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Shortt JA, Ruggiero RP, Cox C, Wacholder AC, Pollock DD. Finding and extending ancient simple sequence repeat-derived regions in the human genome. Mob DNA 2020; 11:11. [PMID: 32095164 PMCID: PMC7027126 DOI: 10.1186/s13100-020-00206-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/04/2020] [Indexed: 12/19/2022] Open
Abstract
Background Previously, 3% of the human genome has been annotated as simple sequence repeats (SSRs), similar to the proportion annotated as protein coding. The origin of much of the genome is not well annotated, however, and some of the unidentified regions are likely to be ancient SSR-derived regions not identified by current methods. The identification of these regions is complicated because SSRs appear to evolve through complex cycles of expansion and contraction, often interrupted by mutations that alter both the repeated motif and mutation rate. We applied an empirical, kmer-based, approach to identify genome regions that are likely derived from SSRs. Results The sequences flanking annotated SSRs are enriched for similar sequences and for SSRs with similar motifs, suggesting that the evolutionary remains of SSR activity abound in regions near obvious SSRs. Using our previously described P-clouds approach, we identified ‘SSR-clouds’, groups of similar kmers (or ‘oligos’) that are enriched near a training set of unbroken SSR loci, and then used the SSR-clouds to detect likely SSR-derived regions throughout the genome. Conclusions Our analysis indicates that the amount of likely SSR-derived sequence in the human genome is 6.77%, over twice as much as previous estimates, including millions of newly identified ancient SSR-derived loci. SSR-clouds identified poly-A sequences adjacent to transposable element termini in over 74% of the oldest class of Alu (roughly, AluJ), validating the sensitivity of the approach. Poly-A’s annotated by SSR-clouds also had a length distribution that was more consistent with their poly-A origins, with mean about 35 bp even in older Alus. This work demonstrates that the high sensitivity provided by SSR-Clouds improves the detection of SSR-derived regions and will enable deeper analysis of how decaying repeats contribute to genome structure.
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Affiliation(s)
- Jonathan A Shortt
- 1Colorado Center for Personalized Medicine, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Robert P Ruggiero
- 2Department of Biology, Southeast Missouri State University, Cape Girardeau, MO 63701 USA
| | - Corey Cox
- 1Colorado Center for Personalized Medicine, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Aaron C Wacholder
- 3Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213 USA
| | - David D Pollock
- 4Department of Biochemistry & Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045 USA
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2
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Holzhausen I, Lendner M, Göhring F, Steinhöfel I, Daugschies A. Distribution of Cryptosporidium parvum gp60 subtypes in calf herds of Saxony, Germany. Parasitol Res 2019; 118:1549-1558. [PMID: 30790038 DOI: 10.1007/s00436-019-06266-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/12/2019] [Indexed: 02/01/2023]
Abstract
Cryptosporidiosis is a common protozoan parasitic infection that causes diarrhoea in neonatal calves. The high shedding of environmentally resistant oocysts facilitates outbreaks of cryptosporidiosis in humans. In total, 58 farms (512 calves) in Germany (Saxony and Brandenburg) were visited three times each. Faecal samples of pre-weaned calves were microscopically examined for oocysts of Cryptosporidium spp. using Heine staining and were scored with regard to their consistency. Overall, 88.9% of calves tested microscopically positive for Cryptosporidium spp. in at least one sample, and the excretion of oocysts was significantly (P < 0.01) associated with a higher faecal score (diarrhoea). After DNA extraction from pooled farm isolates, 47 samples were successfully subtyped by sequence analysis of the 60 kDa glycoprotein gene (gp60). All isolates belonged to subtype family IIa. IIaA15G2R1 was the most common subtype (present on 66% of the farms), followed by IIaA16G3R1 (13%). Subtypes IIaA14G1R1, IIaA14G2R1, IIaA1612R1, IIaA16G2R1, IIaA17G1R1, IIaA17G2R1, IIaA17G4R1 and IIaA19G2R1 were found sporadically. This is the first description of gp60 subtype IIaA17G4R1 in cattle in Germany.
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Affiliation(s)
- I Holzhausen
- Institute of Parasitology, Centre for Infectious Diseases, University of Leipzig, An den Tierkliniken 35, D - 04103, Leipzig, Germany. .,Albrecht - Daniel - Thaer - Institute for Agricultural Sciences e.V., University of Leipzig, An den Tierkliniken 29, D - 04103, Leipzig, Germany.
| | - M Lendner
- Institute of Parasitology, Centre for Infectious Diseases, University of Leipzig, An den Tierkliniken 35, D - 04103, Leipzig, Germany
| | - F Göhring
- Institute of Parasitology, Centre for Infectious Diseases, University of Leipzig, An den Tierkliniken 35, D - 04103, Leipzig, Germany.,Albrecht - Daniel - Thaer - Institute for Agricultural Sciences e.V., University of Leipzig, An den Tierkliniken 29, D - 04103, Leipzig, Germany
| | - I Steinhöfel
- Saxon State Office for Environment, Agriculture and Geology, Am Park 3, D - 04886, Köllitsch, Germany
| | - A Daugschies
- Institute of Parasitology, Centre for Infectious Diseases, University of Leipzig, An den Tierkliniken 35, D - 04103, Leipzig, Germany.,Albrecht - Daniel - Thaer - Institute for Agricultural Sciences e.V., University of Leipzig, An den Tierkliniken 29, D - 04103, Leipzig, Germany
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3
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Next Generation Sequencing uncovers within-host differences in the genetic diversity of Cryptosporidium gp60 subtypes. Int J Parasitol 2017; 47:601-607. [DOI: 10.1016/j.ijpara.2017.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/23/2017] [Accepted: 03/31/2017] [Indexed: 12/21/2022]
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4
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Ahmed MM, Shen C, Khan AQ, Wahid MA, Shaban M, Lin Z. A comparative genomics approach revealed evolutionary dynamics of microsatellite imperfection and conservation in genus Gossypium. Hereditas 2017; 154:12. [PMID: 28529469 PMCID: PMC5437633 DOI: 10.1186/s41065-017-0034-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 04/27/2017] [Indexed: 11/13/2022] Open
Abstract
Background Ongoing molecular processes in a cell could target microsatellites, a kind of repetitive DNA, owing to length variations and motif imperfection. Mutational mechanisms underlying such kind of genetic variations have been extensively investigated in diverse organisms. However, obscure impact of ploidization, an evolutionary process of genome content duplication prevails mostly in plants, on non-coding DNA is poorly understood. Results Genome sequences of diversely originated plant species were examined for genome-wide motif imperfection pattern, and various analytical tools were employed to canvass characteristic relationships among repeat density, imperfection and length of microsatellites. Moreover, comparative genomics approach aided in exploration of microsatellites conservation footprints in Gossypium evolution. Based on our results, motif imperfection in repeat length was found intricately related to genomic abundance of imperfect microsatellites among 13 genomes. Microsatellite decay estimation depicted slower decay of long motif repeats which led to predominant abundance of 5-nt repeat motif in Gossypium species. Short motif repeats exhibited rapid decay through the evolution of Gossypium lineage ensuing drastic decrease of 2-nt repeats, of which, “AT” motif type dilapidated in cultivated tetraploids of cotton. Conclusion The outcome could be a directive to explore comparative evolutionary footprints of simple non-coding genetic elements i.e., repeat elements, through the evolution of genus-specific characteristics in cotton genomes. Electronic supplementary material The online version of this article (doi:10.1186/s41065-017-0034-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Muhammad Mahmood Ahmed
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Chao Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Anam Qadir Khan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Muhammad Atif Wahid
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Muhammad Shaban
