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Primate genome architecture linked with formation mechanisms and functional consequences of structural variation

ABSTRACT: While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, comprising thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques. Non-allelic homologous recombination, linked with genomic architecture, primarily shaped the genomes of great apes resulting in different SV formation mechanism landscapes across species, with distinct functional consequences. Transcriptome analyses across nonhuman primates and humans revealed significant effects of species-specific gene duplications on gene expression, with these effects displaying remarkable diversity in direction and magnitude. Thirteen inter-species gene duplications coincided with the species-specific gain of expression in a new tissue, implicating these duplications in function acquisition.

ORGANISM(S): Pan troglodytes Pongo abelii Macaca mulatta Pongo pygmaeus

PROVIDER: GSE45741 | GEO | 2013/08/10

SECONDARY ACCESSION(S): PRJNA196636

REPOSITORIES: GEO

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Primate genome architecture linked with formation mechanisms and functional consequences of structural variation

Project description:While nucleotide-resolution maps of genomic structural variants (SVs) have provided insights into the origin and impact on phenotypic diversity in humans, comparable maps in nonhuman primates have thus far been lacking. Using massively parallel DNA sequencing we constructed fine-resolution, species-specific structural variation and segmental duplication maps for five chimpanzees, five orang-utans, and five rhesus macaques. The SV maps, comprising thousands of deletions, duplications, and mobile element insertions, revealed a high activity of retrotransposition in macaques. Non-allelic homologous recombination, linked with genomic architecture, primarily shaped the genomes of great apes resulting in different SV formation mechanism landscapes across species, with distinct functional consequences. Transcriptome analyses across nonhuman primates and humans revealed significant effects of species-specific gene duplications on gene expression, with these effects displaying remarkable diversity in direction and magnitude. Thirteen inter-species gene duplications coincided with the species-specific gain of expression in a new tissue, implicating these duplications in function acquisition. Agilent arrays were custom designed for probes to be relatively evenly spaced across the reference genomes of chimpanzee, orang-utan, and rhesus macaque. For each species 9 one million probe arrays were used to cover the autosomes and a single 400k probe array was used for the sex chromosomes.

2013-08-10 | E-GEOD-45741 | biostudies-arrayexpress

Adaptive Structural Variants Contributing to Human Brain Development Revealed by 1,026 Rhesus Macaque Genomes

Project description:Clarifying structural variants (SV) profiles in nonhuman primates could provide insights into the genetic background underlying human-specific traits, but such resources are largely lacking. Here, we report the largest SV atlas generated to date from a population of 1,026 macaques, verified by genome assembly for one of them. This accurate, quantitative map indicates stronger purifying selection on inversions located in regulatory regions, suggesting a strategy for prioritizing those with the most important functions. We then identified 75 human-specific inversions and prioritized them. Notably, the top-ranked inversions have substantially shaped the transcriptome through their dual-effects of reconfiguring the ancestral genomic architecture and introducing regional mutation hotspots. As a proof-of-concept, the overexpression of APCDD1, located on one of these inversions and downregulated during human evolution, significantly accelerated neuronal maturation, while its depletion in mice delays the neuronal maturation and subsequently improved their cognitive ability. This study thus provides a valuable resource to explore human evolution and diseases,and broaden the understanding of the contribution of SVs in shaping the distinct features in human brain development.

2024-04-23 | GSE221928 | GEO

Epigenetics effects of formaldehyde inhalation exposure

Project description:We set out to test the hypothesis that formaldehyde inhalation exposure significantly alters miRNA expression profiles within the nasal epithelium of nonhuman primates. Here, cynomolgus macaques were exposed to 0, 2, and 6 ppm formaldehyde for 6 hours/day across two consecutive days. RNA was extracted from the nasal maxilloturbinate region, a direct target of formaldehyde inhalation exposure. Genome-wide miRNA expression levels were assessed using microarrays. Cynomolgus macaques (Macaca fascicularis) were exposed to 0, 2 and 6 ppm formaldehyde for 6 hours/day across two consecutive days using whole body exposure chambers. RNA was extracted from the nasal maxilloturbinate region, a direct target of formaldehyde inhalation exposure. Genome-wide miRNA expression levels were assessed using microarrays.

