- -

Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina

Mostrar el registro completo del ítem

Mattenberger, F.; Sabater-Muñoz, B.; Toft, C.; Sablok, G.; Fares Riaño, MA. (2017). Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina. DNA Research. 24(6):559-570. https://doi.org/10.1093/dnares/dsx025

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/153360

Ficheros en el ítem

Thumbnail
Nombre: Mattenberger;Saba ...
Tamaño: 1.341Mb
Formato: PDF
Descripción: Versión editorial
Abrir/Preview

Metadatos del ítem

Título: Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina
Autor: Mattenberger, Florian Sabater-Muñoz, Beatriz Toft, Christina Sablok, Gaurav Fares Riaño, Mario Ali
Entidad UPV: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Fecha difusión:
Resumen:
[EN] Gene duplication is an important source of novelties and genome complexity. What genes are preserved as duplicated through long evolutionary times can shape the evolution of innovations. Identifying factors that ...[+]
Palabras clave: Gene expression , Gene duplication , Transcriptional plasticity , Duplicability , Saccharomyces cerevisiae
Derechos de uso: Reconocimiento - No comercial (by-nc)
Fuente:
DNA Research. (issn: 1340-2838 )
DOI: 10.1093/dnares/dsx025
Editorial:
Oxford University Press
Versión del editor: https://doi.org/10.1093/dnares/dsx025
Código del Proyecto:
info:eu-repo/grantAgreement/MINECO//BFU2015-66073-P/ES/CARACTERIZANDO LOS MECANISMOS DE INNOVACION POR DUPLICACION GENICA/
info:eu-repo/grantAgreement/MINECO//JCI-2012-14056/ES/JCI-2012-14056/
info:eu-repo/grantAgreement/AEI//BES-2016-076677/
Agradecimientos:
We would like to thank members of Fares' Lab for a careful reading and discussion of the results in the manuscript. We are also grateful to colleagues at Trinity College for helpful discussions. This work was supported by ...[+]
Tipo: Artículo

References

Ohno, S. (1999). Gene duplication and the uniqueness of vertebrate genomes circa 1970–1999. Seminars in Cell & Developmental Biology, 10(5), 517-522. doi:10.1006/scdb.1999.0332

Lynch, M. (2000). The Evolutionary Fate and Consequences of Duplicate Genes. Science, 290(5494), 1151-1155. doi:10.1126/science.290.5494.1151

Otto, S. P., & Whitton, J. (2000). Polyploid Incidence and Evolution. Annual Review of Genetics, 34(1), 401-437. doi:10.1146/annurev.genet.34.1.401 [+]
Ohno, S. (1999). Gene duplication and the uniqueness of vertebrate genomes circa 1970–1999. Seminars in Cell & Developmental Biology, 10(5), 517-522. doi:10.1006/scdb.1999.0332

Lynch, M. (2000). The Evolutionary Fate and Consequences of Duplicate Genes. Science, 290(5494), 1151-1155. doi:10.1126/science.290.5494.1151

Otto, S. P., & Whitton, J. (2000). Polyploid Incidence and Evolution. Annual Review of Genetics, 34(1), 401-437. doi:10.1146/annurev.genet.34.1.401

Carretero-Paulet, L., & Fares, M. A. (2012). Evolutionary Dynamics and Functional Specialization of Plant Paralogs Formed by Whole and Small-Scale Genome Duplications. Molecular Biology and Evolution, 29(11), 3541-3551. doi:10.1093/molbev/mss162

Cui, L. (2006). Widespread genome duplications throughout the history of flowering plants. Genome Research, 16(6), 738-749. doi:10.1101/gr.4825606

Holub, E. B. (2001). The arms race is ancient history in Arabidopsis, the wildflower. Nature Reviews Genetics, 2(7), 516-527. doi:10.1038/35080508

Lespinet, O. (2002). The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes. Genome Research, 12(7), 1048-1059. doi:10.1101/gr.174302

Wendel, J. F. (2000). Plant Molecular Biology, 42(1), 225-249. doi:10.1023/a:1006392424384

Soltis, D. E., Albert, V. A., Leebens-Mack, J., Bell, C. D., Paterson, A. H., Zheng, C., … Soltis, P. S. (2009). Polyploidy and angiosperm diversification. American Journal of Botany, 96(1), 336-348. doi:10.3732/ajb.0800079

De Peer, Y. V. (2004). Computational approaches to unveiling ancient genome duplications. Nature Reviews Genetics, 5(10), 752-763. doi:10.1038/nrg1449

Hoegg, S., Brinkmann, H., Taylor, J. S., & Meyer, A. (2004). Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish. Journal of Molecular Evolution, 59(2), 190-203. doi:10.1007/s00239-004-2613-z

Grant, S. G. N. (2016). The molecular evolution of the vertebrate behavioural repertoire. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1685), 20150051. doi:10.1098/rstb.2015.0051

Green, S. A., & Bronner, M. E. (2013). Gene duplications and the early evolution of neural crest development. Seminars in Cell & Developmental Biology, 24(2), 95-100. doi:10.1016/j.semcdb.2012.12.006

Conant, G. C., & Wolfe, K. H. (2007). Increased glycolytic flux as an outcome of whole‐genome duplication in yeast. Molecular Systems Biology, 3(1), 129. doi:10.1038/msb4100170

Wolfe, K. H., & Shields, D. C. (1997). Molecular evidence for an ancient duplication of the entire yeast genome. Nature, 387(6634), 708-713. doi:10.1038/42711

Fares, M. A., Keane, O. M., Toft, C., Carretero-Paulet, L., & Jones, G. W. (2013). The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes. PLoS Genetics, 9(1), e1003176. doi:10.1371/journal.pgen.1003176

Blanc, G., & Wolfe, K. H. (2004). Widespread Paleopolyploidy in Model Plant Species Inferred from Age Distributions of Duplicate Genes. The Plant Cell, 16(7), 1667-1678. doi:10.1105/tpc.021345

Blanc, G., & Wolfe, K. H. (2004). Functional Divergence of Duplicated Genes Formed by Polyploidy during Arabidopsis Evolution. The Plant Cell, 16(7), 1679-1691. doi:10.1105/tpc.021410

Conant, G. C., & Wolfe, K. H. (2008). Turning a hobby into a job: How duplicated genes find new functions. Nature Reviews Genetics, 9(12), 938-950. doi:10.1038/nrg2482

Fares, M. A., Byrne, K. P., & Wolfe, K. H. (2005). Rate Asymmetry After Genome Duplication Causes Substantial Long-Branch Attraction Artifacts in the Phylogeny of Saccharomyces Species. Molecular Biology and Evolution, 23(2), 245-253. doi:10.1093/molbev/msj027

Freeling, M. (2009). Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition. Annual Review of Plant Biology, 60(1), 433-453. doi:10.1146/annurev.arplant.043008.092122

Conant, G. C., Birchler, J. A., & Pires, J. C. (2014). Dosage, duplication, and diploidization: clarifying the interplay of multiple models for duplicate gene evolution over time. Current Opinion in Plant Biology, 19, 91-98. doi:10.1016/j.pbi.2014.05.008

Keane, O. M., Toft, C., Carretero-Paulet, L., Jones, G. W., & Fares, M. A. (2014). Preservation of genetic and regulatory robustness in ancient gene duplicates ofSaccharomyces cerevisiae. Genome Research, 24(11), 1830-1841. doi:10.1101/gr.176792.114

Fares, M. A. (2015). The origins of mutational robustness. Trends in Genetics, 31(7), 373-381. doi:10.1016/j.tig.2015.04.008

Gout, J.-F., & Lynch, M. (2015). Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization. Molecular Biology and Evolution, 32(8), 2141-2148. doi:10.1093/molbev/msv095

Altschul, S. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402. doi:10.1093/nar/25.17.3389

Byrne, K. P. (2005). The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Research, 15(10), 1456-1461. doi:10.1101/gr.3672305

Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M., & Usadel, B. (2012). RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40(W1), W622-W627. doi:10.1093/nar/gks540

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2009). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616

Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11(10). doi:10.1186/gb-2010-11-10-r106

Brion, C., Pflieger, D., Souali-Crespo, S., Friedrich, A., & Schacherer, J. (2016). Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. Molecular Biology of the Cell, 27(10), 1694-1705. doi:10.1091/mbc.e15-12-0816

Linde, J., Duggan, S., Weber, M., Horn, F., Sieber, P., Hellwig, D., … Kurzai, O. (2015). Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Research, 43(3), 1392-1406. doi:10.1093/nar/gku1357

Seoighe, C., & Wolfe, K. H. (1999). Yeast genome evolution in the post-genome era. Current Opinion in Microbiology, 2(5), 548-554. doi:10.1016/s1369-5274(99)00015-6

