Limits...
The genetic architecture of gene expression levels in wild baboons.

Tung J, Zhou X, Alberts SC, Stephens M, Gilad Y - Elife (2015)

Bottom Line: Primate evolution has been argued to result, in part, from changes in how genes are regulated.We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substantial evidence for, and surprising power to detect, genetic effects on gene expression levels in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes; interestingly, genes with eQTL significantly overlapped between baboons and a comparable human eQTL data set.Our results suggest that genes vary in their tolerance of genetic perturbation, and that this property may be conserved across species.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.

ABSTRACT
Primate evolution has been argued to result, in part, from changes in how genes are regulated. However, we still know little about gene regulation in natural primate populations. We conducted an RNA sequencing (RNA-seq)-based study of baboons from an intensively studied wild population. We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substantial evidence for, and surprising power to detect, genetic effects on gene expression levels in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes; interestingly, genes with eQTL significantly overlapped between baboons and a comparable human eQTL data set. Our results suggest that genes vary in their tolerance of genetic perturbation, and that this property may be conserved across species. Further, they establish the feasibility of eQTL mapping using RNA-seq data alone, and represent an important step towards understanding the genetic architecture of gene expression in primates.

Show MeSH
PCA projection of YRI samples using the RNA-seq-based pipeline vsindependently typed SNPs.PCA projection of genotype data from the RNA-seq-based pipeline and theHapMap3 data place individual samples very close together.(A) and (B) show the same data, but(B) zooms in on the central cluster for bettervisibility.DOI:http://dx.doi.org/10.7554/eLife.04729.009
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4383332&req=5

fig1s6: PCA projection of YRI samples using the RNA-seq-based pipeline vsindependently typed SNPs.PCA projection of genotype data from the RNA-seq-based pipeline and theHapMap3 data place individual samples very close together.(A) and (B) show the same data, but(B) zooms in on the central cluster for bettervisibility.DOI:http://dx.doi.org/10.7554/eLife.04729.009


The genetic architecture of gene expression levels in wild baboons.

Tung J, Zhou X, Alberts SC, Stephens M, Gilad Y - Elife (2015)

PCA projection of YRI samples using the RNA-seq-based pipeline vsindependently typed SNPs.PCA projection of genotype data from the RNA-seq-based pipeline and theHapMap3 data place individual samples very close together.(A) and (B) show the same data, but(B) zooms in on the central cluster for bettervisibility.DOI:http://dx.doi.org/10.7554/eLife.04729.009
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383332&req=5

fig1s6: PCA projection of YRI samples using the RNA-seq-based pipeline vsindependently typed SNPs.PCA projection of genotype data from the RNA-seq-based pipeline and theHapMap3 data place individual samples very close together.(A) and (B) show the same data, but(B) zooms in on the central cluster for bettervisibility.DOI:http://dx.doi.org/10.7554/eLife.04729.009
Bottom Line: Primate evolution has been argued to result, in part, from changes in how genes are regulated.We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substantial evidence for, and surprising power to detect, genetic effects on gene expression levels in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes; interestingly, genes with eQTL significantly overlapped between baboons and a comparable human eQTL data set.Our results suggest that genes vary in their tolerance of genetic perturbation, and that this property may be conserved across species.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.

ABSTRACT
Primate evolution has been argued to result, in part, from changes in how genes are regulated. However, we still know little about gene regulation in natural primate populations. We conducted an RNA sequencing (RNA-seq)-based study of baboons from an intensively studied wild population. We performed complementary expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses, discovering substantial evidence for, and surprising power to detect, genetic effects on gene expression levels in the baboons. eQTL were most likely to be identified for lineage-specific, rapidly evolving genes; interestingly, genes with eQTL significantly overlapped between baboons and a comparable human eQTL data set. Our results suggest that genes vary in their tolerance of genetic perturbation, and that this property may be conserved across species. Further, they establish the feasibility of eQTL mapping using RNA-seq data alone, and represent an important step towards understanding the genetic architecture of gene expression in primates.

Show MeSH