The evolution of gene expression levels in mammalian organs - PubMed (original) (raw)
. 2011 Oct 19;478(7369):343-8.
doi: 10.1038/nature10532.
Magali Soumillon, Anamaria Necsulea, Philippe Julien, Gábor Csárdi, Patrick Harrigan, Manuela Weier, Angélica Liechti, Ayinuer Aximu-Petri, Martin Kircher, Frank W Albert, Ulrich Zeller, Philipp Khaitovich, Frank Grützner, Sven Bergmann, Rasmus Nielsen, Svante Pääbo, Henrik Kaessmann
Affiliations
- PMID: 22012392
- DOI: 10.1038/nature10532
The evolution of gene expression levels in mammalian organs
David Brawand et al. Nature. 2011.
Abstract
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.
Similar articles
- The molecular evolution of spermatogenesis across mammals.
Murat F, Mbengue N, Winge SB, Trefzer T, Leushkin E, Sepp M, Cardoso-Moreira M, Schmidt J, Schneider C, Mößinger K, Brüning T, Lamanna F, Belles MR, Conrad C, Kondova I, Bontrop R, Behr R, Khaitovich P, Pääbo S, Marques-Bonet T, Grützner F, Almstrup K, Schierup MH, Kaessmann H. Murat F, et al. Nature. 2023 Jan;613(7943):308-316. doi: 10.1038/s41586-022-05547-7. Epub 2022 Dec 21. Nature. 2023. PMID: 36544022 Free PMC article. - Birth and expression evolution of mammalian microRNA genes.
Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu H, Khaitovich P, Kaessmann H. Meunier J, et al. Genome Res. 2013 Jan;23(1):34-45. doi: 10.1101/gr.140269.112. Epub 2012 Oct 3. Genome Res. 2013. PMID: 23034410 Free PMC article. - Mechanisms and evolutionary patterns of mammalian and avian dosage compensation.
Julien P, Brawand D, Soumillon M, Necsulea A, Liechti A, Schütz F, Daish T, Grützner F, Kaessmann H. Julien P, et al. PLoS Biol. 2012;10(5):e1001328. doi: 10.1371/journal.pbio.1001328. Epub 2012 May 15. PLoS Biol. 2012. PMID: 22615540 Free PMC article. - Evolutionary dynamics of coding and non-coding transcriptomes.
Necsulea A, Kaessmann H. Necsulea A, et al. Nat Rev Genet. 2014 Nov;15(11):734-48. doi: 10.1038/nrg3802. Epub 2014 Oct 9. Nat Rev Genet. 2014. PMID: 25297727 Review. - The X factor: X chromosome dosage compensation in the evolutionarily divergent monotremes and marsupials.
Whitworth DJ, Pask AJ. Whitworth DJ, et al. Semin Cell Dev Biol. 2016 Aug;56:117-121. doi: 10.1016/j.semcdb.2016.01.006. Epub 2016 Jan 12. Semin Cell Dev Biol. 2016. PMID: 26806635 Review.
Cited by
- Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance.
Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, Pardo-Manuel de Villena F. Crowley JJ, et al. Nat Genet. 2015 Apr;47(4):353-60. doi: 10.1038/ng.3222. Epub 2015 Mar 2. Nat Genet. 2015. PMID: 25730764 Free PMC article. - Mitochondrial 16S rRNA Is Methylated by tRNA Methyltransferase TRMT61B in All Vertebrates.
Bar-Yaacov D, Frumkin I, Yashiro Y, Chujo T, Ishigami Y, Chemla Y, Blumberg A, Schlesinger O, Bieri P, Greber B, Ban N, Zarivach R, Alfonta L, Pilpel Y, Suzuki T, Mishmar D. Bar-Yaacov D, et al. PLoS Biol. 2016 Sep 15;14(9):e1002557. doi: 10.1371/journal.pbio.1002557. eCollection 2016 Sep. PLoS Biol. 2016. PMID: 27631568 Free PMC article. - Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.
Roy S, Wapinski I, Pfiffner J, French C, Socha A, Konieczka J, Habib N, Kellis M, Thompson D, Regev A. Roy S, et al. Genome Res. 2013 Jun;23(6):1039-50. doi: 10.1101/gr.146233.112. Epub 2013 May 2. Genome Res. 2013. PMID: 23640720 Free PMC article. - Evidence for compensatory evolution within pleiotropic regulatory elements.
Kliesmete Z, Orchard P, Lee VYK, Geuder J, Krauß SM, Ohnuki M, Jocher J, Vieth B, Enard W, Hellmann I. Kliesmete Z, et al. Genome Res. 2024 Oct 29;34(10):1528-1539. doi: 10.1101/gr.279001.124. Genome Res. 2024. PMID: 39255977 Free PMC article. - Expression reduction in mammalian X chromosome evolution refutes Ohno's hypothesis of dosage compensation.
Lin F, Xing K, Zhang J, He X. Lin F, et al. Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11752-7. doi: 10.1073/pnas.1201816109. Epub 2012 Jul 2. Proc Natl Acad Sci U S A. 2012. PMID: 22753487 Free PMC article.
References
- Nat Rev Genet. 2008 Sep;9(9):689-98 - PubMed
- Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2957-62 - PubMed
- Proc Natl Acad Sci U S A. 1978 Nov;75(11):5618-22 - PubMed
- Nature. 2010 Apr 1;464(7289):773-7 - PubMed
- Nature. 2005 Sep 1;437(7055):69-87 - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases