The evolution of gene expression levels in mammalian organs (original) (raw)
Kemp, T. S. The Origin and Evolution of Mammals (Oxford Univ. Press, Oxford, 2005) Google Scholar
Ponting, C. P. The functional repertoires of metazoan genomes. Nature Rev. Genet.9, 689–698 (2008) ArticleCAS Google Scholar
King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science188, 107–116 (1975) ArticleADSCAS Google Scholar
Caceres, M. et al. Elevated gene expression levels distinguish human from non-human primate brains. Proc. Natl Acad. Sci. USA100, 13030–13035 (2003) ArticleADSCAS Google Scholar
Enard, W. et al. Intra- and interspecific variation in primate gene expression patterns. Science296, 340–343 (2002) ArticleADSCAS Google Scholar
Khaitovich, P., Enard, W., Lachmann, M. & Paabo, S. Evolution of primate gene expression. Nature Rev. Genet.7, 693–702 (2006) ArticleCAS Google Scholar
Gilad, Y., Oshlack, A., Smyth, G. K., Speed, T. P. & White, K. P. Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature440, 242–245 (2006) ArticleADSCAS Google Scholar
Uddin, M. et al. Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proc. Natl Acad. Sci. USA101, 2957–2962 (2004) ArticleADSCAS Google Scholar
Liao, B. Y. & Zhang, J. Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol. Biol. Evol.23, 530–540 (2006) ArticleCAS Google Scholar
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev. Genet.10, 57–63 (2009) ArticleCAS Google Scholar
Montgomery, S. B. et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature464, 773–777 (2010) ArticleADSCAS Google Scholar
Pickrell, J. K. et al. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature464, 768–772 (2010) ArticleADSCAS Google Scholar
Blekhman, R., Marioni, J. C., Zumbo, P., Stephens, M. & Gilad, Y. Sex-specific and lineage-specific alternative splicing in primates. Genome Res.20, 180–189 (2010) ArticleCAS Google Scholar
Babbitt, C. C. et al. Both noncoding and protein-coding RNAs contribute to gene expression evolution in the primate brain. Genome Biol. Evol.2, 67–79 (2010) Article Google Scholar
Hubbard, T. J. et al. Ensembl 2009. Nucleic Acids Res.37, D690–D697 (2009) ArticleCAS Google Scholar
Chodroff, R. A. et al. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol.11, R72 (2010) Article Google Scholar
Clark, M. B. et al. The reality of pervasive transcription. PLoS Biol.9, e1000625 (2011) ArticleCAS Google Scholar
Goodman, M. The genomic record of humankind’s evolutionary roots. Am. J. Hum. Genet.64, 31–39 (1999) ArticleCAS Google Scholar
Caswell, J. L. et al. Analysis of chimpanzee history based on genome sequence alignments. PLoS Genet.4, e1000057 (2008) Article Google Scholar
Harcourt, A. H., Harvey, P. H., Larson, S. G. & Short, R. V. Testis weight, body weight and breeding system in primates. Nature293, 55–57 (1981) ArticleADSCAS Google Scholar
Li, W. H., Ellsworth, D. L., Krushkal, J., Chang, B. H. & Hewett-Emmett, D. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet. Evol.5, 182–187 (1996) ArticleCAS Google Scholar
The. Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature437, 69–87 (2005)
Warren, W. C. et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature453, 175–183 (2008) ArticleADSCAS Google Scholar
Keightley, P. D., Lercher, M. J. & Eyre-Walker, A. Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol.3, e42 (2005) Article Google Scholar
Marcus, G. The Birth of the Mind (Basic Books, 2004) Google Scholar
Khaitovich, P. et al. Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science309, 1850–1854 (2005) ArticleADSCAS Google Scholar
Chan, E. T. et al. Conservation of core gene expression in vertebrate tissues. J. Biol.8, 33 (2009) Article Google Scholar
Kaessmann, H. Origins, evolution, and phenotypic impact of new genes. Genome Res.20, 1313–1326 (2010) ArticleCAS Google Scholar
Birkhead, T. R. & Pizzari, T. Postcopulatory sexual selection. Nature Rev. Genet.3, 262–273 (2002) ArticleCAS Google Scholar
Veyrunes, F. et al. Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes. Genome Res.18, 965–973 (2008) ArticleCAS Google Scholar
Potrzebowski, L. et al. Chromosomal gene movements reflect the recent origin and biology of therian sex chromosomes. PLoS Biol.6, e80 (2008) Article Google Scholar
Grützner, F. et al. In the platypus a meiotic chain of ten sex chromosomes shares genes with the bird Z and mammal X chromosomes. Nature432, 913–917 (2004) ArticleADS Google Scholar
