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dc.contributor.authorMaddi, Ali M. A.
dc.contributor.authorKavousi, Kaveh
dc.contributor.authorArabfard, Masoud
dc.contributor.authorOhadi, Hamid
dc.contributor.authorOhadi, Mina
dc.date.accessioned2022-07-28T12:30:13Z
dc.date.available2022-07-28T12:30:13Z
dc.date.issued2022-07-27
dc.identifier.citationMaddi , A M A , Kavousi , K , Arabfard , M , Ohadi , H & Ohadi , M 2022 , ' Tandem repeats ubiquitously flank and contribute to translation initiation sites ' , BMC Genomic Data , vol. 23 , 59 . https://doi.org/10.1186/s12863-022-01075-5en
dc.identifier.issn2730-6844
dc.identifier.otherPURE: 280644519
dc.identifier.otherPURE UUID: 30b85281-cb6e-4307-9700-2165a7b1242c
dc.identifier.otherRIS: urn:5F9966CA4EACB486527FBF34D6B56B2E
dc.identifier.otherRIS: Maddi2022
dc.identifier.otherORCID: /0000-0001-6418-111X/work/116597659
dc.identifier.urihttp://hdl.handle.net/10023/25740
dc.description.abstractBackground While the evolutionary divergence of cis-regulatory sequences impacts translation initiation sites (TISs), the implication of tandem repeats (TRs) in TIS selection remains largely elusive. Here, we employed the TIS homology concept to study a possible link between TRs of all core lengths and repeats with TISs. Methods Human, as reference sequence, and 83 other species were selected, and data was extracted on the entire protein-coding genes (n = 1,611,368) and transcripts (n = 2,730,515) annotated for those species from Ensembl 102. Following TIS identification, two different weighing vectors were employed to assign TIS homology, and the co-occurrence pattern of TISs with the upstream flanking TRs was studied in the selected species. The results were assessed in 10-fold cross-validation. Results On average, every TIS was flanked by 1.19 TRs of various categories within its 120 bp upstream sequence, per species. We detected statistically significant enrichment of non-homologous human TISs co-occurring with human-specific TRs. On the contrary, homologous human TISs co-occurred significantly with non-human-specific TRs. 2991 human genes had at least one transcript, TIS of which was flanked by a human-specific TR. Text mining of a number of the identified genes, such as CACNA1A, EIF5AL1, FOXK1, GABRB2, MYH2, SLC6A8, and TTN, yielded predominant expression and functions in the human brain and/or skeletal muscle. Conclusion We conclude that TRs ubiquitously flank and contribute to TIS selection at the trans-species level. Future functional analyses, such as a combination of genome editing strategies and in vitro protein synthesis may be employed to further investigate the impact of TRs on TIS selection.
dc.format.extent11
dc.language.isoeng
dc.relation.ispartofBMC Genomic Dataen
dc.rightsCopyright © The Author(s) 2022. Article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver applies to the data made available in this article, unless otherwise stated in a credit line to the data.en
dc.subjectGenome-scaleen
dc.subjectTandem repeaten
dc.subjectTranslation initiation siteen
dc.subjectHomologyen
dc.subjectTIS selectionen
dc.subjectQH426 Geneticsen
dc.subjectDASen
dc.subject.lccQH426en
dc.titleTandem repeats ubiquitously flank and contribute to translation initiation sitesen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. School of Physics and Astronomyen
dc.contributor.institutionUniversity of St Andrews. Centre for Designer Quantum Materialsen
dc.identifier.doihttps://doi.org/10.1186/s12863-022-01075-5
dc.description.statusPeer revieweden


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