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Wang L, Zhang S, Fang J, Jin X, Mamut R, Li P. The Chloroplast Genome of the Lichen Photobiont Trebouxiophyceae sp. DW1 and Its Phylogenetic Implications. Genes (Basel) 2022; 13:genes13101840. [PMID: 36292725 PMCID: PMC9601494 DOI: 10.3390/genes13101840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Lichens are symbiotic associations of algae and fungi. The genetic mechanism of the symbiosis of lichens and the influence of symbiosis on the size and composition of the genomes of symbiotic algae have always been intriguing scientific questions explored by lichenologists. However, there were limited data on lichen genomes. Therefore, we isolated and purified a lichen symbiotic alga to obtain a single strain (Trebouxiophyceae sp. DW1), and then obtained its chloroplast genome information by next-generation sequencing (NGS). The chloroplast genome is 129,447 bp in length, and the GC content is 35.2%. Repetitive sequences with the length of 30–35 bp account for 1.27% of the total chloroplast genome. The simple sequence repeats are all mononucleotide repeats. Codon usage analysis showed that the genome tended to use codon ending in A/U. By comparing the length of different regions of Trebouxiophyceae genomes, we found that the changes in the length of exons, introns, and intergenic sequences affect the size of genomes. Trebouxiophyceae had an unstable chloroplast genome structure, with IRs repeatedly losing during evolution. Phylogenetic analysis showed that Trebouxiophyceae is paraphyletic, and Trebouxiophyceae sp. DW1 is sister to the clade of Koliella longiseta and Pabia signiensis.
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Affiliation(s)
- Lidan Wang
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, China
| | - Shenglu Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinjin Fang
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, China
| | - Xinjie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Reyim Mamut
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, China
- Correspondence: (R.M.); (P.L.)
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Correspondence: (R.M.); (P.L.)
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Jiang M, Wu X, Song Y, Shen H, Cui H. Effects of OsMSH6 Mutations on Microsatellite Stability and Homeologous Recombination in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:220. [PMID: 32194600 PMCID: PMC7062918 DOI: 10.3389/fpls.2020.00220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/12/2020] [Indexed: 05/02/2023]
Abstract
DNA mismatch repair (MMR) system is important for maintaining DNA replication fidelity and genome stability by repairing erroneous deletions, insertions and mis-incorporation of bases. With the aim of deciphering the role of the MMR system in genome stability and recombination in rice, we investigated the function of OsMSH6 gene, an import component of the MMR system. To achieve this goal, homeologous recombination and endogenous microsatellite stability were evaluated by using rice mutants carrying a Tos17 insertion into the OsMSH6 gene. Totally 60 microsatellites were analyzed and 15 distributed on chromosome 3, 6, 8, and 10 showed instability in three OsMSH6 mutants, D6011, NF7784 and NF9010, compared with the wild type MSH6WT (the control). The disruption of OsMSH6 gene is associated with modest increases in homeologous recombination, ranging from 2.0% to 32.5% on chromosome 1, 3, 9, and 10 in the BCF2 populations of the mutant ND6011 and NF9010. Our results suggest that the OsMSH6 plays an important role in ensuring genome stability and genetic recombination, providing the first evidence for the MSH6 gene in maintaining microsatellite stability and restricting homeologous recombination in plants.
