Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression variability in human and chimpanzee populations share common determinants

ABSTRACT: Inter-individual variation in gene regulation has been shown to be heritable and it is quite often associated with differences in disease susceptibility between individuals. While many human studies focused on mapping associations between genetic and gene regulatory variation, much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative expression quantitative trait loci (eQTL) mapping study in humans and chimpanzees, using gene expression data from primary heart samples. While expression variability in both species is strongly determined by non-genetic sources, such as cell type heterogeneity, we found evidence that the degree of inter-individual variation in gene regulation is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of genes associated with eQTLs in the two species. We conclude that humans and chimpanzees share sources common determinants of gene expression variability, including genetically regulated constraints from stabilizing and diversifying selection pressures.

ORGANISM(S): Pan troglodytes

PROVIDER: GSE151397 | GEO | 2020/05/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Whole genome sequencing of 39 captive born chimpanzees

Project description:Inter-individual variation in gene regulation has been shown to be heritable and it is quite often associated with differences in disease susceptibility between individuals. While many human studies focused on mapping associations between genetic and gene regulatory variation, much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative expression quantitative trait loci (eQTL) mapping study in humans and chimpanzees, using gene expression data from primary heart samples. While expression variability in both species is strongly determined by non-genetic sources, such as cell type heterogeneity, we found evidence that he degree of inter-individual variation in gene regulation is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of genes associated with eQTLs in the two species. We conclude that humans and chimpanzees share sources common determinants of gene expression variability, including genetically regulated constraints from stabilizing and diversifying selection pressures. Associated with SRA project accession PRJNA635393 and GEO accession GSE151397.

2020-07-21 | PRJEB39475 | EVA

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels

2012-10-01 | GSE37451 | GEO

Study of the consistency, comparability and identity of different Dendritic cells productions for clinical use

Project description:Gene expression profiling of monocyte-derived Dendritic cells manufactured several times from one healthy donor and one single time from 8 different healthy donors to test the sources of variability Sources tested: Assay-related variability (8 samples), Manufacture-related variability (5 samples), Intra-donor-related variability (5 samples), inter-donor-related variability (9 samples)

2012-11-16 | GSE31195 | GEO

Identification of brain transcriptional variability reproduced in peripheral blood: an approach for mapping brain eQTLs

Project description:Genome-wide gene expression studies may provide a comprehensive insight in gene activities and biological pathways differing between individuals and tissues (even closely related tissues building complex organs such as the brain). Our research addressed both kinds of gene expression variation – between brain regions and between individuals – by expression profiling in brain tissues derived from eight brain regions and blood from 12 vervet monkeys (Chlorocebus aethiops sabaeus). We employed the non-human primate model to assure tissue quality and to enhance the probability of precise dissection of the brain tissues, which is difficult to realize in human subjects. We characterized brain regional differences in gene expression levels which may relate to specific functions of brain tissues including disease symptoms affecting specific brain regions. We focused on inter-individual variability of brain transcript levels in different regions that correlates well between blood and brain tissues and therefore could be further reliably studied in easily accessible blood samples. Applying very stringent transcript selection criteria including 1). considerable similarities between brain and blood tissues, 2). consistent repeat measurements in blood, 3). higher inter-individual than intra-individual variability and 4). detection in all tissue samples, allowed us to identify transcripts in which inter-individual variation in brain expression profiles indicates possible genetic factors regulating gene transcript levels. High heritabilities of these transcript levels indicated that our approach focusing on transcripts showing higher inter-individual variability than intra-individual variability identifies transcripts with a strong genetic component.

2009-08-21 | GSE15301 | GEO

Study of the consistency, comparability and identity of different Dendritic cells productions for clinical use

