Molecular evolution of the human chromosome 15 pericentromeric region

Locke, Devin P.; Jiang, Zhaoshi; Pertz, Lisa M.; Misceo, Doriana; Archidiacono, Nicoletta; Eichler, Evan E.

doi:10.1159/000080804

Cited by 21 publications

(18 citation statements)

References 73 publications

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“…Secondary duplications of larger mosaic blocks (termed "pericentromeric swapping" events) occurred subsequently, leading to differential distribution of these blocks among the great-ape and human pericentromeric regions. Detailed analyses of pericentromeric regions (10p11, 10q11, 15q11, 2p11, and 16p11), as well as more global computational analysis, suggest that this is a general principle of human genome evolution (Jackson et al 1999;Guy et al 2000Guy et al , 2003Horvath et al 2000b;Locke et al 2005). Our extended analysis of 2p11 confirms this two-step model (Fig.…”

Section: Discussionsupporting

confidence: 76%

“…In such a scenario, one might expect to find pericentromeric regions with younger or older duplicons depending on differences in the chromatin context in which they emerged. A global analysis of several pericentromeric regions confirms that, in general, younger (<8 Mya) pericentromeric seeding events are a relatively rare occurrence in the human genome (Bailey et al 2002;She et al 2004a;Locke et al 2005). This is not to say that pericentromeric-to-pericentromeric duplications have not continued to occur more recently.…”

Section: Discussionmentioning

confidence: 75%

“…Previous analyses have suggested that pericentromeric regions have been formed via the duplication of euchromatic segments that have colonized pericentromeric DNA over the past 30 Myr of evolution (Eichler et al 1996;Jackson et al 1999;Horvath et al 2000bHorvath et al , 2003Bailey et al 2002;Crosier et al 2002;She et al 2004a;Locke et al 2005). This duplicative transposition of euchromatic segments into pericentromeric regions (which we have termed "pericentromeric seeding") has led to the formation of complex mosaics of segmental duplications consisting of juxtaposed duplicons from diverse euchromatic positions.…”

Section: Discussionmentioning

confidence: 95%

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Punctuated duplication seeding events during the evolution of human chromosome 2p11

et al. 2005

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Primate genomic sequence comparisons are becoming increasingly useful for elucidating the evolutionary history and organization of our own genome. Such studies are particularly informative within human pericentromeric regions-areas of particularly rapid change in genomic structure. Here, we present a systematic analysis of the evolutionary history of one ∼700-kb region of 2p11, including the first autosomal transition from pericentromeric sequence to higher-order ␣-satellite DNA. We show that this region is composed of segmental duplications corresponding to 14 ancestral segments ranging in size from 4 kb to ∼115 kb. These duplicons show 94%-98.5% sequence identity to their ancestral loci. Comparative FISH and phylogenetic analysis indicate that these duplicons are differentially distributed in human, chimpanzee, and gorilla genomes, whereas baboon has a single putative ancestral locus for all but one of the duplications. Our analysis supports a model where duplicative transposition events occurred during a narrow window of evolution after the separation of the human/ape lineage from the Old World monkeys (10-20 million years ago). Although dramatic secondary dispersal events occurred during the radiation of the human, chimpanzee, and gorilla lineages, duplicative transposition seeding events of new material to this particular pericentromeric region abruptly ceased after this time period. The multiplicity of initial duplicative transpositions prior to the separation of humans and great-apes suggests a punctuated model for the formation of highly duplicated pericentromeric regions within the human genome. The data further indicate that factors other than sequence are important determinants for such bursts of duplicative transposition from the euchromatin to pericentromeric regions.

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Section: Discussionsupporting

confidence: 76%

Section: Discussionmentioning

confidence: 75%

Section: Discussionmentioning

confidence: 95%

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Punctuated duplication seeding events during the evolution of human chromosome 2p11

et al. 2005

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“…Indeed, while human and chimpanzee genomes are 98.77% identical within comparable sequences, they show an increased divergence (15%) in the terminal 10 Mbp (millions of base pairs) of chromosomes (The Chimpanzee Sequencing and Analysis Consortium 2005). These highly plastic segments of the human genome show qualitative and quantitative differences in the distribution of segmental duplications when compared with the great apes, consistent with their recent origin and human-specific sequence transfers (Horvath et al 2001;Bailey et al 2002;Horvath et al 2003;Linardopoulou et al 2005;Locke et al 2005). In addition, regions enriched in segmental duplications are more prone to both interspecies and intraspecies structural variation (Newman et al 2005;Sharp et al 2005), since these repeated segments may mediate nonallelic homologous recombination (NAHR) (Hastings et al 2009).…”

supporting

confidence: 55%

“…We assessed the possible association between regions with significantly different epigenetic panorama in humans when compared with other primates (Shulha et al 2012) and genomic segments around loci that were structurally modified during the recent evolution of the human genome, i.e., HSA2 fusion point and ancestral centromere, as well as HSA1 and HSA18 inversion breakpoints (Yunis et al 1980;Dennehey et al 2004;Szamalek et al 2006), with HSA1 also encompassing pericentromeric heterochromatin that is absent in its chimpanzee homolog (Yunis et al 1980). Additionally, we assessed highly plastic segments such as human-specific segmental duplications (Sudmant et al 2013) together with subtelomeric and pericentromeric regions (Yunis et al 1980;Bailey et al 2001;Bailey et al 2002;Horvath et al 2003;The Chimpanzee Sequencing and Analysis Consortium 2005;Linardopoulou et al 2005;Locke et al 2005).…”

Section: Resultsmentioning

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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Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons

Kehrer‐Sawatzki¹,

Cooper²

2007

Hum. Mutat.

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The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome.

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Molecular evolution of the human chromosome 15 pericentromeric region

Cited by 21 publications

References 73 publications

Punctuated duplication seeding events during the evolution of human chromosome 2p11

Punctuated duplication seeding events during the evolution of human chromosome 2p11

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

Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons

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