On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees

Marquès‐Bonet, Tomàs; Sànchez-Ruiz, Jesús; Armengol, Lluı́s; Khaja, Razi; Bertranpetit, Jaume; López‐Bigas, Núria; Rocchi, Mariano; Gazave, Élodie; Navarro, Arcadi

doi:10.1186/gb-2007-8-10-r230

Cited by 24 publications

(27 citation statements)

References 196 publications

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“…However, this was not the case. On the contrary, in some of the inverted regions, a lower degree of divergence has been observed (Lu et al 2003, Zhang et al 2004, Vallender & Lahn 2004, Mikkelsen et al 2005, Szamalek et al 2007, Marques-Bonet et al 2007). …”

Section: Large Pericentric Inversionsmentioning

confidence: 85%

Molecular mechanisms of chromosomal rearrangement during primate evolution

Kehrer‐Sawatzki

Cooper

2008

Chromosome Res

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Breakpoint analysis of the large chromosomal rearrangements which have occurred during primate evolution promises to yield new insights into the underlying mechanisms of mutagenesis. Comparison of these evolutionary breakpoints with those that are disease-associated in humans, and which occur during either meiotic or mitotic cell division, should help to identify basic mechanistic similarities as well as differences. It has recently become clear that segmental duplications (SDs) have had a very significant impact on genome plasticity during primate evolution. In comparisons of the human and chimpanzee genomes, SDs have been found in flanking regions of 70-80% of inversions and approximately 40% of deletions/duplications. A strong spatial association between primate-specific breakpoints and SDs has also become evident from comparisons of human with other mammalian genomes. The lineage-specific hyperexpansion of certain SDs observed in the genomes of human, chimpanzee, gorilla and gibbon is indicative of the intrinsic instability of some SDs in primates. However, since many primate-specific breakpoints map to regions lacking SDs, but containing interspersed high-copy repetitive sequence elements such as SINEs, LINEs, LTRs, alpha-satellites and (AT)( n ) repeats, we may infer that a range of different molecular mechanisms have probably been involved in promoting chromosomal breakage during the evolution of primate genomes.

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Section: Large Pericentric Inversionsmentioning

confidence: 85%

Molecular mechanisms of chromosomal rearrangement during primate evolution

Kehrer‐Sawatzki

Cooper

2008

Chromosome Res

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“…In recent years, intermediate-scale mutations (e.g., insertion, deletion, translocation, and inversion) that result in structural variation have gained considerable attention (1). Although the genome-wide impact of mutations of different sizes (e.g., single-nucleotide changes and structural alterations such as insertion or deletion of genetic material) has been investigated separately, it has long been speculated (2,3), and increasing evidence suggests, that mutations of different sizes are correlated in prokaryotes and eukaryotes (4)(5)(6)(7)(8)(9)(10)(11)(12)(13). Although these studies have provided evidence for such a relationship, how this phenomenon affects functional elements in the genome has not been systematically investigated in humans.…”

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confidence: 99%

A time-invariant principle of genome evolution

Babu

2010

Proc. Natl. Acad. Sci. U.S.A.

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Uncovering general principles of genome evolution that are timeinvariant and that operate in germ and somatic cells has implications for genome-wide association studies (GWAS), gene therapy, and disease genomics. Here we investigate the relationship between structural alterations (e.g., insertions and deletions) and singlenucleotide substitutions by comparing the following genomes that diverged at different times across germ-and somatic-cell lineages: (i) the reference human and chimpanzee genome (in million years), (ii) the reference human and personal genomes (in tens of thousands of years), and (iii) structurally altered regions in cancer and genetically engineered cells (in days). At the species level, genes with structural alteration in nearby regions show increased singlenucleotide changes and tend to evolve faster. In personal genomes, the single-nucleotide substitution rate is higher near sites of structural alteration and decreases with increasing distance. In human cancer cell populations and in cells genetically engineered using zinc-finger nucleases, single-nucleotide changes occur frequently near sites of structural alterations. We present evidence that structural alteration induces single-nucleotide changes in nearby regions and discuss possible molecular mechanisms that contribute to this phenomenon. We propose that the low fidelity of nonreplicative error-prone repair polymerases, which are used during insertion or deletion, result in break-repair-induced single-nucleotide mutations in the vicinity of structural alteration. Thus, in the mutational landscape, structural alterations are linked to single-nucleotide changes across different time scales in both somatic-and germ-cell lineages. We discuss implications for genome evolution, GWAS, disease genomics, and gene therapy and emphasize the need to investigate both types of mutations within a single framework.single-nucleotide substitution | structural alteration | mutation | DNA repair U nderstanding how mutations contribute to genetic variation in a population and drive the evolution of new species is a fundamental problem in the postgenomic era. In recent years, intermediate-scale mutations (e.g., insertion, deletion, translocation, and inversion) that result in structural variation have gained considerable attention (1). Although the genome-wide impact of mutations of different sizes (e.g., single-nucleotide changes and structural alterations such as insertion or deletion of genetic material) has been investigated separately, it has long been speculated (2, 3), and increasing evidence suggests, that mutations of different sizes are correlated in prokaryotes and eukaryotes (4-13). Although these studies have provided evidence for such a relationship, how this phenomenon affects functional elements in the genome has not been systematically investigated in humans. Specifically, the implications for sequence (protein and nucleic acid) evolution and the nature of such dependence in genomes that "diverged" at different time scales, i.e., at the tim...

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“…Indeed the hypothesis that they affected the rate of genetic divergence between humans and chimpanzees does not have enough support (Kehrer-Sawatzki and Cooper 2007). Previous studies revealed no evidence of accelerated evolution for genes on rearranged versus colinear chromosomes (Lu et al 2003;Navarro and Barton 2003;Vallender and Lahn 2004;Zhang et al 2004;The Chimpanzee Sequencing and Analysis Consortium 2005;Marques-Bonet et al 2007) and showed that chromosomal rearrangements have generally no impact on gene expression except in a few particular cases (Munoz and Sankoff 2012). However, chromosomal rearrangements appear to be associated with higher divergence in gene-expression levels in the brain (Marques-Bonet et al 2004) and genes located on rearranged chromosomes showed reduced recombination rate compared with colinear ones (Farre et al 2013).…”

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confidence: 99%

Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures

2014

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Human and chimpanzee genomes are 98.8% identical within comparable sequences. However, they differ structurally in nine pericentric inversions, one fusion that originated human chromosome 2, and content and localization of heterochromatin and lineage-specific segmental duplications. The possible functional consequences of these cytogenetic and structural differences are not fully understood and their possible involvement in speciation remains unclear. We show that subtelomeric regions-regions that have a species-specific organization, are more divergent in sequence, and are enriched in genes and recombination hotspots-are significantly enriched for species-specific histone modifications that decorate transcription start sites in different tissues in both human and chimpanzee. The human lineage-specific chromosome 2 fusion point and ancestral centromere locus as well as chromosome 1 and 18 pericentric inversion breakpoints showed enrichment of human-specific H3K4me3 peaks in the prefrontal cortex. Our results reveal an association between plastic regions and potential novel regulatory elements.

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On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees

Cited by 24 publications

References 196 publications

Molecular mechanisms of chromosomal rearrangement during primate evolution

Molecular mechanisms of chromosomal rearrangement during primate evolution

A time-invariant principle of genome evolution

Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures

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