specific organization of human alpha satellite DNA. Am J Hum Genet 37:524–532
Willard HF, Waye JS (1987) Hierarchical order in chromosome-specific human alpha satellite DNA. Trends Genet 3:192–198
Willard HF, Waye JS, Skolnick MH, Schwartz CE, Powers VE, England SB (1986) Detection of restriction fragment length polymorphisms at the centromeres of human chromosomes using chromosome-specific alpha satellite DNA: implications for the development of centromere-based genetic linkage maps. Proc Natl Acad Sci USA 83:5611–5615
Wolfe J, Darling SM, Erickson RP, Craig I, Buckle V, Rigby P, Willard HF, Goodfellow P (1985) Isolation and characterization of an alphoid centromeric repeat family from the human Y chromosome. J Mol Biol 182:477–485
Worton RG, Duff C, Sylvester JE, Schmickel RD, Willard HF (1984) Duchenne muscular dystrophy involving translocation of the dmd gene next to ribosomal RNA genes. Science 224:1447–1449
Wu JC, Manuelidis L (1980) Sequence definition and organization of a human repeated DNA. J Mol Biol 142:363–386
Yurov YB, Yakovlev AG, Zaitzev IZ, Mitkevich SP, Alexandrov IA, Shapiro YuA, Kramerova IA, Gindilis VM (1986) The cloned fragment of reiterated human DNA specific to the centromeric heterochromatin of chromosome 3. Mol Microbiol Virusol (USSR) 7:17–23
Yurov JB, Mitkevich SP, Alexandrov IA (1987) Application of cloned satellite DNA sequences to molecular cytogenetic analysis of constitutive heterochromatin heteromorphisms in man. Hum Genet 76:157–164
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Waye, J.S., Willard, H.F. Chromosome specificity of satellite DNAs: short- and long-range organization of a diverged dimeric subset of human alpha satellite from chromosome 3. Chromosoma 97, 475–480 (1989). https://doi.org/10.1007/BF00295032
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF00295032