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BMC Genomics. 2009; 10: 335.
Published online Jul 24, 2009. doi:  10.1186/1471-2164-10-335
PMCID: PMC2722678
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation
Claire Lemaitre,#1,2,3,4 Lamia Zaghloul,#2,5 Marie-France Sagot,2,3,4 Christian Gautier,2,3,4 Alain Arneodo,2,5 Eric Tannier,corresponding author2,3,4 and Benjamin Auditcorresponding author2,5
1Université de Bordeaux, Centre de Bioinformatique – Génomique Fonctionnelle Bordeaux, F-33000 Bordeaux, France
2Université de Lyon, F-69000 Lyon, France
3Laboratoire Biométrie et Biologie Evolutive, CNRS, Université Lyon 1, F-69100 Villeurbanne, France
4Équipe BAMBOO, INRIA Rhône-Alpes, 655 avenue de l'Europe, F-38330 Montbonnot Saint-Martin, France
5Laboratoire Joliot-Curie et Laboratoire de Physique, CNRS, Ecole Normale Supérieure de Lyon, F-69007 Lyon, France
corresponding authorCorresponding author.
#Contributed equally.
Claire Lemaitre: claire.lemaitre/at/u-bordeaux2.fr; Lamia Zaghloul: lamia.zaghloul/at/ens-lyon.fr; Marie-France Sagot: marie-france.sagot/at/inria.fr; Christian Gautier: cgautier/at/biomserv.univ-lyon1.fr; Alain Arneodo: alain.arneodo/at/ens-lyon.fr; Eric Tannier: eric.tannier/at/inria.fr; Benjamin Audit: benjamin.audit/at/ens-lyon.fr
Received February 26, 2009; Accepted July 24, 2009.
Abstract
Background
The Intergenic Breakage Model, which is the current model of structural genome evolution, considers that evolutionary rearrangement breakages happen with a uniform propensity along the genome but are selected against in genes, their regulatory regions and in-between. However, a growing body of evidence shows that there exists regions along mammalian genomes that present a high susceptibility to breakage. We reconsidered this question taking advantage of a recently published methodology for the precise detection of rearrangement breakpoints based on pairwise genome comparisons.
Results
We applied this methodology between the genome of human and those of five sequenced eutherian mammals which allowed us to delineate evolutionary breakpoint regions along the human genome with a finer resolution (median size 26.6 kb) than obtained before. We investigated the distribution of these breakpoints with respect to genome organisation into domains of different activity. In agreement with the Intergenic Breakage Model, we observed that breakpoints are under-represented in genes. Surprisingly however, the density of breakpoints in small intergenes (1 per Mb) appears significantly higher than in gene deserts (0.1 per Mb).
More generally, we found a heterogeneous distribution of breakpoints that follows the organisation of the genome into isochores (breakpoints are more frequent in GC-rich regions). We then discuss the hypothesis that regions with an enhanced susceptibility to breakage correspond to regions of high transcriptional activity and replication initiation.
Conclusion
We propose a model to describe the heterogeneous distribution of evolutionary breakpoints along human chromosomes that combines natural selection and a mutational bias linked to local open chromatin state.
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