E-GEOD-17274 - Sex-specific and lineage-specific alternative splicing in primates

Released on 1 December 2009, last updated on 22 August 2013
Homo sapiens, Macaca mulatta, Pan troglodytes
Samples (36)
Protocols (2)
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 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.
Experiment type
RNA-seq of coding RNA 
Ran Blekhman <geo@ncbi.nlm.nih.gov>, John C Marioni, Matthew Stephens, Paul Zumbo, Yoav Gilad
Sex-specific and lineage-specific alternative splicing in primates. Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y. , Europe PMC 20009012
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-17274.idf.txt
Sample and data relationshipE-GEOD-17274.sdrf.txt
Additional data (1)E-GEOD-17274.additional.1.zip