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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.

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Detailed workflow for gene expression level estimation.DOI:http://dx.doi.org/10.7554/eLife.04729.004
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fig1s1: Detailed workflow for gene expression level estimation.DOI:http://dx.doi.org/10.7554/eLife.04729.004

Mentions: We obtained blood samples from 63 individually recognized adult baboons in theAmboseli population (Figure 1—figuresupplement 1). From these samples, we produced a total of 1.89 billionRNA-seq reads (mean of 30.0 ± 4.5 s.d. million reads per individual, with 8.6± 1.8 s.d. million reads uniquely mapped to exons: Supplementary file 1A). Onaverage, 67.2% of reads mapped to the most recent release of the baboon genome(Panu2.0), 69.2% of which could be assigned to aunique location. We used the set of uniquely mapped reads to estimate gene-wise geneexpression levels for NCBI-annotated baboon RefSeq genes. After subsequent readprocessing and normalization steps (‘Materials and methods’, Figure 1—figure supplement 1 and Figure 1—figure supplement 2), weconsidered variation in gene expression levels for 10,409 genes expressed in wholeblood (i.e., all genes for which we could test for cis-actinggenetic effects on gene expression).


The genetic architecture of gene expression levels in wild baboons.

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

Detailed workflow for gene expression level estimation.DOI:http://dx.doi.org/10.7554/eLife.04729.004
© Copyright Policy
Related In: Results  -  Collection

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

fig1s1: Detailed workflow for gene expression level estimation.DOI:http://dx.doi.org/10.7554/eLife.04729.004
Mentions: We obtained blood samples from 63 individually recognized adult baboons in theAmboseli population (Figure 1—figuresupplement 1). From these samples, we produced a total of 1.89 billionRNA-seq reads (mean of 30.0 ± 4.5 s.d. million reads per individual, with 8.6± 1.8 s.d. million reads uniquely mapped to exons: Supplementary file 1A). Onaverage, 67.2% of reads mapped to the most recent release of the baboon genome(Panu2.0), 69.2% of which could be assigned to aunique location. We used the set of uniquely mapped reads to estimate gene-wise geneexpression levels for NCBI-annotated baboon RefSeq genes. After subsequent readprocessing and normalization steps (‘Materials and methods’, Figure 1—figure supplement 1 and Figure 1—figure supplement 2), weconsidered variation in gene expression levels for 10,409 genes expressed in wholeblood (i.e., all genes for which we could test for cis-actinggenetic effects on gene expression).

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