Megasatellite DNA

Yoichi Gondo, RIKEN Genomic Sciences Center, Yokohama, Japan
Joh‐E Ikeda, Tokai University, Isehara, Japan

Published online: January 2006

DOI: 10.1038/npg.els.0006152

Megasatellite DNA, one of the satellite DNA families, is defined as large, head-to-tail, tandem repetitive sequences. The RS447 megasatellite DNA found on human 4p16.1 consists of 20–100 copies of the 4746-base pair (bp) unit sequence, in which an open reading frame of 1590 bp encodes USP17 (ubiquitin-specific protease 17). The copy number of RS447 is hypervariable and highly polymorphic within as well as among mammalian species; on the other hand, the unit sequences of RS447 within species are extremely homologous.

Keywords: megasatellite DNA; satellite DNA family; tandem repeat; deubiquitinase; genomic instability; polymorphism

Figure 1. Southern-blot analyses of RS447 human megasatellite deoxyribonucleic acid (DNA). (a) Highly homogeneous copies of 4746 base pairs (bp) of RS447 are tandemly repeated on human chromosome 4p15. (b) Restriction enzymes such as BamHI and XbaI, which have no recognition sites in the RS447 sequence, give rise to large restriction fragments. These large restriction fragments are separated on pulsed field gel electrophoresis. (c) By contrast, single-cutter enzymes of RS447 (e.g. EcoRI, EcoRV, BglII and PstI) produce exactly the same size and intensity of the unit length of RS447. These enzymes can be used to demonstrate the head-to-tail tandem structure of the repeats. cM: centimorgan; kb: kilobase.
Figure 2. Peptide homology alignment among USP17 encoded by human RS447 with mouse Dub1 (Zhu et al., 1996) and Dub2 (Zhu et al., 1997). The cysteine (Cys) and histidine (His) domains that are conserved in the deubiquitinase gene family are indicated by critical Cys and His residues (triangles) respectively.
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 References
    Charlesworth B, Sniegowski P and Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371: 215–220.
    Epstein ND, Karlsson S, O'Brien S, et al. (1987) A new moderately repetitive DNA sequence family of novel organization. Nucleic Acids Research 15: 2327–2341.
    Giacalone J, Friedes J and Francke U (1992) A novel GC-rich human macrosatellite VNTR in Xq24 is differently methylated on active and inactive X chromosomes. Nature Genetics 1: 137–143.
    Gondo Y, Okada T, Matsuyama N, et al. (1998) Human megasatellite DNA RS447: copy number polymorphisms and interspecies conservation. Genomics 54: 39–49.
    Kogi M, Fukushige S, Lefevre C, Hadano S and Ikeda JE (1997) A novel tandem repeat sequence located on human chromosome 4p: isolation and characterisation. Genomics 42: 278–283.
    Okada T, Gondo Y, Goto J, et al. (2002) Unstable transmission of the RS447 human megasatellite tandem repetitive sequence that contains the USP17 deubiquitinating enzyme gene. Human Genetics 110: 302–313.
    Saitoh Y, Miyamoto N, Okada T, et al. (2000) The RS447 human megasatellite tandem repetitive sequence encodes a novel deubiquitinating enzyme with a functional promoter. Genomics 67: 291–300.
    Zhu Y, Carroll M, Papa FR, Hochstrasser M and D'Andrea AD (1996) DUB-1, a deubiquitinating enzyme with growth suppressing activity. Proceedings of the National Academy of Sciences of the United States of America 93: 3275–3279.
    Zhu Y, Lambert K, Corless C, et al. (1997) DUB-2 is a member of a novel family of cytokine-inducible deubiquitinating enzymes. Journal of Biological Chemistry 272: 51–57.
 Further Reading
    book Strachan T and Read AP (1999) Organization of the human genome. In: Human Molecular Genetics, 2nd edn, pp. 139–168 Oxford, UK: BIOS Scientific.

Related Sub-Topics:

Nucleic Acid Structure | Gene and Genome Structure and Organisation | Chromosomes and Chromatin Modifications | DNA Structure and Function | Evolution of Coding and Functional Modules
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Article Title: Megasatellite DNA
 
How to Cite close
Gondo, Yoichi, and Ikeda, Joh‐E(Jan 2006) Megasatellite DNA. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0006152]