The evolution of gene expression levels in mammalian organs [GSE30352]
Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution. We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes.
The poly (A)+ RNA was dephosphorylated with bacterial alkaline phosphatase (BAP) and then decapped with tabacco acid pyrophosphatase (TAP). The decapped intact mRNA was ligated with DNA-RNA linker including EcoR I site by treatment of T4 RNA ligase and the first strand cDNA was synthesized from oligo dT-selected mRNA by priming with dT-tailed vector. The dT-tailed vector was adjusted to have about 60nt. The cDNA vector was circularized with E. coli DNA ligase after digestion of EcoRI which site is also included in vector. An RNA strand converted to a DNA strand by Okayama-Berg method. The obtained cDNA vectors were used for transformation of competent cells E. coli Top10F' by electroporation method. The cDNA libraries constructed by this method are full-length enriched cDNA library.