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Affiliation(s)
- Meng Jiang
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Science, Zhejiang University, Hangzhou, China
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Xiaojiang Wu
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Science, Zhejiang University, Hangzhou, China
| | - Yue Song
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Science, Zhejiang University, Hangzhou, China
| | - Hongzhe Shen
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Science, Zhejiang University, Hangzhou, China
| | - Hairui Cui
- Key Laboratory of Chinese Ministry of Agriculture for Nuclear-Agricultural Sciences, Institute of Nuclear-Agricultural Science, Zhejiang University, Hangzhou, China
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3
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Heissl A, Betancourt AJ, Hermann P, Povysil G, Arbeithuber B, Futschik A, Ebner T, Tiemann-Boege I. The impact of poly-A microsatellite heterologies in meiotic recombination. Life Sci Alliance 2019; 2:2/2/e201900364. [PMID: 31023833 PMCID: PMC6485458 DOI: 10.26508/lsa.201900364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/27/2019] [Accepted: 03/29/2019] [Indexed: 12/12/2022] Open
Abstract
Meiosis strongly influences the transmission and evolution of heterozygous poly-A repeats as measured experimentally in a large collection of single recombination products in a human hotspot. Meiotic recombination has strong, but poorly understood effects on short tandem repeat (STR) instability. Here, we screened thousands of single recombinant products with sperm typing to characterize the role of polymorphic poly-A repeats at a human recombination hotspot in terms of hotspot activity and STR evolution. We show that the length asymmetry between heterozygous poly-A’s strongly influences the recombination outcome: a heterology of 10 A’s (9A/19A) reduces the number of crossovers and elevates the frequency of non-crossovers, complex recombination products, and long conversion tracts. Moreover, the length of the heterology also influences the STR transmission during meiotic repair with a strong and significant insertion bias for the short heterology (6A/7A) and a deletion bias for the long heterology (9A/19A). In spite of this opposing insertion-/deletion-biased gene conversion, we find that poly-A’s are enriched at human recombination hotspots that could have important consequences in hotspot activation.
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Affiliation(s)
- Angelika Heissl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | | | - Philipp Hermann
- Institute of Applied Statistics, Johannes Kepler University, Linz, Austria
| | - Gundula Povysil
- Institute of Bioinformatics, Johannes Kepler University, Linz, Austria
| | | | - Andreas Futschik
- Institute of Applied Statistics, Johannes Kepler University, Linz, Austria
| | - Thomas Ebner
- Department of Gynecology, Obstetrics and Gynecological Endocrinology, Kepler University Clinic, Linz, Austria
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Bernardi B, Kayacan Y, Wendland J. Expansion of a Telomeric FLO/ALS-Like Sequence Gene Family in Saccharomycopsis fermentans. Front Genet 2018; 9:536. [PMID: 30542368 PMCID: PMC6277891 DOI: 10.3389/fgene.2018.00536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023] Open
Abstract
Non-Saccharomyces species have been recognized for their beneficial contribution to fermented food and beverages based on their volatile compound formation and their ability to ferment glucose into ethanol. At the end of fermentation brewer's yeast flocculate which provides an easy means of separation of yeasts from green beer. Flocculation in Saccharomyces cerevisiae requires a set of flocculation genes. These FLO-genes, FLO1, FLO5, FLO9, FLO10, and FLO11, are located at telomeres and transcription of these adhesins is regulated by Flo8 and Mss11. Here, we show that Saccharomycopsis fermentans, an ascomycete yeast distantly related to S. cerevisiae, possesses a very large FLO/ALS-like Sequence (FAS) family encompassing 34 genes. Fas proteins are variable in size and divergent in sequence and show similarity to the Flo1/5/9 family. Fas proteins show the general build with a signal peptide, an N-terminal carbohydrate binding PA14 domain, a central region differing by the number of repeats and a C-terminus with a consensus sequence for GPI-anchor attachment. Like FLO genes in S. cerevisiae, FAS genes are mostly telomeric with several paralogs at each telomere. We term such genes that share evolutionary conserved telomere localization "telologs" and provide several other examples. Adhesin expression in S. cerevisiae and filamentation in Candida albicans is regulated by Flo8 and Mss11. In Saccharomycopsis we identified only a single protein with similarity to Flo8 based on sequence similarity and the presence of a LisH domain.
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Affiliation(s)
- Beatrice Bernardi
- Department of Bioengineering Sciences, Research Group of Microbiology, Functional Yeast Genomics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yeseren Kayacan
- Department of Bioengineering Sciences, Research Group of Microbiology, Functional Yeast Genomics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jürgen Wendland
- Department of Bioengineering Sciences, Research Group of Microbiology, Functional Yeast Genomics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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McGinty RJ, Mirkin SM. Cis- and Trans-Modifiers of Repeat Expansions: Blending Model Systems with Human Genetics. Trends Genet 2018; 34:448-465. [PMID: 29567336 PMCID: PMC5959756 DOI: 10.1016/j.tig.2018.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/30/2022]
Abstract
Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby (cis) or physically separated from (trans) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis- and trans-modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients.
