Skip to main content

Repetitive DNA

Detection, Annotation, and Analysis

  • Chapter
Introduction to Bioinformatics
  • 1012 Accesses

Abstract

Eukaryotic genomes are composed primarily of nonprotein-coding DNA. The most actively studied portion of this DNA is called repetitive DNA, which is produced in multiple copies by a variety of mechanisms. Repetitive DNA represents the most recent addition to nonprotein coding DNA and is expected to hold important clues to the origin and evolution of genomic DNA. There are good reasons to believe that contemporary mechanisms underlying the origin and evolution of repetitive DNA are essentially the same as mechanisms that generated other nonprotein-coding sequences in the distant past.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Suggested Readings

Introduction

  • Andersson, G., Svensson, A. C., Setterblad, N., and Rask, L. (1998) Retroelements in the human MHC class II region, Trends Genet. 14, 109–114.

    Article  PubMed  CAS  Google Scholar 

  • Hartl, D. L. (2000) Molecular melodies in high and low C, Nature Genet. Rev. 1, 145–149.

    Article  CAS  Google Scholar 

  • Jabbari, K. and Bernardi, G. (1998) CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families, Gene 224, 123–128.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. (1990) Novel families of interspersed repetitive DNA sequences from the human genome Nucleic Acids Res 18 137–141

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. (1998) Repeats in genomic DNA: mining and meaning, Curr. Opin. Struct. Biol. 8, 333–337.

    Article  PubMed  CAS  Google Scholar 

  • Lander, E. S., Linton, L. M., Birren, B., et al. (2001) Initial sequencing and analysis of the human genome, Nature 409, 860–921.

    Article  PubMed  CAS  Google Scholar 

  • Sherry, S. T., Harpending, H. C., Batzer, M. A., and Stoneking, M. (1997) Alu evolution in human populations: using the coalescent to estimate effective population size, Genetics 147, 1977–1982.

    PubMed  CAS  Google Scholar 

  • Shimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., et al. (1997) Molecular evidence from retroposons that whales form a clade within even-toed ungulates, Nature 388, 666–670.

    Article  PubMed  CAS  Google Scholar 

  • Surzycki, S. A. and Belknap, W. R. (1999) Characterization of repetitive DNA elements in Arabidopsis, J. Mol. Evol. 48, 684–691.

    Article  PubMed  CAS  Google Scholar 

Simple Sequence Repeats (SSRs)

  • Hancock, J. M. (1995) The contribution of slippage-like processes to genome evolution, J. Mol. Evol. 41, 1038–1047.

    Article  PubMed  CAS  Google Scholar 

  • Jeffreys, A. J., Barber, R., Bois, P., Buard, J., Dubrova, Y. E., Grant, G., et al. (1999) Human minisatellites, repeat DNA instability and meiotic recombination, Electrophoresis 20, 1665–1675.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. (1995a) Human Repetitive Elements, in: Molecular Biology and Biotechnology. A Comprehensive Desk Reference, (Meyers, R. A., ed.), VCH Publishers Inc., New York, NY, pp. 438–441.

    Google Scholar 

  • Jurka, J. (1998) Repeats in genomic DNA: mining and meaning, Curr. Opin. Struct. Biol. 8, 333–337.

    Article  PubMed  CAS  Google Scholar 

  • Kashi, Y., King, D., and Soller, M. (1997) Simple sequence repeats as a source of quantitative genetic variation, Trends Genet. 13, 74–78.

    Article  PubMed  CAS  Google Scholar 

  • Kidwell, M. G. and Lisch, D. R. (2001) Perspective: transposable elements, parasitic DNA, and genome evolution, Evolution Int. J. Org. Evolution 55, 1–24.

    CAS  Google Scholar 

  • Toth, G., Gaspari, Z., and Jurka, J. (2000) Microsatellites in different eukaryotic genomes: survey and analysis, Genome Res. 10, 967–981.

    Article  PubMed  CAS  Google Scholar 

  • Weber, J. L. and May, P. E. (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction, Am. J. Hum. Genet. 44, 388–396.

    PubMed  CAS  Google Scholar 

  • Transposable Elements (TEs) Jurka, J. (1995a) Human Repetitive Elements, in: Molecular Biology and Biotechnology. A Comprehensive Desk Reference, (Meyers, R. A., ed.), VCH Publishers Inc., New York, NY, pp. 438–441.

    Google Scholar 

  • Jurka, J. (1995b) Origin and evolution of Alu repetitive elements, in: The Impact of Short Interspersed Elements (SINEs) on the Host Genome, (Maraia, R. J., ed.), R. G. Landes Company, Austin, TX, pp. 25–41.