2012-11-16 | E-GEOD-31195 | biostudies-arrayexpress

Genetic studies of human-chimpanzee divergence using stem cell fusions

Project description:Complete genome sequencing has identified millions of DNA changes that differ between humans and chimpanzees. Although a subset of these changes likely underlies important phenotypic differences between humans and chimpanzees, it is currently difficult to distinguish causal from incidental changes and to map specific phenotypes to particular genome locations. To facilitate further genetic study of human-chimpanzee divergence, we have generated human and chimpanzee auto-tetraploids and allo-tetraploids by fusing induced pluripotent stem cells (iPSCs) of each species. The resulting tetraploid iPSCs can be stably maintained and retain the ability to differentiate along ectoderm, mesoderm, and endoderm lineages. RNA sequencing identifies thousands of genes whose expression differs between humans and chimpanzees when assessed in single-species diploid or auto-tetraploid iPSCs. Analysis of gene expression patterns in inter-specific allo-tetraploid iPSCs shows that human-chimpanzee expression differences arise from substantial contributions of both cis-acting changes linked to the genes themselves, and trans-acting changes elsewhere in the genome. To enable further genetic mapping of species differences, we tested chemical treatments for stimulating genome-wide mitotic recombination between human and chimpanzee chromosomes, and CRISPR methods for inducing species-specific changes on particular chromosomes in allo-tetraploid cells. We successfully generated derivative cells with nested deletions or inter-specific recombination on the X chromosome. These studies identify a long distance cis-regulatory domain of the Fragile X-associated gene (FMR1), confirm an important role for the X chromosome in trans-regulation of other expression differences, and illustrate the potential of this system for more detailed mapping of the molecular basis of human and chimpanzee evolution.

2021-11-29 | GSE184768 | GEO

Transcription profiling of human and chimp brain tissues

Project description:We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each other and differ more between individuals than among regions within an individual. In contrast, the transcriptomes of the cerebral cortex, the caudate nucleus, and the cerebellum differ substantially from each other. Between humans and chimpanzees, 10% of genes differ in their expression in at least one region of the brain. The majority of these expression differences are shared among all brain regions. Whereas genes encoding proteins involved in signal transduction and cell differentiation differ significantly between brain regions within individuals, no such pattern is seen between the species. However, a subset of genes that show expression differences between humans and chimpanzees are distributed nonrandomly across the genome. Furthermore, genes that show an elevated expression level in humans are statistically significantly enriched in regions that are recently duplicated in humans

2010-02-12 | E-AFMX-2 | biostudies-arrayexpress

Extensive Variation in Chromatin States Across Humans

Project description:The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

2013-10-18 | GSE50893 | GEO

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels

Project description:Analysis of the extent to which inter-individual variation in mRNA decay contributes to inter-individual variation in gene expression levels in humans. The study examines properties of genome-wide decay rates and the relationship between mRNA decay and gene expression across genes, across individuals, and finally across genotype classes. 70 human lymphoblastoid cell lines were treated with Actinomycin D to arrest transcription. Transcript abundance was measured at 5 timepoints: before transcription (0 hours) and after transcription (0.5 hours, 1 hour, 2 hours, and 4 hours). Data was then used to estimate gene-specific decay rates genome-wide.

2012-10-01 | E-GEOD-37451 | biostudies-arrayexpress

A comparative study of endoderm differentiation in humans and chimpanzees

Project description:There is substantial interest in the genetic regulatory framework that is established in early human development, and in the evolutionary forces that shaped early developmental processes in humans. Progress in these areas has been slow because it is difficult to obtain relevant biological samples. Recent technological developments in the generation and differentiation of inducible pluripotent stem cells (iPSCs) provide the ability to develop in vitro models of early human and non-human primates developmental stages. We have previously established matched iPSC panels from humans and chimpanzees. Using these panels, we comparatively characterized gene regulatory changes through a four-day timecourse differentiation of iPSCs (day 1) into primary streak (day 2), endoderm progenitors (day 3), and definitive endoderm (day 4). As might be expected, we found that differentiation stage (in effect, cell type) is the major driver of variation in gene expression levels in our study, followed by species. We then identified thousands of differentially expressed genes between humans and chimpanzees in each differentiation stage. Yet, when we considered gene-specific dynamic regulatory trajectories throughout the timecourse, we found that 75% of genes, including nearly all known endoderm developmental markers, have conserved trajectories in the two species. Interestingly, we observed a marked reduction of both intra- and inter-species variation in gene expression levels in primitive streak samples compared to the iPSCs, with a recovery of variation in endoderm progenitors. The reduction in variation in gene expression levels at a specific developmental stage, paired with the high degree of conservation of temporal expression across species, is consistent with the dynamics of developmental canalization. Overall, we conclude that endoderm development in iPSC-based models are highly conserved and canalized between humans and our closest evolutionary relative.

2017-05-02 | GSE98411 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data