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Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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6
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Abstract
Eukaryotic genomes contain many repetitive DNA sequences that exhibit size instability. Some repeat elements have the added complication of being able to form secondary structures, such as hairpin loops, slipped DNA, triplex DNA or G-quadruplexes. Especially when repeat sequences are long, these DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks. In turn, repair or replication fork restart attempts within the repeat DNA can lead to addition or removal of repeat elements, which can sometimes lead to disease. One important DNA repair mechanism to maintain genomic integrity is recombination. Though early studies dismissed recombination as a mechanism driving repeat expansion and instability, recent results indicate that mitotic recombination is a key pathway operating within repetitive DNA. The action is two-fold: first, it is an important mechanism to repair nicks, gaps, breaks, or stalled forks to prevent chromosome fragility and protect cell health; second, recombination can cause repeat expansions or contractions, which can be deleterious. In this review, we summarize recent developments that illuminate the role of recombination in maintaining genome stability at DNA repeats.
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Usdin K, House NCM, Freudenreich CH. Repeat instability during DNA repair: Insights from model systems. Crit Rev Biochem Mol Biol 2015; 50:142-67. [PMID: 25608779 DOI: 10.3109/10409238.2014.999192] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The expansion of repeated sequences is the cause of over 30 inherited genetic diseases, including Huntington disease, myotonic dystrophy (types 1 and 2), fragile X syndrome, many spinocerebellar ataxias, and some cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Repeat expansions are dynamic, and disease inheritance and progression are influenced by the size and the rate of expansion. Thus, an understanding of the various cellular mechanisms that cooperate to control or promote repeat expansions is of interest to human health. In addition, the study of repeat expansion and contraction mechanisms has provided insight into how repair pathways operate in the context of structure-forming DNA, as well as insights into non-canonical roles for repair proteins. Here we review the mechanisms of repeat instability, with a special emphasis on the knowledge gained from the various model systems that have been developed to study this topic. We cover the repair pathways and proteins that operate to maintain genome stability, or in some cases cause instability, and the cross-talk and interactions between them.
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Affiliation(s)
- Karen Usdin
- Laboratory of Cell and Molecular Biology, NIDDK, NIH , Bethesda, MD , USA
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Northam MR, Moore EA, Mertz TM, Binz SK, Stith CM, Stepchenkova EI, Wendt KL, Burgers PMJ, Shcherbakova PV. DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures. Nucleic Acids Res 2013; 42:290-306. [PMID: 24049079 PMCID: PMC3874155 DOI: 10.1093/nar/gkt830] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA polymerase ζ (Pol ζ) and Rev1 are key players in translesion DNA synthesis. The error-prone Pol ζ can also participate in replication of undamaged DNA when the normal replisome is impaired. Here we define the nature of the replication disturbances that trigger the recruitment of error-prone polymerases in the absence of DNA damage and describe the specific roles of Rev1 and Pol ζ in handling these disturbances. We show that Pol ζ/Rev1-dependent mutations occur at sites of replication stalling at short repeated sequences capable of forming hairpin structures. The Rev1 deoxycytidyl transferase can take over the stalled replicative polymerase and incorporate an additional 'C' at the hairpin base. Full hairpin bypass often involves template-switching DNA synthesis, subsequent realignment generating multiply mismatched primer termini and extension of these termini by Pol ζ. The postreplicative pathway dependent on polyubiquitylation of proliferating cell nuclear antigen provides a backup mechanism for accurate bypass of these sequences that is primarily used when the Pol ζ/Rev1-dependent pathway is inactive. The results emphasize the pivotal role of noncanonical DNA structures in mutagenesis and reveal the long-sought-after mechanism of complex mutations that represent a unique signature of Pol ζ.
