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| Status |
Public on Dec 01, 2009 |
| Title |
Sex-specific and lineage-specific alternative splicing in primates |
| Organisms |
Macaca mulatta; Pan troglodytes; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here we used recently-developed RNA sequencing protocols, which side-step this limitation, to assess intra- and inter-species variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNAseq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evolve under natural selection in primates. These include a subset of genes with conserved sexually dimorphic expression patterns across the three species, which we found to be enriched for genes involved in lipid metabolism. Our data also suggest that while alternative splicing is tightly regulated within and between species, sex-specific and lineage-specific changes in the expression of different splice forms are also frequent. Intriguingly, among genes in which a change in exon usage occurred exclusively in the human lineage, we found an enrichment of genes involved in anatomical structure and morphogenesis, raising the possibility that differences in the regulation of alternative splicing have been an important force in human evolution.
Keywords: Gene Regulation Study
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| Overall design |
Examination of gene expression levels in livers from three primate species (human, chimpanzee, and rhesus macaque), using 3 male and 3 female samples from each species.
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| Contributor(s) |
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y |
| Citation(s) |
20009012 |
| Submission date |
Jul 23, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Ran Blekhman |
| Organization name |
University of Chicago
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| Street address |
920 E. 58th St.
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (3) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL9160 |
Illumina Genome Analyzer II (Macaca mulatta) |
| GPL9378 |
Illumina Genome Analyzer II (Pan troglodytes) |
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| Samples (36)
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| Relations |
| SRA |
SRP001558 |
| BioProject |
PRJNA119135 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE17274_ReadCountPerLane.txt.gz |
639.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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