Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Unexpected Properties of Short Genomic Tandem Repeats

Irina Glotova, Michael Molla, Arthur L. Delcher, Simon Kasif
doi: https://doi.org/10.1101/165308
Irina Glotova
Bioinformatics Program, Boston University, Boston, Massachusetts, 02215, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Michael Molla
Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, Massachusetts, 02215, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Arthur L. Delcher
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simon Kasif
Department of Biomedical Engineering, Boston University, Boston, 02215, USABoston Children’s Hospital, Boston, 02115, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Length polymorphisms in genomic short tandem repeats have been implicated in a variety of diseases, most notably human neurodegenerative disorders. Expansions of tandem repeats are also associated with genomic instability in cancer. Our previous study of length-3 tandem repeats uncovered a surprising pattern in the length distribution of certain such repeats in the non-coding regions of the human reference genome: a bias towards repeats of length 3n - 1, (n > 3). That is, the observed frequency of repeats of this length in the human genome is higher than expected by chance based on the frequency of shorter repeats.

We have hypothesized that this pattern may be a general property of genomic DNA. If true, this could have implications with regard to the dynamics of repeat expansion generally. To test this hypothesis, we have analyzed the genomic sequences of a broad range of eukaryotic organisms as well as several complete human genomes and obtained a number of thought provoking results. We establish that this unexpected elevation in frequency of 3n - 1 long repeats is statistically significant. We also expanded this analysis to different classes of genomic regions and tandem repeats of length four and five. The specific pattern was found in 13 of the 20 organisms analyzed, including all chordate and insect genomes tested. The bias pattern, however, was not confined to a single branch of the evolutionary tree. For some genomes, such as Drosophila melanogaster, the repeat bias surprisingly was also identified in exons. The pattern is present in both small and large genomes. A similar pattern was also found in tetranucleotide and pentanucleotide repeats in the human genome. Another surprising property was identified for the flanking GC content for triplet repeats of length 3n. These findings indicate a puzzling new genomic phenomenon with possible evolutionary and disease-related implications.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted July 18, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Unexpected Properties of Short Genomic Tandem Repeats
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
Share
Unexpected Properties of Short Genomic Tandem Repeats
Irina Glotova, Michael Molla, Arthur L. Delcher, Simon Kasif
bioRxiv 165308; doi: https://doi.org/10.1101/165308
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Unexpected Properties of Short Genomic Tandem Repeats
Irina Glotova, Michael Molla, Arthur L. Delcher, Simon Kasif
bioRxiv 165308; doi: https://doi.org/10.1101/165308

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (1519)
  • Biochemistry (2472)
  • Bioengineering (1726)
  • Bioinformatics (9647)
  • Biophysics (3881)
  • Cancer Biology (2960)
  • Cell Biology (4173)
  • Clinical Trials (135)
  • Developmental Biology (2620)
  • Ecology (4083)
  • Epidemiology (2031)
  • Evolutionary Biology (6867)
  • Genetics (5195)
  • Genomics (6482)
  • Immunology (2176)
  • Microbiology (6908)
  • Molecular Biology (2746)
  • Neuroscience (17196)
  • Paleontology (125)
  • Pathology (425)
  • Pharmacology and Toxicology (703)
  • Physiology (1050)
  • Plant Biology (2478)
  • Scientific Communication and Education (642)
  • Synthetic Biology (826)
  • Systems Biology (2680)
  • Zoology (429)