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Affiliation(s)
- Matthew R Northam
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68118, USA and Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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9
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Revay T, King WA. Sister chromatid exchange assessment by chromosome orientation-fluorescence in situ hybridization on the bovine sex chromosomes and autosomes 16 and 26. Cytogenet Genome Res 2012; 136:107-16. [PMID: 22286126 DOI: 10.1159/000335749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2011] [Indexed: 11/19/2022] Open
Abstract
Mammalian genome replication and maintenance are intimately coupled with the mechanisms that ensure cohesion between the resultant sister chromatids and the repair of DNA breaks. Although a sister chromatid exchange (SCE) is an error-free swapping of precisely matched and identical DNA strands, repetitive elements adjacent to the break site can act as alternative template sites and an unequal sister chromatid exchange can result, leading to structural variations and copy number change. Here we test the vulnerability for SCEs of the repeat-rich bovine Y chromosome in comparison with X, 16 and 26 chromosomes, using chromosome orientation-fluorescence in situ hybridization. The mean SCE rate of the Y chromosome (0.065 ± 0.029) was similar to that of BTA16 and BTA26 (0.065, 0.055), but was only approximately half of that of the X chromosome (0.142). As the chromosomal length affects the number of SCE events, we adjusted the SCE rates of the Y, 16, and 26 chromosomes to the length of the largest chromosome X resulting in very similar adjusted SCE (SCE(adj)) rates in all categories. Our results - based on 3 independent bulls - show that, although the cattle Y chromosome is a chest full of repeated elements, their presence and the documented activity of repeats in SCE formation does not manifest in significantly higher SCE(adj) rates and suggest the importance of the structural organization of the Y chromosome and the role of alternative mitotic DNA repair mechanisms.
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Affiliation(s)
- T Revay
- Department of Biomedical Sciences, University of Guelph, Guelph, Ont., Canada
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Friedreich's ataxia (GAA)n•(TTC)n repeats strongly stimulate mitotic crossovers in Saccharomyces cerevisae. PLoS Genet 2011; 7:e1001270. [PMID: 21249181 PMCID: PMC3020933 DOI: 10.1371/journal.pgen.1001270] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 12/07/2010] [Indexed: 11/19/2022] Open
Abstract
Expansions of trinucleotide GAA•TTC tracts are associated with the human disease Friedreich's ataxia, and long GAA•TTC tracts elevate genome instability in yeast. We show that tracts of (GAA)230•(TTC)230 stimulate mitotic crossovers in yeast about 10,000-fold relative to a “normal” DNA sequence; (GAA)n•(TTC)n tracts, however, do not significantly elevate meiotic recombination. Most of the mitotic crossovers are associated with a region of non-reciprocal transfer of information (gene conversion). The major class of recombination events stimulated by (GAA)n•(TTC)n tracts is a tract-associated double-strand break (DSB) that occurs in unreplicated chromosomes, likely in G1 of the cell cycle. These findings indicate that (GAA)n•(TTC)n tracts can be a potent source of loss of heterozygosity in yeast. Although meiotic recombination has been much more studied than mitotic recombination, mitotic recombination is a universal property. Meiotic recombination rates are quite variable within the genome, with some chromosomal regions (hotspots) having much higher levels of exchange than other regions (coldspots). For mitotic recombination, although some types of DNA sequences are known to be associated with elevated recombination rates (highly-transcribed genes, inverted repeated sequences), relatively few hotspots have been described. In this report, we show that a 690 base pair region consisting of 230 copies of the (GAA)n•(TTC)n trinucleotide repeat stimulates mitotic crossovers in yeast 10,000-fold more strongly than an “average” yeast sequence. This sequence is a preferred site for chromosome breakage in stationary phase yeast cells. Our findings may be relevant to understanding the expansions of the (GAA)n•(TTC)n trinucleotide repeat tracts that are associated with the human disease Friedreich's ataxia.