    Google Scholar 

  • Jurka, J. (1997) Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons, Proc. Natl. Acad. Sci. USA 94, 1872–1877.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. and Kapitonov, V. V. (1999) Sectorial mutagenesis by transposable elements, Genetica 107, 239–248.

    Article  PubMed  CAS  Google Scholar 

Reference Collections of Repeats

  • Jurka, J. (1990) Novel families of interspersed repetitive DNA sequences from the human genome, Nucleic Acids Res. 18, 137–141.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J., Walichiewicz, J., and Milosavljevic, A. (1992) Prototypic sequences for human repetitive DNA, J. Mol. Evol. 35, 286–291.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J., Kaplan, D. J., Duncan, C. H., Walichiewicz, J., Milosavljevic, A., Murali, G., and Solus, J. F. (1993) Identification and characterization of new human medium reiteration frequency repeats, Nucleic Acids Res. 21, 1273–1279.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. (2000) Repbase Update: a database and an electronic journal of repetitive elements, Trends Genet. 16, 418–420.

    Article  PubMed  CAS  Google Scholar 

  • Kaplan, D. J. and Duncan, C. H. (1990) Novel short interspersed repeat in human DNA, Nucleic Acids Res. 18, 192.

    Article  PubMed  CAS  Google Scholar 

  • Kaplan, D. J., Jurka, J., Solus, S. F., and Duncan, C. H. (1991) Medium reiteration frequency repetitive sequences in the human genome, Nucleic Acids Res. 19, 4731–4738.

    Article  PubMed  CAS  Google Scholar 

  • Smit, A. F. (1993) Identification of a new, abundant superfamily of mammalian LTRtransposons, Nucleic Acids Res. 21, 1863–1872.

    Article  PubMed  CAS  Google Scholar 

  • Smit, A. F., Toth, G., Riggs, A. D., and Jurka, J. (1995) Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences, J. Mol. Biol. 246, 401–417.

    Article  PubMed  CAS  Google Scholar 

Annotations Based on Repbase Update

  • Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., et al. (2001) Initial sequencing and analysis of the human genome, Nature 409, 860–921.

    Article  PubMed  CAS  Google Scholar 

Nomenclature

  • Iris, F., Bougueleret, L., Prieur, S., Caterina, D., Primas, G., Perrot, V., et al. (1993) Dense Alu clustering and a potential new member of the NFkappaB family within a 90 kilobase HLA class III segment, Nature Genet. 3, 137–145.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. (1990) Novel families of interspersed repetitive DNA sequences from the human genome, Nucleic Acids Res. 18, 137–141.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J., Kaplan, D. J., Duncan, C. H., Walichiewicz, J., Milosavljevic, A., Murali, G., and Solus, J. F. (1993) Identification and characterization of new human medium reiteration frequency repeats, Nucleic Acids Res. 21, 1273–1279.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J., Kapitonov, V. V., and Smit, A. F. A. (2003) Repetitive DNA, detection of, in: Encyclopedia of the Human Genome, (Cooper, D. N., ed.) Nature Publishing Group, New York, NY.

    Google Scholar 

  • Kaplan, D. J. and Duncan, C. H. (1990) Novel short interspersed repeat in human DNA, Nucleic Acids Res. 18, 192.

    Article  PubMed  CAS  Google Scholar 

  • Kaplan, D. J., Jurka, J., Solus, S. F., and Duncan, C. H. (1991) Medium reiteration frequency repetitive sequences in the human genome, Nucleic Acids Res. 19, 4731–4738.

    Article  PubMed  CAS  Google Scholar 

  • Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., et al. (2001) Initial sequencing and analysis of the human genome, Nature 409, 860–921.

    Article  PubMed  CAS  Google Scholar 

  • Smit, A. F. A. and Riggs, A-.D. (1996) Tiggers and other DNA transposon fossils in the human genome, Proc. Natl. Acad. Sci. USA 93, 1443–1448.

    Article  PubMed  CAS  Google Scholar 

Analysis of Repetitive DNA Identification and Annotation of Known Repeats

  • Bedell, J. A., Korf, I., and Gish, W. (2000) MaskerAid: a performance enhancement to RepeatMasker, Bioinformatics 16, 1040–1041.

    Article  PubMed  CAS  Google Scholar 

  • Claverie, J. M. (1994) Large scale sequence analysis, in: Automated DNA Sequencing and Analysis, (Adams, M. D., Fields, C., and Venter, J. C., eds.), Academic Press, San Diego, CA, pp. 267–279.