Aury, J.-M., Jaillon, O., Duret, L., Noel, B., Jubin, C., Porcel, B. M., … Wincker, P. (2006). Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature, 444(7116), 171-178. doi:10.1038/nature05230

Gout, J.-F., Kahn, D., & Duret, L. (2010). The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution. PLoS Genetics, 6(5), e1000944. doi:10.1371/journal.pgen.1000944

McGrath, C. L., Gout, J.-F., Doak, T. G., Yanagi, A., & Lynch, M. (2014). Insights into Three Whole-Genome Duplications Gleaned from theParamecium caudatumGenome Sequence. Genetics, 197(4), 1417-1428. doi:10.1534/genetics.114.163287

McGrath, C. L., Gout, J.-F., Johri, P., Doak, T. G., & Lynch, M. (2014). Differential retention and divergent resolution of duplicate genes following whole-genome duplication. Genome Research, 24(10), 1665-1675. doi:10.1101/gr.173740.114

Albert, F. W., Muzzey, D., Weissman, J. S., & Kruglyak, L. (2014). Genetic Influences on Translation in Yeast. PLoS Genetics, 10(10), e1004692. doi:10.1371/journal.pgen.1004692

Gout, J.-F., Duret, L., & Kahn, D. (2009). Differential Retention of Metabolic Genes Following Whole-Genome Duplication. Molecular Biology and Evolution, 26(5), 1067-1072. doi:10.1093/molbev/msp026

Papp, B., Pál, C., & Hurst, L. D. (2003). Dosage sensitivity and the evolution of gene families in yeast. Nature, 424(6945), 194-197. doi:10.1038/nature01771

Qian, W., Liao, B.-Y., Chang, A. Y.-F., & Zhang, J. (2010). Maintenance of duplicate genes and their functional redundancy by reduced expression. Trends in Genetics, 26(10), 425-430. doi:10.1016/j.tig.2010.07.002

Birchler, J. A., & Veitia, R. A. (2012). Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines. Proceedings of the National Academy of Sciences, 109(37), 14746-14753. doi:10.1073/pnas.1207726109

Pu, S., Wong, J., Turner, B., Cho, E., & Wodak, S. J. (2008). Up-to-date catalogues of yeast protein complexes. Nucleic Acids Research, 37(3), 825-831. doi:10.1093/nar/gkn1005

Scannell, D. R., Byrne, K. P., Gordon, J. L., Wong, S., & Wolfe, K. H. (2006). Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature, 440(7082), 341-345. doi:10.1038/nature04562

Landry, C. R., Lemos, B., Rifkin, S. A., Dickinson, W. J., & Hartl, D. L. (2007). Genetic Properties Influencing the Evolvability of Gene Expression. Science, 317(5834), 118-121. doi:10.1126/science.1140247

Lehner, B. (2010). Conflict between Noise and Plasticity in Yeast. PLoS Genetics, 6(11), e1001185. doi:10.1371/journal.pgen.1001185

Mattenberger, F., Sabater-Muñoz, B., Hallsworth, J. E., & Fares, M. A. (2017). Glycerol stress inSaccharomyces cerevisiae: Cellular responses and evolved adaptations. Environmental Microbiology, 19(3), 990-1007. doi:10.1111/1462-2920.13603

Mattenberger, F., Sabater-Muñoz, B., Toft, C., & Fares, M. A. (2016). The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations. G3: Genes|Genomes|Genetics, 7(1), 63-75. doi:10.1534/g3.116.035329

Blake, W. J., Balázsi, G., Kohanski, M. A., Isaacs, F. J., Murphy, K. F., Kuang, Y., … Collins, J. J. (2006). Phenotypic Consequences of Promoter-Mediated Transcriptional Noise. Molecular Cell, 24(6), 853-865. doi:10.1016/j.molcel.2006.11.003

Raser, J. M. (2005). Noise in Gene Expression: Origins, Consequences, and Control. Science, 309(5743), 2010-2013. doi:10.1126/science.1105891

Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., & Weissman, J. S. (2006). Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature, 441(7095), 840-846. doi:10.1038/nature04785

Tirosh, I., Weinberger, A., Carmi, M., & Barkai, N. (2006). A genetic signature of interspecies variations in gene expression. Nature Genetics, 38(7), 830-834. doi:10.1038/ng1819

[-]

recommendations

 

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro completo del ítem