Potrzebowski, L., Vinckenbosch, N. & Kaessmann, H. The emergence of new genes on the young therian X. Trends Genet.26, 1–4 (2010) ArticleCAS Google Scholar
Ross, M. T. et al. The DNA sequence of the human X chromosome. Nature434, 325–337 (2005) ArticleADSCAS Google Scholar
Rice, W. R. Sex chromosomes and the evolution of sexual dimorphism. Evolution38, 735–742 (1984) Article Google Scholar
Charlesworth, B. Model for evolution of Y chromosomes and dosage compensation. Proc. Natl Acad. Sci. USA75, 5618–5622 (1978) ArticleADSCAS Google Scholar
Zhang, Y. E., Vibranovski, M. D., Landback, P., Marais, G. A. & Long, M. Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome. PLoS Biol.8, e1000494 (2010) Article Google Scholar
Wilson, M. A. & Makova, K. D. Evolution and survival on eutherian sex chromosomes. PLoS Genet.5, e1000568 (2009) Article Google Scholar
Bachtrog, D., Jensen, J. D. & Zhang, Z. Accelerated adaptive evolution on a newly formed X chromosome. PLoS Biol.7, e82 (2009) Article Google Scholar
Ihmels, J., Bergmann, S. & Barkai, N. Defining transcription modules using large-scale gene expression data. Bioinformatics20, 1993–2003 (2004) ArticleCAS Google Scholar
Xiong, Y. et al. RNA sequencing shows no dosage compensation of the active X-chromosome. Nature Genet.42, 1043–1047 (2010) ArticleCAS Google Scholar
Kemkemer, C., Kohn, M., Kehrer-Sawatzki, H., Fundele, R. H. & Hameister, H. Enrichment of brain-related genes on the mammalian X chromosome is ancient and predates the divergence of synapsid and sauropsid lineages. Chromosome Res.17, 811–820 (2009) ArticleCAS Google Scholar
Haygood, R., Babbitt, C. C., Fedrigo, O. & Wray, G. A. Contrasts between adaptive coding and noncoding changes during human evolution. Proc. Natl Acad. Sci. USA107, 7853–7857 (2010) ArticleADSCAS Google Scholar
Schoenemann, P. T., Sheehan, M. J. & Glotzer, L. D. Prefrontal white matter volume is disproportionately larger in humans than in other primates. Nature Neurosci.8, 242–252 (2005) ArticleCAS Google Scholar
Duret, L. & Galtier, N. Biased gene conversion and the evolution of mammalian genomic landscapes. Annu. Rev. Genomics Hum. Genet.10, 285–311 (2009) ArticleCAS Google Scholar
Nielsen, R. et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol.3, e170 (2005) Article Google Scholar
Fyfe, J. C. et al. An approximately 140-kb deletion associated with feline spinal muscular atrophy implies an essential LIX1 function for motor neuron survival. Genome Res.16, 1084–1090 (2006) ArticleCAS Google Scholar
Tong, Y., Xu, Y., Scearce-Levie, K., Ptacek, L. J. & Fu, Y. H. COL25A1 triggers and promotes Alzheimer’s disease-like pathology in vivo . Neurogenetics11, 41–52 (2010) ArticleCAS Google Scholar
Vauti, F. et al. The mouse Trm1-like gene is expressed in neural tissues and plays a role in motor coordination and exploratory behaviour. Gene389, 174–185 (2007) ArticleCAS Google Scholar
Kircher, M., Stenzel, U. & Kelso, J. Improved base calling for the Illumina Genome Analyzer using machine learning strategies. Genome Biol.10, R83 (2009) Article Google Scholar
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics25, 1105–1111 (2009) ArticleCAS Google Scholar
Hubbard, T. J. et al. Ensembl 2009. Nucleic Acids Res.37, D690–D697 (2009) ArticleCAS Google Scholar
Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature456, 470–476 (2008) ArticleADSCAS Google Scholar
Picard, F., Robin, S., Lebarbier, E. & Daudin, J. J. A segmentation/clustering model for the analysis of array CGH data. Biometrics63, 758–766 (2007) ArticleMathSciNetCAS Google Scholar
Vilella, A. J. et al. EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res.19, 327–335 (2009) ArticleCAS Google Scholar
Blanchette, M. et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res.14, 708–715 (2004) ArticleCAS Google Scholar
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol.10, R25 (2009) Article Google Scholar
Kaessmann, H., Vinckenbosch, N. & Long, M. RNA-based gene duplication: mechanistic and evolutionary insights. Nature Rev. Genet.10, 19–31 (2009) ArticleCAS Google Scholar
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods5, 621–628 (2008) ArticleCAS Google Scholar
Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics20, 289–290 (2004) ArticleCAS Google Scholar