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Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-3885
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dc.contributor.authorSchaper, Elke-
dc.contributor.authorGascuel, Olivier-
dc.contributor.authorAnisimova, Maria-
dc.date.accessioned2018-07-17T15:10:12Z-
dc.date.available2018-07-17T15:10:12Z-
dc.date.issued2014-
dc.identifier.issn0737-4038de_CH
dc.identifier.issn1537-1719de_CH
dc.identifier.urihttps://digitalcollection.zhaw.ch/handle/11475/8268-
dc.description.abstractTandem repeats (TRs) are a major element of protein sequences in all domains of life. They are particularly abundant in mammals, where by conservative estimates one in three proteins contain a TR. High generation-scale duplication and deletion rates were reported for nucleic TR units. However, it is not known whether protein TR units can also be frequently lost or gained providing a source of variation for rapid adaptation of protein function, or alternatively, tend to have conserved TR unit configurations over long evolutionary times. To obtain a systematic picture for proteins TRs, we performed a proteome-wide analysis of the mode of evolution for human TRs. For this purpose, we propose a novel method for the detection of orthologous TRs based on circular profile hidden Markov models. For all detected TRs we reconstructed bi-species TR unit phylogenies across 61 eukaryotes ranging from human to yeast. Moreover, we performed additional analyses to correlate functional and structural annotations of human TRs with their mode of evolution. Surprisingly, we find that the vast majority of human TRs are ancient, with TR unit number and order preserved intact since distant speciation events. For example, ≥61% of all human TRs have been strongly conserved at least since the root of all mammals, approximately 300 Mya ago. Further, we find no human protein TR that shows evidence for strong recent duplications and deletions. The results are in contrast to high generation-scale mutability of nucleic TRs. Presumably, most protein TRs fold into stable and conserved structures that are indispensable for the function of the TR-containing protein. All of our data and results are available for download from http://www.atgc-montpellier.fr/TRE.de_CH
dc.language.isoende_CH
dc.publisherOxford University Pressde_CH
dc.relation.ispartofMolecular Biology and Evolutionde_CH
dc.rightshttp://creativecommons.org/licenses/by/3.0/de_CH
dc.subjectProtein evolutionde_CH
dc.subjectTandem repeatde_CH
dc.subjectConservationde_CH
dc.subjectPhylogenetic analysisde_CH
dc.subject.ddc572: Biochemiede_CH
dc.titleDeep conservation of human protein tandem repeats within the eukaryotesde_CH
dc.typeBeitrag in wissenschaftlicher Zeitschriftde_CH
dcterms.typeTextde_CH
zhaw.departementLife Sciences und Facility Managementde_CH
zhaw.organisationalunitInstitut für Computational Life Sciences (ICLS)de_CH
dc.identifier.doi10.21256/zhaw-3885-
dc.identifier.doi10.1093/molbev/msu062de_CH
zhaw.funding.euNode_CH
zhaw.issue5de_CH
zhaw.originated.zhawYesde_CH
zhaw.pages.end1148de_CH
zhaw.pages.start1132de_CH
zhaw.publication.statuspublishedVersionde_CH
zhaw.volume31de_CH
zhaw.publication.reviewPeer review (Publikation)de_CH
zhaw.webfeedComputational Genomicsde_CH
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Schaper, E., Gascuel, O., & Anisimova, M. (2014). Deep conservation of human protein tandem repeats within the eukaryotes. Molecular Biology and Evolution, 31(5), 1132–1148. https://doi.org/10.21256/zhaw-3885
Schaper, E., Gascuel, O. and Anisimova, M. (2014) ‘Deep conservation of human protein tandem repeats within the eukaryotes’, Molecular Biology and Evolution, 31(5), pp. 1132–1148. Available at: https://doi.org/10.21256/zhaw-3885.
E. Schaper, O. Gascuel, and M. Anisimova, “Deep conservation of human protein tandem repeats within the eukaryotes,” Molecular Biology and Evolution, vol. 31, no. 5, pp. 1132–1148, 2014, doi: 10.21256/zhaw-3885.
SCHAPER, Elke, Olivier GASCUEL und Maria ANISIMOVA, 2014. Deep conservation of human protein tandem repeats within the eukaryotes. Molecular Biology and Evolution. 2014. Bd. 31, Nr. 5, S. 1132–1148. DOI 10.21256/zhaw-3885
Schaper, Elke, Olivier Gascuel, and Maria Anisimova. 2014. “Deep Conservation of Human Protein Tandem Repeats within the Eukaryotes.” Molecular Biology and Evolution 31 (5): 1132–48. https://doi.org/10.21256/zhaw-3885.
Schaper, Elke, et al. “Deep Conservation of Human Protein Tandem Repeats within the Eukaryotes.” Molecular Biology and Evolution, vol. 31, no. 5, 2014, pp. 1132–48, https://doi.org/10.21256/zhaw-3885.


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