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Genome-wide inter-primate comparison of gene expression profiles in multiple tissues

ABSTRACT: Regulatory changes have long been hypothesized to play an important role in primate evolution. To identify adaptive regulatory changes in humans, we performed a genome-wide survey for genes whose regulation evolves under natural selection. To do so, we used a novel multi-species microarray to measure gene expression levels in livers, kidneys, and hearts from six humans, chimpanzees, and rhesus macaques.

ORGANISM(S): Pan troglodytes Homo sapiens Macaca mulatta

PROVIDER: GSE11560 | GEO | 2008/09/17

SECONDARY ACCESSION(S): PRJNA106295

REPOSITORIES: GEO

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Genome-wide inter-primate comparison of gene expression profiles in multiple tissues

Project description:Regulatory changes have long been hypothesized to play an important role in primate evolution. To identify adaptive regulatory changes in humans, we performed a genome-wide survey for genes whose regulation evolves under natural selection. To do so, we used a novel multi-species microarray to measure gene expression levels in livers, kidneys, and hearts from six humans, chimpanzees, and rhesus macaques. Using the multi-species microarray, we compared gene expression levels within and between species in three tissues: Livers, Kidneys (cortex) and Heart muscle. For each tissue, we hybridized RNA samples from 6 individuals from each of the three species, and preformed two technical replicates for each sample. The total number of arrays analyzed is therefore 108 (= 3 species X 3 tissues X 6 individuals X 2 technical replicates). Following hybridization, washing, and scanning, raw data was extracted from the images using the NimbleScan software (version 2.4). We performed background correction using the normexp function in limma with an offset of 32, and normalization using an adaptation of the quantile normalization approach.

2008-09-17 | E-GEOD-11560 | biostudies-arrayexpress

Quantification of gene expression from primate tissue samples

Project description:We have quantified gene expression in five tissues (brain, heart, kidney, liver and testis) from humans, chimpanzees and rhesus macaques using the Illumina NlaIII Digital Gene Expression (DGE) protocol. This dataset extends a previous microarray study by Khaitovich et al. (Khaitovich et al. 2005) with the rhesus macaque outgroup and complements other previously generated tissue transcriptome profiles from primates (Enard et al. 2002; Khaitovich et al. 2006; Somel et al. 2009; Babbitt et al. 2010; Blekhman et al. 2010; Wetterbom et al. 2010). contributor: Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany Samples were obtained from brain (pre-frontal cortex), heart, kidney, liver, and testis tissues of male humans, chimpanzees and rhesus macaques. Illumina NlaIII DGE libraries for all samples were generated in tissue batches, randomizing species in library preparation and sequencing. Human samples originate from different, probably unrelated, individuals for each tissue. For chimpanzees and rhesus macaques the libraries for all tissues come from the same set of individuals and among these are individuals related at the half- and full-sibling level. Due to limited access to samples, the analysis could not be limited to individuals of similar age. Human individuals vary between 5 and 88 years of age, chimpanzees between 6 years and 35 years of age and rhesus macaques between 3 and 9 years of age.

2013-10-01 | E-GEOD-50782 | biostudies-arrayexpress

Epigenetic aging of the prefrontal cortex and cerebellum in humans, chimpanzees, and rhesus macaques

Project description:Genome-wide prefrontal cortex and cerebellum DNA methylation profiles of younger and older adult humans, captive chimpanzees, and captive rhesus macaques

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Quantification of gene expression from primate tissue samples

2013-10-01 | GSE50782 | GEO

Gene expression changes during primate postnatal brain development

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Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

Project description:While genome sequencing has identified numerous non-coding alterations between primate species, which of these are regulatory and potentially relevant to the evolution of the human brain is unclear. Here, we annotate cis-regulatory elements (CREs) in the human, rhesus macaque and chimpanzee genome using ChIP-sequencing in different anatomical parts of the adult brain. We find high similarity in the genomic positioning of CREs between rhesus macaque and humans, suggesting that the majority of these elements were already present in a common ancestor 25 million years ago. Most of the observed regulatory changes between humans and rhesus macaque occurred prior to the ancestral separation of humans and chimpanzee, leaving a modest set of regulatory elements with predicted human-specificity. Our data refine previous predictions and hypotheses on the consequences of genomic changes between primate species, and allow the identification of regulatory alterations relevant to the evolution of the brain. ChIP-Sequencing for H3K27ac on 8 distinct brain regions from human (three biological replicates per brain region), chimpanzee (two biological replicates per brain region) and rhesus macaque (three biological replicates per brain region).

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Gene expression changes during primate postnatal brain development

Project description:In development, timing is of the utmost importance, and the timing of various developmental processes are often changed during evolution. During human evolution sexual maturation has been delayed relative to other primates and this may have played a critical role for both the increase of human brain size and the rise of human-specific cognitive traits . We measured the timing of gene expression changes in the brains of humans, chimpanzees, and rhesus macaques throughout postnatal development. Human, chimpanzee and rhesus macaque post-mortem brain samples from the dorsolateral prefrontal cortex region were collected. The caudate nucleus region was additionally sampled for humans. The age ranges of the individuals in all three species covered the respective species' postnatal maturation period from infancy to young adulthood. RNA extracted from the dissected tissue was hybridized to Affymetrix® U133-plus2.0 GeneChip® arrays.

2009-03-09 | E-GEOD-11512 | biostudies-arrayexpress

Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee and macaque brains

Project description:we used RNA-Seq to quantify the RNA editing level at more than 8,000 previously annotated exonic A-to-I RNA editing sites in two brain regions - prefrontal cortex and cerebellum - of humans, chimpanzees and rhesus macaques. We observed substantial conservation of RNA editing levels between the brain regions, as well as among the three primate species. Evolutionary changes in RNA editing were nonetheless evident among the species. Across lifespan, we observed an increase of the RNA editing level with advanced age in both brain regions of all three primate species.

2014-01-07 | GSE45244 | GEO

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

Transcription profiling by array of brain in humans, chimpanzees and macaques, and brain, heart, kidney and liver in orangutans

Project description:An experiment was performed to study positive selection on expression regulation in human tissues by comparing expression values in humans to those in chimpanzees, orangutans and rhesus macaques.

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