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, Hubei 430070 China
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5
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Willems T, Gymrek M, Poznik G, Tyler-Smith C, Erlich Y, Erlich Y. Population-Scale Sequencing Data Enable Precise Estimates of Y-STR Mutation Rates. Am J Hum Genet 2016; 98:919-933. [PMID: 27126583 DOI: 10.1016/j.ajhg.2016.04.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 04/01/2016] [Indexed: 01/23/2023] Open
Abstract
Short tandem repeats (STRs) are mutation-prone loci that span nearly 1% of the human genome. Previous studies have estimated the mutation rates of highly polymorphic STRs by using capillary electrophoresis and pedigree-based designs. Although this work has provided insights into the mutational dynamics of highly mutable STRs, the mutation rates of most others remain unknown. Here, we harnessed whole-genome sequencing data to estimate the mutation rates of Y chromosome STRs (Y-STRs) with 2-6 bp repeat units that are accessible to Illumina sequencing. We genotyped 4,500 Y-STRs by using data from the 1000 Genomes Project and the Simons Genome Diversity Project. Next, we developed MUTEA, an algorithm that infers STR mutation rates from population-scale data by using a high-resolution SNP-based phylogeny. After extensive intrinsic and extrinsic validations, we harnessed MUTEA to derive mutation-rate estimates for 702 polymorphic STRs by tracing each locus over 222,000 meioses, resulting in the largest collection of Y-STR mutation rates to date. Using our estimates, we identified determinants of STR mutation rates and built a model to predict rates for STRs across the genome. These predictions indicate that the load of de novo STR mutations is at least 75 mutations per generation, rivaling the load of all other known variant types. Finally, we identified Y-STRs with potential applications in forensics and genetic genealogy, assessed the ability to differentiate between the Y chromosomes of father-son pairs, and imputed Y-STR genotypes.
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Affiliation(s)
| | | | | | | | | | - Yaniv Erlich
- New York Genome Center, New York, NY 10013, USA; Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02139, USA; Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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6
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Behura SK, Severson DW. Motif mismatches in microsatellites: insights from genome-wide investigation among 20 insect species. DNA Res 2014; 22:29-38. [PMID: 25378245 PMCID: PMC4379975 DOI: 10.1093/dnares/dsu036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We present a detailed genome-wide comparative study of motif mismatches of microsatellites among 20 insect species representing five taxonomic orders. The results show that varying proportions (∼15-46%) of microsatellites identified in these species are imperfect in motif structure, and that they also vary in chromosomal distribution within genomes. It was observed that the genomic abundance of imperfect repeats is significantly associated with the length and number of motif mismatches of microsatellites. Furthermore, microsatellites with a higher number of mismatches tend to have lower abundance in the genome, suggesting that sequence heterogeneity of repeat motifs is a key determinant of genomic abundance of microsatellites. This relationship seems to be a general feature of microsatellites even in unrelated species such as yeast, roundworm, mouse and human. We provide a mechanistic explanation of the evolutionary link between motif heterogeneity and genomic abundance of microsatellites by examining the patterns of motif mismatches and allele sequences of single-nucleotide polymorphisms identified within microsatellite loci. Using Drosophila Reference Genetic Panel data, we further show that pattern of allelic variation modulates motif heterogeneity of microsatellites, and provide estimates of allele age of specific imperfect microsatellites found within protein-coding genes.