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Zhang M, Wang H, Dong Z, Qi B, Xu K, Liu B. Tissue culture-induced variation at simple sequence repeats in sorghum (Sorghum bicolor L.) is genotype-dependent and associated with down-regulated expression of a mismatch repair gene, MLH3. PLANT CELL REPORTS 2010; 29:51-59. [PMID: 19908047 DOI: 10.1007/s00299-009-0797-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Revised: 10/19/2009] [Accepted: 10/25/2009] [Indexed: 05/28/2023]
Abstract
Somaclonal variation is a common phenomenon associated with plant tissue culture. Microsatellites or simple sequence repeats (SSRs) are ubiquitous components of eukaryotic genomes, and are intrinsically unstable under various stress conditions including tissue culture. Here, we assessed genetic stability of a set of 29 mapped SSR loci in calli and regenerated plants derived from a pair of reciprocal sorghum inter-strain F1 hybrids and their pure line parents. We further measured the steady-state transcripts of a set of nine mismatch repair (MMR)-encoding genes and a DEMETER (DME), a DNA glycosylase domain protein-encoding gene in these lines, and tested for a possible relationship between altered expression of a given MMR or DME gene and the SSR variations. We found that SSR variations occurred in calli and regenerated plants of both the studied pure lines though at sharply different frequencies (20.7 vs. 6.9%), but no variation was detected in calli and regenerated plants of the pair of F1 hybrids. Compared with the donor seed plants, markedly altered expression of all nine studied MMR genes and the DME gene was observed in calli, and more conspicuously, in the regenerated plants. However, only one gene, i.e., MLH3, showed an altered expression pattern that is genotype specific and significantly correlated with the occurrence of SSR instability.
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Affiliation(s)
- Meishan Zhang
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, People's Republic of China
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12
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Double-strand break repair pathways protect against CAG/CTG repeat expansions, contractions and repeat-mediated chromosomal fragility in Saccharomyces cerevisiae. Genetics 2009; 184:65-77. [PMID: 19901069 DOI: 10.1534/genetics.109.111039] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Trinucleotide repeats can form secondary structures, whose inappropriate repair or replication can lead to repeat expansions. There are multiple loci within the human genome where expansion of trinucleotide repeats leads to disease. Although it is known that expanded repeats accumulate double-strand breaks (DSBs), it is not known which DSB repair pathways act on such lesions and whether inaccurate DSB repair pathways contribute to repeat expansions. Using Saccharomyces cerevisiae, we found that CAG/CTG tracts of 70 or 155 repeats exhibited significantly elevated levels of breakage and expansions in strains lacking MRE11, implicating the Mre11/Rad50/Xrs2 complex in repairing lesions at structure-forming repeats. About two-thirds of the expansions that occurred in the absence of MRE11 were dependent on RAD52, implicating aberrant homologous recombination as a mechanism for generating expansions. Expansions were also elevated in a sae2 deletion background and these were not dependent on RAD52, supporting an additional role for Mre11 in facilitating Sae2-dependent hairpin processing at the repeat. Mre11 nuclease activity and Tel1-dependent checkpoint functions were largely dispensable for repeat maintenance. In addition, we found that intact homologous recombination and nonhomologous end-joining pathways of DSB repair are needed to prevent repeat fragility and that both pathways also protect against repeat instability. We conclude that failure of principal DSB repair pathways to repair breaks that occur within the repeats can result in the accumulation of atypical intermediates, whose aberrant resolution will then lead to CAG expansions, contractions, and repeat-mediated chromosomal fragility.
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Shishkin AA, Voineagu I, Matera R, Cherng N, Chernet BT, Krasilnikova MM, Narayanan V, Lobachev KS, Mirkin SM. Large-scale expansions of Friedreich's ataxia GAA repeats in yeast. Mol Cell 2009; 35:82-92. [PMID: 19595718 PMCID: PMC2722067 DOI: 10.1016/j.molcel.2009.06.017] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 01/07/2009] [Accepted: 06/18/2009] [Indexed: 12/12/2022]
Abstract
Large-scale expansions of DNA repeats are implicated in numerous hereditary disorders in humans. We describe a yeast experimental system to analyze large-scale expansions of triplet GAA repeats responsible for the human disease Friedreich's ataxia. When GAA repeats were placed into an intron of the chimeric URA3 gene, their expansions caused gene inactivation, which was detected on the selective media. We found that the rates of expansions of GAA repeats increased exponentially with their lengths. These rates were only mildly dependent on the repeat's orientation within the replicon, whereas the repeat-mediated replication fork stalling was exquisitely orientation dependent. Expansion rates were significantly elevated upon inactivation of the replication fork stabilizers, Tof1 and Csm3, but decreased in the knockouts of postreplication DNA repair proteins, Rad6 and Rad5, and the DNA helicase Sgs1. We propose a model for large-scale repeat expansions based on template switching during replication fork progression through repetitive DNA.
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Affiliation(s)
| | - Irina Voineagu
- Department of Biology, Tufts University, Medford, MA 02155
| | - Robert Matera
- Department of Biology, Tufts University, Medford, MA 02155
| | - Nicole Cherng
- Department of Biology, Tufts University, Medford, MA 02155
| | | | - Maria M. Krasilnikova
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802
| | - Vidhya Narayanan
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Kirill S. Lobachev
- School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332
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14
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Morales C, García MJ, Ribas M, Miró R, Muñoz M, Caldas C, Peinado MA. Dihydrofolate reductase amplification and sensitization to methotrexate of methotrexate-resistant colon cancer cells. Mol Cancer Ther 2009; 8:424-32. [DOI: 10.1158/1535-7163.mct-08-0759] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Ouyang D, Yi L, Liu L, Mu HT, Xi Z. In vitro expansion of DNA triplet repeats with bulge binders and different DNA polymerases. FEBS J 2008; 275:4510-21. [DOI: 10.1111/j.1742-4658.2008.06593.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Replication stalling at unstable inverted repeats: interplay between DNA hairpins and fork stabilizing proteins. Proc Natl Acad Sci U S A 2008; 105:9936-41. [PMID: 18632578 DOI: 10.1073/pnas.0804510105] [Citation(s) in RCA: 199] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA inverted repeats (IRs) are hotspots of genomic instability in both prokaryotes and eukaryotes. This feature is commonly attributed to their ability to fold into hairpin- or cruciform-like DNA structures interfering with DNA replication and other genetic processes. However, direct evidence that IRs are replication stall sites in vivo is currently lacking. Here, we show by 2D electrophoretic analysis of replication intermediates that replication forks stall at IRs in bacteria, yeast, and mammalian cells. We found that DNA hairpins, rather than DNA cruciforms, are responsible for the replication stalling by comparing the effects of specifically designed imperfect IRs with varying lengths of their central spacer. Finally, we report that yeast fork-stabilizing proteins, Tof1 and Mrc1, are required to counteract repeat-mediated replication stalling. We show that the function of the Tof1 protein at DNA structure-mediated stall sites is different from its previously described effect on protein-mediated replication fork barriers.
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17
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Nag DK, Cavallo SJ. Effects of mutations in SGS1 and in genes functionally related to SGS1 on inverted repeat-stimulated spontaneous unequal sister-chromatid exchange in yeast. BMC Mol Biol 2007; 8:120. [PMID: 18166135 PMCID: PMC2254439 DOI: 10.1186/1471-2199-8-120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 12/31/2007] [Indexed: 11/11/2022] Open
Abstract
Background The presence of inverted repeats (IRs) in DNA poses an obstacle to the normal progression of the DNA replication machinery, because these sequences can form secondary structures ahead of the replication fork. A failure to process and to restart the stalled replication machinery can lead to the loss of genome integrity. Consistently, IRs have been found to be associated with a high level of genome rearrangements, including deletions, translocations, inversions, and a high rate of sister-chromatid exchange (SCE). The RecQ helicase Sgs1, in Saccharomyces cerevisiae, is believed to act on stalled replication forks. To determine the role of Sgs1 when the replication machinery stalls at the secondary structure, we measured the rates of IR-associated and non-IR-associated spontaneous unequal SCE events in the sgs1 mutant, and in strains bearing mutations in genes that are functionally related to SGS1. Results The rate of SCE in sgs1 cells for both IR and non-IR-containing substrates was higher than the rate in the wild-type background. The srs2 and mus81 mutations had modest effects, compared to sgs1. The exo1 mutation increased SCE rates for both substrates. The sgs1 exo1 double mutant exhibited synergistic effects on spontaneous SCE. The IR-associated SCE events in sgs1 cells were partially MSH2-dependent. Conclusions These results suggest that Sgs1 suppresses spontaneous unequal SCE, and SGS1 and EXO1 regulate spontaneous SCE by independent mechanisms. The mismatch repair proteins, in contradistinction to their roles in mutation avoidance, promote secondary structure-associated genetic instability.
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Affiliation(s)
- Dilip K Nag
- Division of Molecular Medicine, Wadsworth Center, Center for Medical Sciences, 150 New Scotland Avenue, Albany, NY 12208, USA.