    Google Scholar 

  • Karlin, S. and Altschul, S. F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes, Proc. Natl. Acad. Sci. USA 87, 2264–2268.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. and Milosavljevic, A. (1991) Reconstruction and analysis of human Alu genes, J. Mol. Evol. 32, 105–121.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J., Walichiewicz, J., and Milosavljevic, A. (1992) Prototypic sequences for human repetitive DNA, J. Mol. Evol. 35, 286–291.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. (1994) Approaches to identification and analysis of interspersed repetitive DNA sequences, in: Automated DNA Sequencing and Analysis (Adams, M. D., Fields, C., and Venter, J. C., eds.), Academic Press, San Diego, CA, pp. 294–298.

    Google Scholar 

  • Jurka, J. and Pethiyagoda, C. (1995) Simple repetitive DNA sequences from primates: compilation and analysis, J. Mol.Evol. 40, 120–126.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J., Klonowski, P., Dagman, V., and Pelton, P. (1996) CENSOR-a program for identification and elimination of repetitive elements from DNA sequences, Comput. Chem. 20, 119–121.

    Article  PubMed  CAS  Google Scholar 

  • Milosavljevic, A. and Jurka, J. (1993) Discovering simple DNA sequences by the algorithmic significance method, Comput. Applic. Biosci. 9, 407–411.

    CAS  Google Scholar 

  • Milosavljevic, A. (1998) Repeat analysis, in: ICRF Handbook of Genome Analysis, vol. 2, (Spurr, N. K., Young, B. D., and Bryant, S. P., eds.), Blackwell Science Inc., Malden, MA, pp. 617–628.

    Google Scholar 

  • Pearson, W. R. and Lipman, D. J. (1988) Improved tools for biological sequence comparison, Proc. Natl.Acad. Sci. USA 85, 2444–2448.

    Article  PubMed  CAS  Google Scholar 

  • Silva, R. and Burch, J. B. (1987) Evidence that chicken CR1 elements represent a novel family of retroposons, Mol. Cell. Biol. 9, 3563–3566.

    Google Scholar 

  • Smith, T. F. and Waterman, M. S. (1981) Identification of common molecular subsequences, J. Mol. Biol. 147, 195–197.

    Article  PubMed  CAS  Google Scholar 

  • Wootton, J. C. and Federhen, S. (1996) Analysis of compositionally biased regions in sequence databases, Meth. Enzymol. 266, 554–571.

    Article  PubMed  CAS  Google Scholar 

Analysis of Repetitive DNA Identification, Reconstruction and Classification of New TEs

  • Bao, Z. and Eddy, S. R. (2002) Automated de novo identification of repeat sequence families in sequenced genomes, Genome Res. 12, 1269–1276.

    Article  PubMed  CAS  Google Scholar 

  • Faulkner, D. V. and Jurka, J. (1988) Multiple Aligned Sequence Editor (MASE), Trends Biochem. Sci 13, 321–322.

    Article  PubMed  CAS  Google Scholar 

  • Galtier, N., Gouy, M., and Gautier, C. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny, Comp. Appl. Biosci. 12, 543–548.

    PubMed  CAS  Google Scholar 

  • Ivics, Z., Hackett, P. B., Plasterk, R. H., and Izsvak, Z. (1997) Molecular reconstruction of Sleeping Beauty, a Tcl-like transposon from fish, and its transposition in human cells, Cell 91, 501–510.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. and Milosavljevic, A. (1991) Reconstruction and analysis of human Alu genes, J. Mol. Evol. 32, 105–121.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. (1994) Approaches to identification and analysis of interspersed repetitive DNA sequences, in: Automated DNA Sequencing and Analysis (Adams, M. D., Fields, C. and Venter, J. C., eds.), Academic Press, San Diego, CA, pp. 294–298.

    Google Scholar 

  • Jurka, J. (1998) Repeats in genomic DNA: mining and meaning, Curr. Opin. Struct. Biol. 8, 333–337.

    Article  PubMed  CAS  Google Scholar 

  • Jurka, J. and Smith, T. (1988) A fundamental division in the Alu family of repeated sequences, Proc. Natl. Acad. Sci. USA 85, 4775–4778.

    Article  PubMed  CAS  Google Scholar 

  • Kapitonov, V. V. and Jurka, J. (2001) Rolling-circle transposons in eukaryotes, Proc. Natl. Acad. Sci. USA 98, 8714–8719.

    Article  PubMed  CAS  Google Scholar 

  • Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res. 22, 4673–4680.

    Article  PubMed  CAS  Google Scholar 

Download references

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer Science+Business Media New York

About this chapter

Cite this chapter

Jurka, J. (2003). Repetitive DNA. In: Krawetz, S.A., Womble, D.D. (eds) Introduction to Bioinformatics. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59259-335-4_8

Download citation

  • DOI: https://doi.org/10.1007/978-1-59259-335-4_8

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-58829-241-4

  • Online ISBN: 978-1-59259-335-4

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics