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Valeeva LR, Sannikova AV, Shafigullina NR, Abdulkina LR, Sharipova MR, Shakirov EV. Telomere Length Variation in Model Bryophytes. PLANTS (BASEL, SWITZERLAND) 2024; 13:387. [PMID: 38337920 PMCID: PMC10856949 DOI: 10.3390/plants13030387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
The ends of linear chromosomes of most eukaryotes consist of protein-bound DNA arrays called telomeres, which play essential roles in protecting genome integrity. Despite general evolutionary conservation in function, telomeric DNA is known to drastically vary in length and sequence between different eukaryotic lineages. Bryophytes are a group of early diverging land plants that include mosses, liverworts, and hornworts. This group of ancient land plants recently emerged as a new model for important discoveries in genomics and evolutionary biology, as well as for understanding plant adaptations to a terrestrial lifestyle. We measured telomere length in different ecotypes of model bryophyte species, including Physcomitrium patens, Marchantia polymorpha, Ceratodon purpureus, and in Sphagnum isolates. Our data indicate that all analyzed moss and liverwort genotypes have relatively short telomeres. Furthermore, all analyzed ecotypes and isolates of model mosses and liverworts display evidence of substantial natural variation in telomere length. Interestingly, telomere length also differs between male and female strains of the dioecious liverwort M. polymorpha and dioecious moss C. purpureus. Given that bryophytes are extraordinarily well adapted to different ecological niches from polar to tropical environments, our data will contribute to understanding the impact of natural telomere length variation on evolutionary adaptations in this ancient land plant lineage.
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Affiliation(s)
- Liia R. Valeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (A.V.S.); (L.R.A.)
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
| | - Anastasia V. Sannikova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (A.V.S.); (L.R.A.)
| | - Nadiya R. Shafigullina
- Institute of Environmental Sciences, Department of General Ecology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia
| | - Liliia R. Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (A.V.S.); (L.R.A.)
| | - Margarita R. Sharipova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia; (A.V.S.); (L.R.A.)
| | - 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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Shakirov EV, Chen JJL, Shippen DE. Plant telomere biology: The green solution to the end-replication problem. THE PLANT CELL 2022; 34:2492-2504. [PMID: 35511166 PMCID: PMC9252485 DOI: 10.1093/plcell/koac122] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/14/2022] [Indexed: 05/04/2023]
Abstract
Telomere maintenance is a fundamental cellular process conserved across all eukaryotic lineages. Although plants and animals diverged over 1.5 billion years ago, lessons learned from plants continue to push the boundaries of science, revealing detailed molecular mechanisms in telomere biology with broad implications for human health, aging biology, and stress responses. Recent studies of plant telomeres have unveiled unexpected divergence in telomere sequence and architecture, and the proteins that engage telomeric DNA and telomerase. The discovery of telomerase RNA components in the plant kingdom and some algae groups revealed new insight into the divergent evolution and the universal core of telomerase across major eukaryotic kingdoms. In addition, resources cataloging the abundant natural variation in Arabidopsis thaliana, maize (Zea mays), and other plants are providing unparalleled opportunities to understand the genetic networks that govern telomere length polymorphism and, as a result, are uncovering unanticipated crosstalk between telomeres, environmental factors, organismal fitness, and plant physiology. Here we recap current advances in plant telomere biology and put this field in perspective relative to telomere and telomerase research in other eukaryotic lineages.
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Affiliation(s)
- Eugene V Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia 25701, USA
| | - Julian J -L Chen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
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Choi JY, Abdulkina LR, Yin J, Chastukhina IB, Lovell JT, Agabekian IA, Young PG, Razzaque S, Shippen DE, Juenger TE, Shakirov EV, Purugganan MD. Natural variation in plant telomere length is associated with flowering time. THE PLANT CELL 2021; 33:1118-1134. [PMID: 33580702 PMCID: PMC8599780 DOI: 10.1093/plcell/koab022] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/14/2021] [Indexed: 05/05/2023]
Abstract
Telomeres are highly repetitive DNA sequences found at the ends of chromosomes that protect the chromosomes from deterioration duringcell division. Here, using whole-genome re-sequencing and terminal restriction fragment assays, we found substantial natural intraspecific variation in telomere length in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). Genome-wide association study (GWAS) mapping in A. thaliana identified 13 regions with GWAS-significant associations underlying telomere length variation, including a region that harbors the telomerase reverse transcriptase (TERT) gene. Population genomic analysis provided evidence for a selective sweep at the TERT region associated with longer telomeres. We found that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life-history traits and chromosome integrity. Our results point to several possible reasons for this correlation, including the possibility that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier). Our work suggests that chromosomal structure itself might be an adaptive trait associated with plant life-history strategies.
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Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003, NY, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
| | - Liliia R Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - Jun Yin
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Inna B Chastukhina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Alabama 35806, USA
| | - Inna A Agabekian
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - Pierce G Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
| | - Samsad Razzaque
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Eugene V Shakirov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
- Department of Biological Sciences, College of Science, Marshall University, West Virginia 25701, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, West Virginia 25755, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003, NY, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
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Potlapalli BP, Schubert V, Metje-Sprink J, Liehr T, Houben A. Application of Tris-HCl Allows the Specific Labeling of Regularly Prepared Chromosomes by CRISPR-FISH. Cytogenet Genome Res 2020; 160:156-165. [PMID: 32200382 DOI: 10.1159/000506720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2020] [Indexed: 11/19/2022] Open
Abstract
Visualizing the spatiotemporal organization of the genome will improve our understanding of how chromatin structure and function are intertwined. Here, we describe the further development of the RNA-guided endonuclease-in situ labeling (RGEN-ISL) method CRISPR-FISH. Using soybean and mouse chromosomes, we demonstrate that the treatment of conventionally fixed chromosomes (in ethanol or methanol:acetic acid) with 40 mM Tris-HCl (pH 9.0) for 30 minutes at 37°C prior to CRISPR-FISH allows the application of this method for the detection of high-copy sequences. Wheat, rye, maize, and Nicotiana benthamiana were used to confirm the applicability of the identified CRISPR-FISH conditions also in other species.
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Fulcher N, Teubenbacher A, Kerdaffrec E, Farlow A, Nordborg M, Riha K. Genetic architecture of natural variation of telomere length in Arabidopsis thaliana. Genetics 2015; 199:625-35. [PMID: 25488978 PMCID: PMC4317667 DOI: 10.1534/genetics.114.172163] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/25/2014] [Indexed: 11/18/2022] Open
Abstract
Telomeres represent the repetitive sequences that cap chromosome ends and are essential for their protection. Telomere length is known to be highly heritable and is derived from a homeostatic balance between telomeric lengthening and shortening activities. Specific loci that form the genetic framework underlying telomere length homeostasis, however, are not well understood. To investigate the extent of natural variation of telomere length in Arabidopsis thaliana, we examined 229 worldwide accessions by terminal restriction fragment analysis. The results showed a wide range of telomere lengths that are specific to individual accessions. To identify loci that are responsible for this variation, we adopted a quantitative trait loci (QTL) mapping approach with multiple recombinant inbred line (RIL) populations. A doubled haploid RIL population was first produced using centromere-mediated genome elimination between accessions with long (Pro-0) and intermediate (Col-0) telomere lengths. Composite interval mapping analysis of this population along with two established RIL populations (Ler-2/Cvi-0 and Est-1/Col-0) revealed a number of shared and unique QTL. QTL detected in the Ler-2/Cvi-0 population were examined using near isogenic lines that confirmed causative regions on chromosomes 1 and 2. In conclusion, this work describes the extent of natural variation of telomere length in A. thaliana, identifies a network of QTL that influence telomere length homeostasis, examines telomere length dynamics in plants with hybrid backgrounds, and shows the effects of two identified regions on telomere length regulation.
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Affiliation(s)
- Nick Fulcher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Astrid Teubenbacher
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Envel Kerdaffrec
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Ashley Farlow
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria
| | - Karel Riha
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna 1030, Austria Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, Czech Republic
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Andorf CM, Kopylov M, Dobbs D, Koch KE, Stroupe ME, Lawrence CJ, Bass HW. G-Quadruplex (G4) Motifs in the Maize (Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status, Hypoxia, Low Sugar, and Nutrient Deprivation. J Genet Genomics 2014; 41:627-47. [DOI: 10.1016/j.jgg.2014.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 10/16/2014] [Accepted: 10/24/2014] [Indexed: 02/07/2023]
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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 2013; 42:e21. [PMID: 24366880 PMCID: PMC3919618 DOI: 10.1093/nar/gkt1315] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Telomeres comprise the protective caps of natural chromosome ends and function in the suppression of DNA damage signaling and cellular senescence. Therefore, techniques used to determine telomere length are important in a number of studies, ranging from those investigating telomeric structure to effects on human disease. Terminal restriction fragment (TRF) analysis has for a long time shown to be one of the most accurate methods for quantification of absolute telomere length and range from a number of species. As this technique centers on standard Southern blotting, telomeric DNA is observed on resulting autoradiograms as a heterogeneous smear. Methods to accurately determine telomere length from telomeric smears have proven problematic, and no reliable technique has been suggested to obtain mean telomere length values. Here, we present TeloTool, a new program allowing thorough statistical analysis of TRF data. Using this new method, a number of methodical biases are removed from previously stated techniques, including assumptions based on probe intensity corrections. This program provides a standardized mean for quick and reliable extraction of quantitative data from TRF autoradiograms; its wide application will allow accurate comparison between datasets generated in different laboratories.
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Affiliation(s)
- Janett Göhring
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna 1030, Austria, Gregor Mendel Institute, Vienna 1030, Austria, Institute for Applied Physics, Johannes Kepler University Linz, Linz 4040, Austria and Upper Austria University of Applied Sciences, Campus Linz, Linz 4020, Austria
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Bragg JN, Wu J, Gordon SP, Guttman ME, Thilmony R, Lazo GR, Gu YQ, Vogel JP. Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection. PLoS One 2012; 7:e41916. [PMID: 23028431 PMCID: PMC3444500 DOI: 10.1371/journal.pone.0041916] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 06/29/2012] [Indexed: 11/18/2022] Open
Abstract
The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optimized our Agrobacterium tumefaciens-mediated high-efficiency transformation method and generated 8,491 Brachypodium T-DNA lines. We used inverse PCR to sequence the DNA flanking the insertion sites in the mutants. Using these flanking sequence tags (FSTs) we were able to assign 7,389 FSTs from 4,402 T-DNA mutants to 5,285 specific insertion sites (ISs) in the Brachypodium genome. More than 29% of the assigned ISs are supported by multiple FSTs. T-DNA insertions span the entire genome with an average of 19.3 insertions/Mb. The distribution of T-DNA insertions is non-uniform with a larger number of insertions at the distal ends compared to the centromeric regions of the chromosomes. Insertions are correlated with genic regions, but are biased toward UTRs and non-coding regions within 1 kb of genes over exons and intron regions. More than 1,300 unique genes have been tagged in this population. Information about the Western Regional Research Center Brachypodium insertional mutant population is available on a searchable website (http://brachypodium.pw.usda.gov) designed to provide researchers with a means to order T-DNA lines with mutations in genes of interest.
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Affiliation(s)
- Jennifer N. Bragg
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- University of California Davis, Davis, California, United States of America
| | - Jiajie Wu
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- University of California Davis, Davis, California, United States of America
| | - Sean P. Gordon
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Mara E. Guttman
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Roger Thilmony
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Gerard R. Lazo
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - Yong Q. Gu
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- United States Department of Agriculture- Agriculture Research Service (USDA-ARS), Western Regional Research Center, Albany, California, United States of America
- * E-mail:
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Howe ES, Clemente TE, Bass HW. Maize histone H2B-mCherry: a new fluorescent chromatin marker for somatic and meiotic chromosome research. DNA Cell Biol 2012; 31:925-38. [PMID: 22662764 PMCID: PMC3378959 DOI: 10.1089/dna.2011.1514] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/26/2012] [Accepted: 01/26/2012] [Indexed: 11/12/2022] Open
Abstract
Cytological studies of fluorescent proteins are rapidly yielding insights into chromatin structure and dynamics. Here we describe the production and cytological characterization of new transgenic maize lines expressing a fluorescent histone fusion protein, H2B-mCherry. The transgene is expressed under the control of the maize ubiquitin1 promoter, including its first exon and intron. Polymerase chain reaction-based genotyping and root-tip microscopy showed that most of the lines carrying the transgene also expressed it, producing bright uniform staining of nuclei. Further, plants showing expression in root tips at the seedling stage also showed expression during meiosis, late in the life cycle. Detailed high-resolution three-dimensional imaging of cells and nuclei from various somatic and meiotic cell types showed that H2B-mCherry produced remarkably clear images of chromatin and chromosome fiber morphology, as seen in somatic, male meiotic prophase, and early microgametophyte cells. H2B-mCherry also yielded distinct nucleolus staining and was shown to be compatible with fluorescence in situ hybridization. We found several instances where H2B-mCherry was superior to DAPI as a generalized chromatin stain. Our study establishes these histone H2B-mCherry lines as new biological reagents for visualizing chromatin structure, chromosome morphology, and nuclear dynamics in fixed and living cells in a model plant genetic system.
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Affiliation(s)
- Elizabeth S. Howe
- Department of Biological Science, Florida State University, Tallahassee, Florida
| | - Thomas E. Clemente
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, Florida
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