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Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder

Telomeres are regions of tandem repeated sequences at the ends of linear chromosomes that protect against DNA damage and chromosome fusion. Telomeres are associated with senescence and cancers and have attracted the attention of an increasing number of researchers. However, few telomeric motif seque...

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Autores principales: Sun, Qing, Wang, Hao, Tao, Shiheng, Xi, Xuguang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10100673/
https://www.ncbi.nlm.nih.gov/pubmed/36847562
http://dx.doi.org/10.1128/spectrum.03928-22
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author Sun, Qing
Wang, Hao
Tao, Shiheng
Xi, Xuguang
author_facet Sun, Qing
Wang, Hao
Tao, Shiheng
Xi, Xuguang
author_sort Sun, Qing
collection PubMed
description Telomeres are regions of tandem repeated sequences at the ends of linear chromosomes that protect against DNA damage and chromosome fusion. Telomeres are associated with senescence and cancers and have attracted the attention of an increasing number of researchers. However, few telomeric motif sequences are known. Given the mounting interest in telomeres, an efficient computational tool for the de novo detection of the telomeric motif sequence of new species is needed since experimental-based methods are costly in terms of time and effort. Here, we report the development of TelFinder, an easy-to-use and freely available tool for the de novo detection of telomeric motif sequences from genomic data. The vast quantity of readily available genomic data makes it possible to apply this tool to any species of interest, which will undoubtedly inspire studies requiring telomeric repeat information and improve the utilization of these genomic data sets. We have tested TelFinder on telomeric sequences available in the Telomerase Database, and the detection accuracy reaches 90%. In addition, variation analyses in telomere sequences can be performed by TelFinder for the first time. The telomere variation preference of different chromosomes and even at the ends of the chromosome can provide clues regarding the underlying mechanisms of telomeres. Overall, these results shed new light on the divergent evolution of telomeres. IMPORTANCE Telomeres are reported to be highly correlated with the cell cycle and aging. As a result, research on telomere composition and evolution has become more and more urgent. However, using experimental methods to detect telomeric motif sequences is slow and costly. To combat this challenge, we developed TelFinder, a computational tool for the de novo detection of the telomere composition only using genomic data. In this study, we showed that a lot of complicated telomeric motifs could be identified by TelFinder only using genomic data. In addition, TelFinder can be used to check variation analyses in telomere sequences, which could lead to a deeper understanding of telomere sequences.
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spelling pubmed-101006732023-04-14 Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder Sun, Qing Wang, Hao Tao, Shiheng Xi, Xuguang Microbiol Spectr Methods and Protocols Telomeres are regions of tandem repeated sequences at the ends of linear chromosomes that protect against DNA damage and chromosome fusion. Telomeres are associated with senescence and cancers and have attracted the attention of an increasing number of researchers. However, few telomeric motif sequences are known. Given the mounting interest in telomeres, an efficient computational tool for the de novo detection of the telomeric motif sequence of new species is needed since experimental-based methods are costly in terms of time and effort. Here, we report the development of TelFinder, an easy-to-use and freely available tool for the de novo detection of telomeric motif sequences from genomic data. The vast quantity of readily available genomic data makes it possible to apply this tool to any species of interest, which will undoubtedly inspire studies requiring telomeric repeat information and improve the utilization of these genomic data sets. We have tested TelFinder on telomeric sequences available in the Telomerase Database, and the detection accuracy reaches 90%. In addition, variation analyses in telomere sequences can be performed by TelFinder for the first time. The telomere variation preference of different chromosomes and even at the ends of the chromosome can provide clues regarding the underlying mechanisms of telomeres. Overall, these results shed new light on the divergent evolution of telomeres. IMPORTANCE Telomeres are reported to be highly correlated with the cell cycle and aging. As a result, research on telomere composition and evolution has become more and more urgent. However, using experimental methods to detect telomeric motif sequences is slow and costly. To combat this challenge, we developed TelFinder, a computational tool for the de novo detection of the telomere composition only using genomic data. In this study, we showed that a lot of complicated telomeric motifs could be identified by TelFinder only using genomic data. In addition, TelFinder can be used to check variation analyses in telomere sequences, which could lead to a deeper understanding of telomere sequences. American Society for Microbiology 2023-02-27 /pmc/articles/PMC10100673/ /pubmed/36847562 http://dx.doi.org/10.1128/spectrum.03928-22 Text en Copyright © 2023 Sun et al. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Methods and Protocols
Sun, Qing
Wang, Hao
Tao, Shiheng
Xi, Xuguang
Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder
title Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder
title_full Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder
title_fullStr Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder
title_full_unstemmed Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder
title_short Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder
title_sort large-scale detection of telomeric motif sequences in genomic data using telfinder
topic Methods and Protocols
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10100673/
https://www.ncbi.nlm.nih.gov/pubmed/36847562
http://dx.doi.org/10.1128/spectrum.03928-22
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