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Affiliation(s)
- Susanta K Behura
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - David W Severson
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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7
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Grinberg A, Biggs P, Dukkipati V, George T. Extensive intra-host genetic diversity uncovered in Cryptosporidium parvum using Next Generation Sequencing. INFECTION GENETICS AND EVOLUTION 2013; 15:18-24. [DOI: 10.1016/j.meegid.2012.08.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 08/28/2012] [Accepted: 08/28/2012] [Indexed: 11/28/2022]
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8
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Fonville NC, Ward RM, Mittelman D. Stress-induced modulators of repeat instability and genome evolution. J Mol Microbiol Biotechnol 2012; 21:36-44. [PMID: 22248541 DOI: 10.1159/000332748] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Evolution hinges on the ability of organisms to adapt to their environment. A key regulator of adaptability is mutation rate, which must be balanced to maintain genome fidelity while permitting sufficient plasticity to cope with environmental changes. Multiple mechanisms govern an organism's mutation rate. Constitutive mechanisms include mutator alleles that drive global, permanent increases in mutation rates, but these changes are confined to the subpopulation that carries the mutator allele. Other mechanisms focus mutagenesis in time and space to improve the chances that adaptive mutations can spread through the population. For example, environmental stress can induce mechanisms that transiently relax the fidelity of DNA repair to bring about a temporary increase in mutation rates during times when an organism experiences a reduced fitness for its surroundings, as has been demonstrated for double-strand break repair in Escherichia coli. Still, other mechanisms control the spatial distribution of mutations by directing changes to especially mutable sequences in the genome. In eukaryotic cells, for example, the stress-sensitive chaperone Hsp90 can regulate the length of trinucleotide repeats to fine-tune gene function and can regulate the mobility of transposable elements to enable larger functional changes. Here, we review the regulation of mutation rate, with special emphasis on the roles of tandem repeats and environmental stress in genome evolution.
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9
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Macdonald AJ, Sarre SD, Fitzsimmons NN, Aitken N. Determining microsatellite genotyping reliability and mutation detection ability: an approach using small-pool PCR from sperm DNA. Mol Genet Genomics 2010; 285:1-18. [PMID: 20957392 DOI: 10.1007/s00438-010-0577-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 09/10/2010] [Indexed: 11/26/2022]
Abstract
Microsatellite genotyping from trace DNA is now common in fields as diverse as medicine, forensics and wildlife genetics. Conversely, small-pool PCR (SP-PCR) has been used to investigate microsatellite mutation mechanisms in human DNA, but has had only limited application to non-human species. Trace DNA and SP-PCR studies share many challenges, including problems associated with allelic drop-out, false alleles and other PCR artefacts, and the need to reliably identify genuine alleles and/or mutations. We provide a framework for the validation of such studies without a multiple tube approach and demonstrate the utility of that approach with an analysis of microsatellite mutations in the tammar wallaby (Macropus eugenii). Specifically, we amplified three autosomal microsatellites from somatic DNA to characterise efficiency and reliability of PCR from low-template DNA. Reconstruction experiments determined our ability to discriminate mutations from parental alleles. We then developed rules to guide data interpretation. We estimated mutation rates in sperm DNA to range from 1.5 × 10(-2) to 2.2 × 10(-3) mutations per locus per generation. Large multi-step mutations were observed, providing evidence for complex mutation processes at microsatellites and potentially violating key assumptions in the stepwise mutation model. Our data demonstrate the necessity of actively searching for large mutation events when investigating microsatellite evolution and highlight the need for a thorough understanding of microsatellite amplification characteristics before embarking on SP-PCR or trace DNA studies.
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Affiliation(s)
- Anna J Macdonald
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2601, Australia.
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10
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Richard GF, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 2008; 72:686-727. [PMID: 19052325 PMCID: PMC2593564 DOI: 10.1128/mmbr.00011-08] [Citation(s) in RCA: 335] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.
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Affiliation(s)
- Guy-Franck Richard
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie, UFR927, 25 rue du Dr. Roux, F-75015, Paris, France.