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Abstract
Nearly 30 hereditary disorders in humans result from an increase in the number of copies of simple repeats in genomic DNA. These DNA repeats seem to be predisposed to such expansion because they have unusual structural features, which disrupt the cellular replication, repair and recombination machineries. The presence of expanded DNA repeats alters gene expression in human cells, leading to disease. Surprisingly, many of these debilitating diseases are caused by repeat expansions in the non-coding regions of their resident genes. It is becoming clear that the peculiar structures of repeat-containing transcripts are at the heart of the pathogenesis of these diseases.
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Affiliation(s)
- Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA.
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Abstract
DNA palindromes are a source of instability in eukaryotic genomes but remain under-investigated because they are difficult to study. Nonetheless, progress in the last year or so has begun to form a coherent picture of how DNA palindromes cause damage in eukaryotes and how this damage is opposed by cellular mechanisms. In yeast, the features of double strand DNA interruptions that appear at palindromic sites in vivo suggest that a resolvase-type activity creates the fractures by attacking a palindrome after it extrudes into a cruciform structure. Induction of DNA breaks in this fashion could be deterred through a Center-Break palindrome revision process as investigated in detail in mice. The MRX/MRN likely plays a pivotal role in prevention of palindrome-induced genome damage in eukaryotes.
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Affiliation(s)
- Susanna M Lewis
- Graduate Department of Molecular and Medical Genetics, University of Toronto, Ont., Canada.
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Mirkin SM. DNA structures, repeat expansions and human hereditary disorders. Curr Opin Struct Biol 2006; 16:351-8. [PMID: 16713248 DOI: 10.1016/j.sbi.2006.05.004] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2006] [Revised: 04/20/2006] [Accepted: 05/08/2006] [Indexed: 11/28/2022]
Abstract
Expansions of simple DNA repeats are responsible for more than two dozen hereditary disorders in humans, including fragile X syndrome, myotonic dystrophy, Huntington's disease, various spinocerebellar ataxias, Friedreich's ataxia and others. During the past decade, it became clear that unusual structural features of expandable repeats greatly contribute to their instability and could lead to their expansion. Furthermore, DNA replication, repair and recombination are implicated in the formation of repeat expansions, as shown in various experimental systems. The replication model of repeat expansion stipulates that unusual structures of expandable repeats stall replication fork progression, whereas extra repeats are added during replication fork restart. It also explains the bias toward repeat expansion or contraction that was observed in different organisms.
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Affiliation(s)
- Sergei M Mirkin
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
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Nag DK, Fasullo M, Dong Z, Tronnes A. Inverted repeat-stimulated sister-chromatid exchange events are RAD1-independent but reduced in a msh2 mutant. Nucleic Acids Res 2005; 33:5243-9. [PMID: 16166656 PMCID: PMC1216339 DOI: 10.1093/nar/gki835] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Inverted repeats (IRs) and trinucleotide repeats (TNRs) that have the potential to form secondary structures in vivo are known to cause genome rearrangements. Expansions of TNRs in humans are associated with several neurological disorders. Both IRs and TNRs stimulate spontaneous unequal sister-chromatid exchange (SCE) in yeast. Secondary structure-associated SCE events occur via double-strand break repair. Here we show that the rate of spontaneous IR-stimulated unequal SCE events in yeast is significantly reduced in strains with mutations in the mismatch repair genes MSH2 or MSH3, but unaffected by a mutation in the nucleotide excision-repair gene RAD1. Non-IR-associated unequal SCE events are increased in both MMR- and rad1-mutant cells; however, SCE events for both IR- and non-IR-containing substrates occur at a higher level in the exo1 background. Our results suggest that spontaneous SCE occurs by a template switching mechanism. Like IRs, TNRs have been shown to generate double-strand breaks (DSBs) in yeast. TNR expansions in mice are MSH2-dependent. Since IR-mediated SCE events are reduced in msh2 cells, we propose that TNR expansion mutations arise when DSBs are repaired using the sister or the homolog as a template.
