Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes

Marta Farré,Francesc López-Giráldez,Aurora Ruiz-Herrera,Montserrat Bosch,Montserrat Ponsà

doi:10.1371/journal.pone.0027239

Marta Farré, Francesc López-Giráldez + Show 3 more

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https://doi.org/10.1371/journal.pone.0027239

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Journal: PloS one	Publication Date: Nov 4, 2011
Citations: 94	License type: CC BY 4.0

Affiliation: Autonomous University of Barcelona, Yale University

Abstract

BackgroundAncestral reconstructions of mammalian genomes have revealed that evolutionary breakpoint regions are clustered in regions that are more prone to break and reorganize. What is still unclear to evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal.Methodology and Principal FindingsHere we present a comprehensive study of the distribution of tandem repeats in great apes. We analyzed the distribution of tandem repeats in relation to the localization of evolutionary breakpoint regions in the human, chimpanzee, orangutan and macaque genomes. We observed an accumulation of tandem repeats in the genomic regions implicated in chromosomal reorganizations. In the case of the human genome our analyses revealed that evolutionary breakpoint regions contained more base pairs implicated in tandem repeats compared to synteny blocks, being the AAAT motif the most frequently involved in evolutionary regions. We found that those AAAT repeats located in evolutionary regions were preferentially associated with Alu elements.SignificanceOur observations provide evidence for the role of tandem repeats in shaping mammalian genome architecture. We hypothesize that an accumulation of specific tandem repeats in evolutionary regions can promote genome instability by altering the state of the chromatin conformation or by promoting the insertion of transposable elements.

Highlights

Since the earliest cytogenetic studies, evolutionary biologists have sought to understand how mammalian genomes are organized
Different approaches have been developed in order to define homologous synteny blocks (HSBs; i.e. regions where the gene order has been conserved among species) and evolutionary breakpoint regions (EBRs; i.e. regions where the synteny has been disrupted by chromosomal reorganizations) among mammalian genomes
HSBs represented more than 70% of the human genome, reaching 91.88% for the human/orangutan comparison (Table 1), reflecting the high conservation of mammalian genomes

Summary

Introduction

Since the earliest cytogenetic studies, evolutionary biologists have sought to understand how mammalian genomes are organized. Advances in molecular cytogenetic techniques, such as cross-species in situ hybridization, increased the level of resolution for defining orthologous regions as well as the number of species studied [3]. The integration of cross-species chromosome painting studies performed in more than 100 mammalian species [4,5] has revealed that evolutionary breakpoints (i.e., the disruption of two orthologous chromosomal segments) are not homogeneously distributed but rather concentrated in certain regions across the human genome. Different approaches have been developed in order to define homologous synteny blocks (HSBs; i.e. regions where the gene order has been conserved among species) and evolutionary breakpoint regions (EBRs; i.e. regions where the synteny has been disrupted by chromosomal reorganizations) among mammalian genomes. What is still unclear to evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal

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