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11
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Boyer JC, Hawk JD, Stefanovic L, Farber RA. Sequence-dependent effect of interruptions on microsatellite mutation rate in mismatch repair-deficient human cells. Mutat Res 2007; 640:89-96. [PMID: 18242644 DOI: 10.1016/j.mrfmmm.2007.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Revised: 11/21/2007] [Accepted: 12/11/2007] [Indexed: 11/18/2022]
Abstract
Although microsatellite mutation rates generally increase with increasing length of the repeat tract, interruptions in a microsatellite may stabilize it. We have performed a direct analysis of the effect of microsatellite interruptions on mutation rate and spectrum in cultured mammalian cells. Two mononucleotide sequences (G(17) and A(17)) and a dinucleotide [(CA)(17)] were compared with interrupted repeats of the same size and with sequences of 8 repeat units. MMR-deficient (MMR(-)) cells were used for these studies to eliminate effects of this repair process. Mutation rates were determined by fluctuation analysis on cells containing a microsatellite sequence at the 5' end of an antibiotic-resistance gene; the vector carrying this sequence was integrated in the genome of the cells. In general, interrupted sequences had lower mutation rates than perfect ones of the same size, but the magnitude of the difference was dependent upon the sequence of the interrupting base(s). Some interrupted repeats had mutation rates that were lower than those of perfect sequences of the same length but similar to those of half the length. This suggests that interrupting bases effectively divide microsatellites into smaller repeat runs with mutational characteristics different from those of the corresponding full-length microsatellite. We conclude that interruptions decrease microsatellite mutation rate and influence the spectrum of frameshift mutations. The sequence of the interrupting base(s) determines the magnitude of the effect on mutation rate.
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Affiliation(s)
- Jayne C Boyer
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, CB #7525, Chapel Hill, NC 27599, United States.
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12
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Buschiazzo E, Gemmell NJ. The rise, fall and renaissance of microsatellites in eukaryotic genomes. Bioessays 2006; 28:1040-50. [PMID: 16998838 DOI: 10.1002/bies.20470] [Citation(s) in RCA: 190] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Microsatellites are among the most versatile of genetic markers, being used in an impressive number of biological applications. However, the evolutionary dynamics of these markers remain a source of contention. Almost 20 years after the discovery of these ubiquitous simple sequences, new genomic data are clarifying our understanding of the structure, distribution and variability of microsatellites in genomes, especially for the eukaryotes. While these new data provide a great deal of descriptive information about the nature and abundance of microsatellite sequences within eukaryotic genomes, there have been few attempts to synthesise this information to develop a global concept of evolution. This review provides an up-to-date account of the mutational processes, biases and constraints believed to be involved in the evolution of microsatellites, particularly with respect to the creation and degeneration of microsatellites, which we assert may be broadly viewed as a life cycle. In addition, we identify areas of contention that require further research and propose some possible directions for future investigation.
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Affiliation(s)
- Emmanuel Buschiazzo
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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13
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Schwartz S, Alazzouzi H, Perucho M. Mutational dynamics in human tumors confirm the neutral intrinsic instability of the mitochondrial D-loop poly-cytidine repeat. Genes Chromosomes Cancer 2006; 45:770-80. [PMID: 16708351 DOI: 10.1002/gcc.20340] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Somatic mutations at a mitochondrial noncoding polycytidine (C)(n) repeat (polyC) have been associated with tumor progression. We analyzed whether these alterations are due to the inherent mutability of repeated sequences. Insertion and deletion mutations were found in colon (n = 114), stomach (n = 105), endometrium (n = 53), breast (n = 45), lung (n = 35), and prostate (n = 20) tumors. The mutation frequency in colon, gastric, and endometrial tumors was 23, 17, and 11%, respectively, which paralleled the relative extent of microsatellite instability in long mononucleotide repeats observed in tumors with mismatch repair deficiency (colon > stomach > endometrium, relative ratio 10:8:4). Colon tumors with mutations of more than one nucleotide were more advanced in tumor progression. Further, two tumors showing a T > C mutation that restored the homopolymeric repeat, harbored sequential deletion mutations of up to 4 and 6 nucleotides. These results illustrate that the increased mutability of repeated mitochondrial sequences is dependent on the repetitive structure of the DNA molecule and suggest that mutations in the (C)(n) repeat, whether homoplasmic or not, and by extrapolation, mitochondrial mutations in general, are not the result of selective pressure during tumorigenesis. We also suggest that the (C)(n) repeat may be used as an universal molecular clock to estimate the relative mitotic history of tumors.