2012-09-01 | E-GEOD-34978 | biostudies-arrayexpress

Neutrophil extracellular traps and alveolar barrier disruption contribute to varicella pneumonia pathology

Project description:Varicella pneumonia is the most common and severe complication of primary varicella-zoster virus (VZV) infection in adults. Pathogenesis of varicella pneumonia is largely unknown, mainly due to limited availability of clinical specimens and lack of appropriate VZV animal models. Simian varicella virus (SVV) infection of nonhuman primates closely recapitulates clinical and pathogenic features of human VZV disease. This study aimed to elucidate the virus and host factors that contribute to the pathogenesis of varicella pneumonia. The deposited data present changes in gene expression in the lung of SVV-infected cynomolgus macaques (Macaca fascicularis) at 3, 6 and 9 days after infection, and mock-infected control macaques at 3 days after infection.

2020-09-01 | E-MTAB-8485 | biostudies-arrayexpress

Formaldehyde and Epigenetic Alterations: MicroRNA Changes in the Nasal Epithelium of Nonhuman Primates

2012-09-01 | GSE34978 | GEO

Validation of genomic structural variation predictions in fruit flies

Project description:Whole-genome tiling arrays were used to validate deletions and tandem duplications that were inferred based on next-generation sequencing data. The arrays were generated for six samples of the Drosophila melanogaster Genetic Reference Panel (DGRP) as well as the Berkeley reference strain. Structural variations (SVs) were assessed by comparing probe intensities within the region of interest between the sample for which the SV was predicted and the reference strain.

2012-11-29 | E-MTAB-1105 | biostudies-arrayexpress

Gene expression differences among primates are associated with changes in a histone epigenetic modification

Project description:Changes in gene regulation are thought to play an important role in speciation and adaptation, especially in primates. However, we still know relatively little about the mechanisms underlying regulatory evolution. In particular, the extent to which epigenetic modifications underlie gene expression differences between primates is not yet known. Our study focuses on an epigenetic histone modification, H3K4me3, which is thought to promote transcription. To investigate the contribution of H3K4me3 to regulatory differences between species, we collected gene expression data and identified H3K4me3-associated genomic regions in lymphoblastoid cell lines (LCLs) from humans, chimpanzees, and rhesus macaques, using three cell lines from each species. We found strong evidence for conservation of H3K4me3 localization in primates. Moreover, regardless of species, H3K4me3 is consistently enriched near annotated transcription start sites (TSS), and highly expressed genes are more likely than lowly expressed genes to have the histone modification near their TSS. Interestingly, we observed an enrichment of interspecies differences in H3K4me3 at the TSS of genes that are differentially expressed between species. We estimate that as much as 7% of gene expression differences between the LCLs of humans, chimpanzees, and rhesus macaques may be explained, at least in part, by changes in the status of H3K4me3 histone modifications. Our results suggest a modest, yet important role for epigenetic changes in gene expression differences between primates. Examination of H3K4me3 profiles in lymphoblastoid cell lines (LCLs) from three primate species (human, chimpanzee, and rhesus macaque), using 3 samples from each species, compared to a pooled input control from each species. Expression profiling was also done in the same LCL samples.

2011-02-15 | E-GEOD-24111 | biostudies-arrayexpress

RNA-Seq of baboon kidney cortex biopsies [high sodium diet]

Project description:Blood pressure and the kidney cortex transcriptome response to sodium diet challenge in female nonhuman primates

2022-09-01 | GSE181248 | GEO

Deep transcriptional sequencing of mucosal challenge compartment from rhesus macaques acutely infected with simian immunodeficiency virus implicates loss of cell adhesion preceding immune activation

Project description:Recent studies of nonhuman primates (NHPs) have suggested that during the acute phase of infection, antiviral mucosal immunity is restricting viral replication in the primary infection compartment. These studies imply that HIV achieves systemic infection as a consequence of a failure in host antiviral immunity. Here, we used high-dose intrarectal inoculation of rhesus macaques with SIVmac251 to examine how the mucosal immune system is overcome by SIV during acute infection. The host response in rectal mucosa was characterized by mRNA deep sequencing (mRNA-seq) at 3 and 12 days post inoculation (DPI) in 4 animals for each time point.

2014-04-17 | GSE56845 | GEO

Gene expression differences among primates are associated with changes in a histone epigenetic modification

2011-02-15 | GSE24111 | GEO

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