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Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-22627
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dc.contributor.authorVerbiest, Max-
dc.contributor.authorDelucchi, Matteo-
dc.contributor.authorBilgin Sonay, Tugce-
dc.contributor.authorAnisimova, Maria-
dc.date.accessioned2021-06-11T13:03:01Z-
dc.date.available2021-06-11T13:03:01Z-
dc.date.issued2021-06-08-
dc.identifier.issn2673-7647de_CH
dc.identifier.urihttps://digitalcollection.zhaw.ch/handle/11475/22627-
dc.description.abstractShort tandem repeats (STRs) are abundant in genomic sequences and are known for comparatively high mutation rates; STRs therefore are thought to be a potent source of genetic diversity. In protein-coding sequences STRs primarily encode disorder-promoting amino acids and are often located in intrinsically disordered regions (IDRs). STRs are frequently studied in the scope of microsatellite instability (MSI) in cancer, with little focus on the connection between protein STRs and IDRs. We believe, however, that this relationship should be explicitly included when ascertaining STR functionality in cancer. Here we explore this notion using all canonical human proteins from SwissProt, wherein we detected 3,699 STRs. Over 80% of these consisted completely of disorder promoting amino acids. 62.1% of amino acids in STR sequences were predicted to also be in an IDR, compared to 14.2% for non-repeat sequences. Over-representation analysis showed STR-containing proteins to be primarily located in the nucleus where they perform protein- and nucleotide-binding functions and regulate gene expression. They were also enriched in cancer-related signaling pathways. Furthermore, we found enrichments of STR-containing proteins among those correlated with patient survival for cancers derived from eight different anatomical sites. Intriguingly, several of these cancer types are not known to have a MSI-high (MSI-H) phenotype, suggesting that protein STRs play a role in cancer pathology in non MSI-H settings. Their intrinsic link with IDRs could therefore be an attractive topic of future research to further explore the role of STRs and IDRs in cancer. We speculate that our observations may be linked to the known dosage-sensitivity of disordered proteins, which could hint at a concentration-dependent gain-of-function mechanism in cancer for proteins containing STRs and IDRs.de_CH
dc.language.isoende_CH
dc.publisherFrontiers Research Foundationde_CH
dc.relation.ispartofFrontiers in Bioinformaticsde_CH
dc.rightshttp://creativecommons.org/licenses/by/4.0/de_CH
dc.subjectShort tandem repeatsde_CH
dc.subjectMicrosatellitesde_CH
dc.subjectMicrosatellite instabilityde_CH
dc.subjectIntrinsic disorderde_CH
dc.subjectCancerde_CH
dc.subjectComputational biologyde_CH
dc.subjectProtein bioinformaticsde_CH
dc.subject.ddc572: Biochemiede_CH
dc.titleBeyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancerde_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.doi10.3389/fbinf.2021.685844de_CH
dc.identifier.doi10.21256/zhaw-22627-
zhaw.funding.euinfo:eu-repo/grantAgreement/EC/H2020/823886//Repeat protein Function Refinement, Annotation and Classification of Topologies/REFRACTde_CH
zhaw.issue685844de_CH
zhaw.originated.zhawYesde_CH
zhaw.publication.statuspublishedVersionde_CH
zhaw.volume1de_CH
zhaw.publication.reviewPeer review (Publikation)de_CH
zhaw.funding.snf193832de_CH
zhaw.webfeedComputational Genomicsde_CH
zhaw.webfeedMedical Image Analysis & Data Modelingde_CH
zhaw.funding.zhawTrans-omic approach to colorectal cancer: an integrative computational and clinical perspectivede_CH
zhaw.author.additionalNode_CH
zhaw.display.portraitYesde_CH
zhaw.monitoring.costperiod2021de_CH
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Verbiest, M., Delucchi, M., Bilgin Sonay, T., & Anisimova, M. (2021). Beyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancer. Frontiers in Bioinformatics, 1(685844). https://doi.org/10.3389/fbinf.2021.685844
Verbiest, M. et al. (2021) ‘Beyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancer’, Frontiers in Bioinformatics, 1(685844). Available at: https://doi.org/10.3389/fbinf.2021.685844.
M. Verbiest, M. Delucchi, T. Bilgin Sonay, and M. Anisimova, “Beyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancer,” Frontiers in Bioinformatics, vol. 1, no. 685844, Jun. 2021, doi: 10.3389/fbinf.2021.685844.
VERBIEST, Max, Matteo DELUCCHI, Tugce BILGIN SONAY und Maria ANISIMOVA, 2021. Beyond microsatellite instability : intrinsic disorder as a potential link between protein short tandem repeats and cancer. Frontiers in Bioinformatics. 8 Juni 2021. Bd. 1, Nr. 685844. DOI 10.3389/fbinf.2021.685844
Verbiest, Max, Matteo Delucchi, Tugce Bilgin Sonay, and Maria Anisimova. 2021. “Beyond Microsatellite Instability : Intrinsic Disorder as a Potential Link between Protein Short Tandem Repeats and Cancer.” Frontiers in Bioinformatics 1 (685844). https://doi.org/10.3389/fbinf.2021.685844.
Verbiest, Max, et al. “Beyond Microsatellite Instability : Intrinsic Disorder as a Potential Link between Protein Short Tandem Repeats and Cancer.” Frontiers in Bioinformatics, vol. 1, no. 685844, June 2021, https://doi.org/10.3389/fbinf.2021.685844.


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