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Affiliation(s)
- Simó Schwartz
- Molecular Oncology and Aging Group, Centre d'Investigacions en Bioquimica i Biologia Molecular (CIBBIM), Hospital Universitari Vall d'Hebron, Centre Docent Universitat Autònoma de Barcelona, Spain.
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14
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Vauhkonen H, Sajantila A. Intrinsic structural variation of the complex microsatellite marker MYCL1 in Finnish and Somali populations and its relevance to gastrointestinal tumors. Genet Mol Biol 2006. [DOI: 10.1590/s1415-47572006000400005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Sansom OJ, Bishop SM, Bird A, Clarke AR. MBD4 deficiency does not increase mutation or accelerate tumorigenesis in mice lacking MMR. Oncogene 2004; 23:5693-6. [PMID: 15184874 DOI: 10.1038/sj.onc.1207767] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mbd4 (methyl-binding domain 4) has been shown to be mutated in a high percentage of mismatch repair (MMR)-deficient colorectal tumours that exhibit microsatellite instability (MSI). However, the significance of these mutations is still unclear as they are predominantly monoallelic and the majority occur at a poly-A tract. Apart from MMR-deficient tumours, no other reports of mutations of Mbd4 in human neoplasia are as yet published. To address the significance of loss of Mbd4 in the absence of MMR, we have crossed Mbd4-deficient mice to mice lacking DNA MMR. We show that, in the context of MMR deficiency, additional loss of Mbd4 does not alter spontaneous mutation frequency at the endogenous Dlb-1b locus, nor does it modify tumour onset, tumour spectrum or MSI compared to singly mutant Msh2 or Mlh1 mice. Taken together, these findings show that nullizygosity or heterozygosity for Mbd4 does not affect MMR-dependent tumorigenesis.
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Affiliation(s)
- Owen J Sansom
- School of Biosciences, University of Cardiff, Museum Avenue, PO Box 911, Cardiff CF10 3US, UK
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16
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Affiliation(s)
- Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
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17
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Leopoldino AM, Pena SDJ. The mutational spectrum of human autosomal tetranucleotide microsatellites. Hum Mutat 2003; 21:71-9. [PMID: 12497633 DOI: 10.1002/humu.10153] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We studied by multiplex amplification and single-run electrophoretic analysis 10 microsatellite loci, composed of nine tetranucleotide-repeats (D1S1612, D3S2387, D4S2431, D5S2501, D10S1237, D15S657, D16S2622, D18S1270, and IFNAR-ALU) and one trinucleotide repeat (D2S1353). After elimination of proven null allele events involving D1S1612 and D5S2501 and of all data of D3S2387, in which we suspected but could not prove the occurrence of null alleles, we were left with nine loci, encompassing 24,224 meioses and 23 mutations. Twenty-two of the mutations (96%) were single-step events. Moreover, 18 of the mutations were paternal, four were maternal, and one was indeterminate. There was no significant difference between the number of additions and deletions in the mutants. Our findings are compatible with a simple model in which tetranucleotide microsatellites mutate primarily in paternal germinative cells by DNA slippage, such that the vast majority of mutations are equiprobable additions or deletions of a single-repeat unit. By combining the data from our tetranucleotide loci with literature information of highly and lowly mutable microsatellites, we observed a very highly significant correlation between mutation rate and the geometric mean of the length of the longest perfect repeat region (LRPR), compatible with a power or exponential relationship. The variation of the length of the LRPR explained as much as 80% of the variance of the mutation rate of autosomal tetranucleotide microsatellites.
