WALTER: an easy way to online evaluate telomere lengths from terminal restriction fragment analysis

. 2021 Mar 22 ; 22 (1) : 145. [epub] 20210322

Jazyk angličtina Země Velká Británie, Anglie Médium electronic

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid33752601

Grantová podpora
18-07027S Grantová Agentura České Republiky
CZ.02.1.01/0.0 /0.0/15_003/0000477 European Regional and Development Fund

Odkazy

PubMed 33752601
PubMed Central PMC7986547
DOI 10.1186/s12859-021-04064-0
PII: 10.1186/s12859-021-04064-0
Knihovny.cz E-zdroje

BACKGROUND: Telomeres, nucleoprotein structures comprising short tandem repeats and delimiting the ends of linear eukaryotic chromosomes, play an important role in the maintenance of genome stability. Therefore, the determination of the length of telomeres is of high importance for many studies. Over the last years, new methods for the analysis of the length of telomeres have been developed, including those based on PCR or analysis of NGS data. Despite that, terminal restriction fragment (TRF) method remains the gold standard to this day. However, this method lacks universally accepted and precise tool capable to analyse and statistically evaluate TRF results. RESULTS: To standardize the processing of TRF results, we have developed WALTER, an online toolset allowing rapid, reproducible, and user-friendly analysis including statistical evaluation of the data. Given its web-based nature, it provides an easily accessible way to analyse TRF data without any need to install additional software. CONCLUSIONS: WALTER represents a major upgrade from currently available tools for the image processing of TRF scans. This toolset enables a rapid, highly reproducible, and user-friendly evaluation of almost any TRF scan including in-house statistical evaluation of the data. WALTER platform together with user manual describing the evaluation of TRF scans in detail and presenting tips and troubleshooting, as well as test data to demo the software are available at https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51/tab?tabId=125#WALTER and the source code at https://github.com/mlyc93/WALTER .

Zobrazit více v PubMed

Montpetit AJ, Alhareeri AA, Montpetit M, Starkweather AR, Elmore LW, Filler K, et al. Telomere length: a review of methods for measurement. Nurs Res. 2014;63:289–299. doi: 10.1097/NNR.0000000000000037. PubMed DOI PMC

Lee M, Napier CE, Yang SF, Arthur JW, Reddel RR, Pickett HA. Comparative analysis of whole genome sequencing-based telomere length measurement techniques. Methods. 2017;114:4–15. doi: 10.1016/j.ymeth.2016.08.008. PubMed DOI

Petracek ME, Lefebvre PA, Silflow CD, Berman J. Chlamydomonas telomere sequences are A + T-rich but contain three consecutive G·C base pairs. Proc Natl Acad Sci USA. 1990;87:8222–8226. doi: 10.1073/pnas.87.21.8222. PubMed DOI PMC

Fajkus J, Kovařík A, Královics R, Bezděk M. Organization of telomeric and subtelomeric chromatin in the higher plant Nicotiana tabacum. Mol Gen Genet. 1995;247:633–638. doi: 10.1007/BF00290355. PubMed DOI

Fojtova M, Fajkus P, Polanska P, Fajkus J. Terminal restriction fragments (TRF) method to analyze telomere lengths. Bio-protocol. 2015;5:66.

Grant JD, Broccoli D, Muquit M, Manion FJ, Tisdall J, Ochs MF. Telometric: a tool providing simplified, reproducible measurements of telomeric DNA from constant field agarose gels. Biotechniques. 2001;31:1314–1318. doi: 10.2144/01316bc02. PubMed DOI

Göhring J, Fulcher N, Jacak J, Riha K. TeloTool: a new tool for telomere length measurement from terminal restriction fragment analysis with improved probe intensity correction. Nucleic Acids Res. 2014;42:e21. doi: 10.1093/nar/gkt1315. PubMed DOI PMC

Chang W, Cheng J, Allaire JJ, Xie Y and McPherson J. shiny: Web Application Framework for R. https://CRAN.R-project.org/package=shiny.

Wan X, Wang W, Liu J, Tong T. Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range. BMC Med Res Methodol. 2014;14:135. doi: 10.1186/1471-2288-14-135. PubMed DOI PMC

Higgins JPT, Thomas J, Chandler J, Cumpston M, Li T, Page MJ, Welch VA (editors). Cochrane handbook for systematic reviews of interventions. 2nd ed. Wiley; 2019. 10.1002/9781119536604. PubMed PMC

Bryan TM, Englezou A, Gupta J, Bacchetti S, Reddel RR. Telomere elongation in immortal human cells without detectable telomerase activity. EMBO J. 1995;14:4240–4248. doi: 10.1002/j.1460-2075.1995.tb00098.x. PubMed DOI PMC

Kimura M, Stone RC, Hunt SC, Skurnick J, Lu X, Cao X, et al. Measurement of telomere length by the southern blot analysis of terminal restriction fragment lengths. Nat Protoc. 2010;5:1596–1607. doi: 10.1038/nprot.2010.124. PubMed DOI

Mender I, Shay J. Telomere restriction fragment (TRF) analysis. Bio-protocol. 2015;5:66. PubMed PMC

Jenkins FJ, Kerr CM, Fouquerel E, Bovbjerg DH, Opresko PL. Modified terminal restriction fragment analysis for quantifying telomere length using in-gel hybridization. J Vis Exp. 2017;125:e56001. PubMed PMC

Lincz LF, Scorgie FE, Garg MB, Gilbert J, Sakoff JA. A simplified method to calculate telomere length from Southern blot images of terminal restriction fragment lengths. Biotechniques. 2020;68:28–34. doi: 10.2144/btn-2019-0082. PubMed DOI

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...