Cis and trans regulatory effects contribute to natural variation in transcriptome of Drosophila melanogaster - PubMed (original) (raw)
Cis and trans regulatory effects contribute to natural variation in transcriptome of Drosophila melanogaster
Anne Genissel et al. Mol Biol Evol. 2008 Jan.
Abstract
The dissection of intraspecific variation in transcriptome is a central theme of many recent quantitative genomic analyses. Transcript level variation has been attributed to factors at the gene itself (cis) and elsewhere in the genome (trans). Previous analyses of Drosophila intraspecific transcriptome variation pointed toward a larger contribution of trans factors. However, data from other genera, and from interspecific comparisons within Drosophila, are more consistent with a major role for cis factors. We investigated the relative amount of cis and trans variation in Drosophila melanogaster, using whole-genome expression from an oligonucleotide microarray in the 2 extensively studied genotypes Ore and 2b3, and 6 recombinant inbred (RI) lines derived from these parents. We examined 2 types of models to decompose cis and trans contributions to genetic variation in transcript level: 1) an infinitesimal model assuming that the transcription variation is highly polygenic and due to many small effects and 2) contrast models assuming that a few large effects contribute to the transcriptional variation. We explicitly fitted cis-by-trans interactions and extended our analyses to consider regulation of alternatively spliced transcripts. We estimated that approximately 10% of the transcriptome was differentially regulated among the lines. We were able to identify cis and trans effects that contribute to this differential regulation for 1,340 genes. Our analyses revealed numerous cis effects (90%) but much fewer trans effects, perhaps due to reduced power of detection for trans effects. In addition, we identified 15 genes that have alternative splice variants differentially regulated in cis.
Similar articles
- Evolutionary changes in cis and trans gene regulation.
Wittkopp PJ, Haerum BK, Clark AG. Wittkopp PJ, et al. Nature. 2004 Jul 1;430(6995):85-8. doi: 10.1038/nature02698. Nature. 2004. PMID: 15229602 - Regulatory changes underlying expression differences within and between Drosophila species.
Wittkopp PJ, Haerum BK, Clark AG. Wittkopp PJ, et al. Nat Genet. 2008 Mar;40(3):346-50. doi: 10.1038/ng.77. Epub 2008 Feb 17. Nat Genet. 2008. PMID: 18278046 - Genomic inferences of the cis-regulatory nucleotide polymorphisms underlying gene expression differences between Drosophila melanogaster mating races.
Osada N, Kohn MH, Wu CI. Osada N, et al. Mol Biol Evol. 2006 Aug;23(8):1585-91. doi: 10.1093/molbev/msl023. Epub 2006 Jun 5. Mol Biol Evol. 2006. PMID: 16754642 - Unraveling cis-regulatory mechanisms at the abdominal-A and Abdominal-B genes in the Drosophila bithorax complex.
Akbari OS, Bousum A, Bae E, Drewell RA. Akbari OS, et al. Dev Biol. 2006 May 15;293(2):294-304. doi: 10.1016/j.ydbio.2006.02.015. Epub 2006 Mar 20. Dev Biol. 2006. PMID: 16545794 Review. - [From genetics of intraspecific differences to genetics of intraspecific similarity].
Chadov BF, Chadova EV, Kopyl SA, Artemova EV, Khotskina EA, Fedorova NB. Chadov BF, et al. Genetika. 2004 Sep;40(9):1157-72. Genetika. 2004. PMID: 15559143 Review. Russian.
Cited by
- Genome-wide expression QTL mapping reveals the highly dynamic regulatory landscape of a major wheat pathogen.
Abraham LN, Croll D. Abraham LN, et al. BMC Biol. 2023 Nov 20;21(1):263. doi: 10.1186/s12915-023-01763-3. BMC Biol. 2023. PMID: 37981685 Free PMC article. - Power calculator for detecting allelic imbalance using hierarchical Bayesian model.
Sherbina K, León-Novelo LG, Nuzhdin SV, McIntyre LM, Marroni F. Sherbina K, et al. BMC Res Notes. 2021 Nov 27;14(1):436. doi: 10.1186/s13104-021-05851-x. BMC Res Notes. 2021. PMID: 34838135 Free PMC article. - Contributions of cis- and trans-Regulatory Evolution to Transcriptomic Divergence across Populations in the Drosophila mojavensis Larval Brain.
Benowitz KM, Coleman JM, Allan CW, Matzkin LM. Benowitz KM, et al. Genome Biol Evol. 2020 Aug 1;12(8):1407-1418. doi: 10.1093/gbe/evaa145. Genome Biol Evol. 2020. PMID: 32653899 Free PMC article. - Basal hsp70 expression levels do not explain adaptive variation of the warm- and cold-climate O3 + 4 + 7 and OST gene arrangements of Drosophila subobscura.
Puig Giribets M, Santos M, García Guerreiro MP. Puig Giribets M, et al. BMC Evol Biol. 2020 Jan 31;20(1):17. doi: 10.1186/s12862-020-1584-z. BMC Evol Biol. 2020. PMID: 32005133 Free PMC article. - The Evolution of Gene Expression in cis and trans.
Signor SA, Nuzhdin SV. Signor SA, et al. Trends Genet. 2018 Jul;34(7):532-544. doi: 10.1016/j.tig.2018.03.007. Epub 2018 Apr 18. Trends Genet. 2018. PMID: 29680748 Free PMC article. Review.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Molecular Biology Databases