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Affiliation(s)
- Andréia M Leopoldino
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Andrew SE, Peters AC. DNA instability and human disease. AMERICAN JOURNAL OF PHARMACOGENOMICS : GENOMICS-RELATED RESEARCH IN DRUG DEVELOPMENT AND CLINICAL PRACTICE 2002; 1:21-8. [PMID: 12173310 DOI: 10.2165/00129785-200101010-00003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
It is now well established that non-Mendelian examples of DNA instability are associated with human disease. Most malignancies are associated with various chromosomal instabilities, such as aneuploidy, gene amplification, and chromosomal deletion. Furthermore, widespread microsatellite instability (MSI) is associated with a variety of tumors, and instability at specific dynamic repeat expansions underlies a family of neurologic disorders. Inactivation of DNA mismatch repair genes results in genomic instabilities affecting microsatellite regions. Mutations in genes involved in DNA polymerization or Okazaki fragment processing are also associated with MSI. Such instabilities convey a 'mutator' phenotype which is pathogenic. The mechanisms controlling trinucleotide repeat expansions are less well understood. Why this type of genomic instability is particularly pathogenic to neurons is also not clear. An understanding of what normally maintains stability is the first step towards preventing such loss of control and maintaining health.
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Affiliation(s)
- S E Andrew
- Department of Medical Genetics, University of Alberta, Edmonton, Canada
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Bacon AL, Farrington SM, Dunlop MG. Mutation frequency in coding and non-coding repeat sequences in mismatch repair deficient cells derived from normal human tissue. Oncogene 2001; 20:7464-71. [PMID: 11709717 DOI: 10.1038/sj.onc.1204973] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2001] [Revised: 09/05/2001] [Accepted: 09/13/2001] [Indexed: 01/02/2023]
Abstract
Repetitive tracts within the coding regions of TGFBR2 and BAX are frequently mutated in mismatch repair deficient tumours and are implicated in tumour progression. However, there has been little study of the balance between selection pressure and inherent instability at sequences within these genes. To determine whether TGFBR2 and BAX are inherently prone to mutations in the presence of MMR defects, we studied MMR deficient cells derived from B-lymphocytes. By analysing cells derived from normal tissue we aimed to minimize the effects of selection pressures that bias the apparent frequency of mutation. We definitively show that certain sequences, usually repaired by MMR, are inherently unstable. Using a small pool PCR technique we confirmed these cells exhibit microsatellite instability. Additionally, we demonstrate that MMR deficiency results in an excess of mutations, specifically at the poly(A)(10) tract compared to other regions of the TGFBR2 gene (P<0.001). Conversely, an excess of mutations does not appear to arise at the poly(G)(8) tract of the BAX gene. These studies provide insight into the mechanism by which TGFBR2 and BAX genes become mutated during tumorigenesis. These findings invoke the notion of "unmasking" specific hypermutable sequences in particular genes adding further complexity to the concept of the mutator phenotype.
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Affiliation(s)
- A L Bacon
- Department of Oncology and MRC Human Genetics Unit, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
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Bacon AL, Dunlop MG, Farrington SM. Hypermutability at a poly(A/T) tract in the human germline. Nucleic Acids Res 2001; 29:4405-13. [PMID: 11691928 PMCID: PMC60178 DOI: 10.1093/nar/29.21.4405] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Poly(A/T) tracts are abundant simple sequence repeats (SSRs) within the human genome. They constitute part of the coding sequence of a variety of genes, encoding polylysine stretches that are important for protein function. Assessment of poly(A/T) tract stability is also used to identify microsatellite unstable colorectal cancers, which are characteristic of tumours defective in DNA mismatch repair. Despite their importance, little is known about the stability of poly(A/T) SSRs in the human germline. We have determined the stability of a paradigm poly(A/T) tract, BAT-40, by study of population allele frequencies, mutation frequency in families and mutation frequency in sperm DNA. We show that the locus is polymorphic, with a level of heterozygosity of 59.7%. Germline mutation was observed in 13 of 187 germline transmissions (7.0%) in 10 families suggesting BAT-40 is unstable in the germline. Further evidence for germline instability at BAT-40 was provided by small pool PCR analysis of matched blood and sperm DNA templates, revealing a significantly elevated frequency of mutation in the germline (P < 0.001). These findings provide insight into poly(A/T) tract stability in the germline. They also have relevance to the study of gene expression and to determination of microsatellite instability in tumours.
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Affiliation(s)
- A L Bacon
- University of Edinburgh Department of Oncology and MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
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