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Characterization and potential functional significance of human-chimpanzee large INDEL variation

Nalini Polavarapu2, Gaurav Arora1, Vinay K Mittal1 and John F McDonald1*

Author Affiliations

1 Parker H Petit Institute for Bioengineering & Bioscience, School of Biology, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA 30332, USA

2 Monsanto Co, 800 North Lindberg Boulevard, St Louis, MO 63146, USA

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Mobile DNA 2011, 2:13  doi:10.1186/1759-8753-2-13

Published: 25 October 2011



Although humans and chimpanzees have accumulated significant differences in a number of phenotypic traits since diverging from a common ancestor about six million years ago, their genomes are more than 98.5% identical at protein-coding loci. This modest degree of nucleotide divergence is not sufficient to explain the extensive phenotypic differences between the two species. It has been hypothesized that the genetic basis of the phenotypic differences lies at the level of gene regulation and is associated with the extensive insertion and deletion (INDEL) variation between the two species. To test the hypothesis that large INDELs (80 to 12,000 bp) may have contributed significantly to differences in gene regulation between the two species, we categorized human-chimpanzee INDEL variation mapping in or around genes and determined whether this variation is significantly correlated with previously determined differences in gene expression.


Extensive, large INDEL variation exists between the human and chimpanzee genomes. This variation is primarily attributable to retrotransposon insertions within the human lineage. There is a significant correlation between differences in gene expression and large human-chimpanzee INDEL variation mapping in genes or in proximity to them.


The results presented herein are consistent with the hypothesis that large INDELs, particularly those associated with retrotransposons, have played a significant role in human-chimpanzee regulatory evolution.

insertion and deletion; differential gene expression; retrotransposon; noninterspersed sequence; human insertion; short interspersed nuclear element