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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Alu pair exclusions in the human genome.

George W Cook1, Miriam K Konkel, James D Major

  • 1Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803, USA. mbatzer@lsu.edu.

Mobile DNA
|September 28, 2011
PubMed
Summary

Direct pairs of Alu elements are more common than inverted pairs within 350,000 base pairs in the human genome. This imbalance might contribute to genomic instability.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Human Genetics

Background:

  • Alu elements constitute over 10% of human DNA.
  • Previous studies noted an imbalance in Alu pair orientations (direct vs. inverted) for short distances.

Purpose of the Study:

  • To comprehensively analyze the ratio of inverted to direct Alu pairs across the entire human genome.
  • To investigate if the previously observed imbalance extends to larger genomic distances.

Main Methods:

  • Genome-wide analysis of over 800,000 full-length Alu elements.
  • Statistical analysis of the inverted to direct (I:D) Alu pair ratio.
  • Polymerase Chain Reaction (PCR) to verify Alu pair exclusions.

Main Results:

  • A significant depression in the I:D ratio was observed for Alu pairs separated by up to 350,000 base pairs.
  • Direct Alu pairs significantly outnumber inverted pairs within this 350,000 bp 'imbalance bubble'.
  • Experimental verification confirmed deletions causing inverted Alu pair exclusions.

Conclusions:

  • Over 50 million full-length Alu pairs exist within this imbalance region.
  • The collective effect of these Alu pairs may be a previously uncharacterized source of genomic instability.