ArticleBMC genomics2009
Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organisation.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 63 citations in OpenAlex.
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- Random, fragile, or correlated: Mechanisms of synteny decay in mammals.bioRxiv : the preprint server for biology · 2025Article
- Evolution of the ancestral mammalian karyotype and syntenic regions.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness.Genome research · 2022Article
- A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals.GigaScience · 2021Article
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- Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.Genome research · 2018Article
- Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats.BMC genomics · 2017Article
- Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies.Frontiers in genetics · 2017Article
- Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia.Genome biology and evolution · 2016Article
- Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation.Genome biology and evolution · 2016Article
- Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process.Journal of mathematical biology · 2016Article
- Embryonic stem cell specific "master" replication origins at the heart of the loss of pluripotency.PLoS computational biology · 2015Article
- Chromosome Architecture and Genome Organization.PloS one · 2015Article
- Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions.BMC genomics · 2014Article
- Genetic and epigenetic determinants mediate proneness of oncogene breakpoint sites for involvement in TCR translocations.Genes and immunity · 2014Article
- Review
- Human genome replication proceeds through four chromatin states.PLoS computational biology · 2013Article
- Linking the DNA strand asymmetry to the spatio-temporal replication program: II. Accounting for neighbor-dependent substitution rates.The European physical journal. E, Soft matter · 2012Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsWe 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.
conclusionWe 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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