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Abdulkina LR, Agabekian IA, Valeeva LR, Kozlova OS, Sharipova MR, Shakirov EV. Comparative Application of Terminal Restriction Fragment Analysis Tools to Large-Scale Genomic Assays. Int J Mol Sci 2023; 24:17194. [PMID: 38139024 PMCID: PMC10742804 DOI: 10.3390/ijms242417194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
The analysis of telomere length is an important component of many studies aiming to characterize the role of telomere maintenance mechanisms in cellular lifespan, disease, or in general chromosome protection and DNA replication pathways. Several powerful methods to accurately measure the telomere length from Southern blots have been developed, but their utility for large-scale genomic studies has not been previously evaluated. Here, we performed a comparative analysis of two recently developed programs, TeloTool and WALTER, for the extraction of mean telomere length values from Southern blots. Using both software packages, we measured the telomere length in two extensive experimental datasets for the model plant Arabidopsis thaliana, consisting of 537 natural accessions and 65 T-DNA (transfer DNA for insertion mutagenesis) mutant lines in the reference Columbia (Col-0) genotype background. We report that TeloTool substantially overestimates the telomere length in comparison to WALTER, especially for values over 4500 bp. Importantly, the TeloTool- and WALTER-calculated telomere length values correlate the most in the 2100-3500 bp range, suggesting that telomeres in this size interval can be estimated by both programs equally well. We further show that genome-wide association studies using datasets from both telomere length analysis tools can detect the most significant SNP candidates equally well. However, GWAS analysis with the WALTER dataset consistently detects fewer significant SNPs than analysis with the TeloTool dataset, regardless of the GWAS method used. These results imply that the telomere length data generated by WALTER may represent a more stringent approach to GWAS and SNP selection for the downstream molecular screening of candidate genes. Overall, our work reveals the unanticipated impact of the telomere length analysis method on the outcomes of large-scale genomic screens.
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Affiliation(s)
- Liliia R. Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (L.R.A.); (I.A.A.); (L.R.V.); (O.S.K.); (M.R.S.)
| | - Inna A. Agabekian
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (L.R.A.); (I.A.A.); (L.R.V.); (O.S.K.); (M.R.S.)
| | - Liia R. Valeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (L.R.A.); (I.A.A.); (L.R.V.); (O.S.K.); (M.R.S.)
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
| | - Olga S. Kozlova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (L.R.A.); (I.A.A.); (L.R.V.); (O.S.K.); (M.R.S.)
| | - Margarita R. Sharipova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (L.R.A.); (I.A.A.); (L.R.V.); (O.S.K.); (M.R.S.)
| | - Eugene V. Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
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