Detection of Restriction Fragment Length Polymorphisms at the Centromeres of Human Chromosomes by Using Chromosome-specific Alpha Satellite DNA Probes: Implications for Development of Centromere-based Genetic Linkage Maps

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1986 Aug 1

PMID 3016709

Citations 54

Authors

H F Willard

J S Waye

M H Skolnick

C E Schwartz

V E Powers

S B England

Affiliations

Soon will be listed here.

Abstract

We describe a general strategy for the detection of high-frequency restriction fragment length polymorphisms in the centromeric regions of human chromosomes by molecular analysis of alpha satellite DNA, a diverse family of tandemly repeated DNA located near the centromeres of all human chromosomes. To illustrate this strategy, cloned alpha satellite repeats isolated from two human chromosomes, 17 and X, have been used under high-stringency conditions that take advantage of the chromosome-specific organization of this divergent repeated DNA family. Multiple high-frequency restriction fragment length polymorphisms are described for the centromeric region of both chromosome 17 and X chromosome. Mendelian inheritance of the variants is demonstrated. The X-linked alpha satellite polymorphisms in particular are highly informative and constitute a virtually unique centromeric DNA marker for each X chromosome examined. Since the strategy we describe is a general one, the alpha satellite family of DNA should provide a rich source of molecular variation in the human genome and should contribute to the development of centromere-based genetic linkage maps of human chromosomes.

Citing Articles

Telomere-to-telomere assembly of diploid chromosomes with Verkko.

Rautiainen M, Nurk S, Walenz B, Logsdon G, Porubsky D, Rhie A Nat Biotechnol. 2023; 41(10):1474-1482.

PMID: 36797493 PMC: 10427740. DOI: 10.1038/s41587-023-01662-6.

The Role of Human Centromeric RNA in Chromosome Stability.

Leclerc S, Kitagawa K Front Mol Biosci. 2021; 8:642732.

PMID: 33869284 PMC: 8044762. DOI: 10.3389/fmolb.2021.642732.

Improved contiguity of the threespine stickleback genome using long-read sequencing.

Nath S, Shaw D, White M G3 (Bethesda). 2021; 11(2).

PMID: 33598708 PMC: 8022941. DOI: 10.1093/g3journal/jkab007.

Centromere Repeats: Hidden Gems of the Genome.

Hartley G, ONeill R Genes (Basel). 2019; 10(3).

PMID: 30884847 PMC: 6471113. DOI: 10.3390/genes10030223.

Alpha satellite DNA biology: finding function in the recesses of the genome.

McNulty S, Sullivan B Chromosome Res. 2018; 26(3):115-138.

PMID: 29974361 PMC: 6121732. DOI: 10.1007/s10577-018-9582-3.

References

Smith G . Unequal crossover and the evolution of multigene families. Cold Spring Harb Symp Quant Biol. 1974; 38:507-13. DOI: 10.1101/sqb.1974.038.01.055. View

Devilee P, Slagboom P, Cornelisse C, Pearson P . Sequence heterogeneity within the human alphoid repetitive DNA family. Nucleic Acids Res. 1986; 14(5):2059-73. PMC: 339643. DOI: 10.1093/nar/14.5.2059. View

Southern E . Long range periodicities in mouse satellite DNA. J Mol Biol. 1975; 94(1):51-69. DOI: 10.1016/0022-2836(75)90404-0. View

Jacobs P . Human chromosome heteromorphisms (variants). Prog Med Genet. 1977; 2:251-74. DOI: 10.1016/0378-1119(77)90004-x. View

Manuelidis L . Chromosomal localization of complex and simple repeated human DNAs. Chromosoma. 1978; 66(1):23-32. DOI: 10.1007/BF00285813. View

Manuelidis L, Wu J . Homology between human and simian repeated DNA. Nature. 1978; 276(5683):92-4. DOI: 10.1038/276092a0. View

Jeffreys A . DNA sequence variants in the G gamma-, A gamma-, delta- and beta-globin genes of man. Cell. 1979; 18(1):1-10. DOI: 10.1016/0092-8674(79)90348-9. View

Botstein D, White R, Skolnick M, Davis R . Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 1980; 32(3):314-31. PMC: 1686077. View

MCKUSICK V . The Wilhelmine E. Key 1979 Invitational Lecture: The anatomy of the human genome. J Hered. 1980; 71(6):370-91. DOI: 10.1093/oxfordjournals.jhered.a109392. View

10.

Ruddle F . A new era in mammalian gene mapping: somatic cell genetics and recombinant DNA methodologies. Nature. 1981; 294(5837):115-20. DOI: 10.1038/294115a0. View

11.

Murray J, Davies K, Harper P, Meredith L, Mueller C, Williamson R . Linkage relationship of a cloned DNA sequence on the short arm of the X chromosome to Duchenne muscular dystrophy. Nature. 1982; 300(5887):69-71. DOI: 10.1038/300069a0. View

12.

Yang T, Hansen S, Oishi K, Ryder O, Hamkalo B . Characterization of a cloned repetitive DNA sequence concentrated on the human X chromosome. Proc Natl Acad Sci U S A. 1982; 79(21):6593-7. PMC: 347174. DOI: 10.1073/pnas.79.21.6593. View

13.

Rieder C . The formation, structure, and composition of the mammalian kinetochore and kinetochore fiber. Int Rev Cytol. 1982; 79:1-58. DOI: 10.1016/s0074-7696(08)61672-1. View

14.

Willard H, Smith K, Sutherland J . Isolation and characterization of a major tandem repeat family from the human X chromosome. Nucleic Acids Res. 1983; 11(7):2017-33. PMC: 325859. DOI: 10.1093/nar/11.7.2017. View

15.

Gusella J, Wexler N, Conneally P, Naylor S, Anderson M, Tanzi R . A polymorphic DNA marker genetically linked to Huntington's disease. Nature. 1983; 306(5940):234-8. DOI: 10.1038/306234a0. View

16.

Jabs E, Wolf S, MIGEON B . 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; 81(15):4884-8. PMC: 391596. DOI: 10.1073/pnas.81.15.4884. View

17.

Blackburn E . The molecular structure of centromeres and telomeres. Annu Rev Biochem. 1984; 53:163-94. DOI: 10.1146/annurev.bi.53.070184.001115. View

18.

White R, Leppert M, Bishop D, Barker D, BERKOWITZ J, Brown C . Construction of linkage maps with DNA markers for human chromosomes. Nature. 1985; 313(5998):101-5. DOI: 10.1038/313101a0. View

19.

Gray K, White J, Costanzi C, Gillespie D, Schroeder W, Calabretta B . Recent amplification of an alpha satellite DNA in humans. Nucleic Acids Res. 1985; 13(2):521-35. PMC: 341012. DOI: 10.1093/nar/13.2.521. View

20.

Waye J, Willard H . Chromosome-specific alpha satellite DNA: nucleotide sequence analysis of the 2.0 kilobasepair repeat from the human X chromosome. Nucleic Acids Res. 1985; 13(8):2731-43. PMC: 341190. DOI: 10.1093/nar/13.8.2731. View