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Affiliation(s)
- Dilip K. Nag
- Molecular Genetics Program, Wadsworth Center, Center for Medical Sciences150 New Scotland Avenue, Albany, NY 12208, USA
- Department of Biomedical Sciences, School of Public Health, State University of New YorkAlbany, NY 12201, USA
- To whom correspondence should be addressed. Tel: 518 473 6327; Fax: 518 474 3181;
| | - Michael Fasullo
- Ordway Research Institute, Wadsworth Center, Center for Medical Sciences150 New Scotland Avenue, Albany, NY 12208, USA
- Department of Biomedical Sciences, School of Public Health, State University of New YorkAlbany, NY 12201, USA
| | - Zheng Dong
- Ordway Research Institute, Wadsworth Center, Center for Medical Sciences150 New Scotland Avenue, Albany, NY 12208, USA
| | - Ashlie Tronnes
- Molecular Genetics Program, Wadsworth Center, Center for Medical Sciences150 New Scotland Avenue, Albany, NY 12208, USA
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Braun BR, van het Hoog M, d'Enfert C, Martchenko M, Dungan J, Kuo A, Inglis DO, Uhl MA, Hogues H, Berriman M, Lorenz M, Levitin A, Oberholzer U, Bachewich C, Harcus D, Marcil A, Dignard D, Iouk T, Zito R, Frangeul L, Tekaia F, Rutherford K, Wang E, Munro CA, Bates S, Gow NA, Hoyer LL, Köhler G, Morschhäuser J, Newport G, Znaidi S, Raymond M, Turcotte B, Sherlock G, Costanzo M, Ihmels J, Berman J, Sanglard D, Agabian N, Mitchell AP, Johnson AD, Whiteway M, Nantel A. A human-curated annotation of the Candida albicans genome. PLoS Genet 2005; 1:36-57. [PMID: 16103911 PMCID: PMC1183520 DOI: 10.1371/journal.pgen.0010001] [Citation(s) in RCA: 252] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2005] [Accepted: 03/14/2005] [Indexed: 11/24/2022] Open
Abstract
Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.
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Affiliation(s)
- Burkhard R Braun
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Marco van het Hoog
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Christophe d'Enfert
- Unité Postulante Biologie et Pathogénicité Fongiques, INRA USC 2019, Institut Pasteur, Paris, France
| | - Mikhail Martchenko
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Jan Dungan
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Alan Kuo
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Diane O Inglis
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - M. Andrew Uhl
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Hervé Hogues
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | | | - Michael Lorenz
- Department of Microbiology and Molecular Genetics, Utah-Houston Medical School, Houston, Texas, United States of America
| | - Anastasia Levitin
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Ursula Oberholzer
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Catherine Bachewich
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Doreen Harcus
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Anne Marcil
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Daniel Dignard
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Tatiana Iouk
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Rosa Zito
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Lionel Frangeul
- Plate-Forme Intégration et Analyse Génomique, Institut Pasteur, Paris, France
| | - Fredj Tekaia
- Unité de Génétique Moléculaire des Levures, Institut Pasteur, Paris, France
| | | | - Edwin Wang
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - Carol A Munro
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Steve Bates
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Neil A Gow
- School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, United Kingdom
| | - Lois L Hoyer
- Department of Veterinary Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gerwald Köhler
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Joachim Morschhäuser
- Institut für Molekulare Infektionsbiologie, Universität Wurzburg, Wurzburg, Germany
| | - George Newport
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Sadri Znaidi
- Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada
| | - Martine Raymond
- Institut de Recherches Cliniques de Montreal, Montreal, Quebec, Canada
| | - Bernard Turcotte
- Department of Medicine, Royal Victoria Hospital, McGill University, Montreal, Quebec, Canada
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Maria Costanzo
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California, United States of America
| | - Jan Ihmels
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Judith Berman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Dominique Sanglard
- Institute of Microbiology, University Hospital Lausanne, Lausanne, Switzerland
| | - Nina Agabian
- Department of Stomatology, University of California, San Francisco, California, United States of America
| | - Aaron P Mitchell
- Department of Microbiology and Institute of Cancer Research, Columbia University, New York, New York, United States of America
| | - Alexander D Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, California, United States of America
| | - Malcolm Whiteway
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
| | - André Nantel
- Biotechnology Research Institute, National Research Council Canada, Montreal, Quebec, Canada
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