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Mehrdad SA, Cucchiarini A, Mergny JL, Noureini SK. Heavy metal ions interactions with G-quadruplex-prone DNA sequences. Biochimie 2024:S0300-9084(24)00123-8. [PMID: 38821199 DOI: 10.1016/j.biochi.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/02/2024]
Abstract
The industrial world exposes living organisms to a variety of metal pollutants. Here we investigated whether such elements affect G-rich sequences susceptible to fold into G-quadruplex (GQ) structures. Thermal stability and conformation of these oligoncleotides was studied at various molar ratios of a variety of heavy metal salts using thermal FRET, transition-FRET (t-FRET) and circular dichroism. Metal ions affected the thermal stability of the GQs to different extents; some metals had no effect on Tm while other metals caused small to moderate changes in Tm at 1:1 or 1:10 molar ratio. While most of the metals had no major effect, Al3+, Cd2+, Pb2+, Hg2+ and Zn2+ altered the thermal stability and structural features of the GQs. Some metals such as Pb2+ and Hg2+ exhibit differential interactions with telomere, c-myc and c-kit GQs. Overall, toxic heavy metals affect G-quadruplex stability in a sequence and topology dependent manner. This study provides new insight into how heavy metal exposure may affect gene expression and cellular responses.
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Affiliation(s)
- Seyyed-Ali Mehrdad
- Department of Biology, Faculty of Basic Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Anne Cucchiarini
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Jean-Louis Mergny
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Sakineh Kazemi Noureini
- Department of Biology, Faculty of Basic Science, Hakim Sabzevari University, Sabzevar, Iran.
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2
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Cellier G, Nordey T, Cortada L, Gauche M, Rasoamanana H, Yahiaoui N, Rébert E, Prior P, Chéron JJ, Poussier S, Pruvost O. Molecular Epidemiology of Ralstonia pseudosolanacearum Phylotype I Strains in the Southwest Indian Ocean Region and Their Relatedness to African Strains. PHYTOPATHOLOGY 2023; 113:423-435. [PMID: 36399027 DOI: 10.1094/phyto-09-22-0355-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The increasing requirement for developing tools enabling fine strain traceability responsible for epidemics is tightly linked with the need to understand factors shaping pathogen populations and their environmental interactions. Bacterial wilt caused by the Ralstonia solanacearum species complex (RSSC) is one of the most important plant diseases in tropical and subtropical regions. Sadly, little, outdated, or no information on its epidemiology is reported in the literature, although alarming outbreaks are regularly reported as disasters. A large set of phylotype I isolates (n = 2,608) was retrieved from diseased plants in fields across the Southwest Indian Ocean (SWIO) and Africa. This collection enabled further assessment of the epidemiological discriminating power of the previously published RS1-MLVA14 scheme. Thirteen markers were validated and characterized as not equally informative. Most had little infra-sequevar polymorphism, and their performance depended on the sequevar. Strong correlation was found with a previous multilocus sequence typing scheme. However, 2 to 3% of sequevars were not correctly assigned through endoglucanase gene sequence. Discriminant analysis of principal components (DAPC) revealed four groups with strong phylogenetic relatedness to sequevars 31, 33, and 18. Phylotype I-31 isolates were highly prevalent in the SWIO and Africa, but their dissemination pathways remain unclear. Tanzania and Mauritius showed the greatest diversity of RSSC strains, as the four DAPC groups were retrieved. Mauritius was the sole territory harboring a vast phylogenetic diversity and all DAPC groups. More research is still needed to understand the high prevalence of phylotype I-31 at such a large geographic scale.
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Affiliation(s)
- Gilles Cellier
- Anses, Plant Health Laboratory, Saint Pierre, Reunion Island
| | | | - Laura Cortada
- East Africa Hub, International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Nematology Section, Department of Biology, Ghent University, Ghent, Belgium
| | - Mirana Gauche
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Hasina Rasoamanana
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Noura Yahiaoui
- Anses, Plant Health Laboratory, Saint Pierre, Reunion Island
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Emeline Rébert
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Philippe Prior
- INRAE, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint-Pierre, Reunion Island
| | - Jean Jacques Chéron
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Stéphane Poussier
- University of Reunion Island, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
| | - Olivier Pruvost
- CIRAD, UMR Peuplements végétaux et bioagresseurs en milieu tropical, Saint Pierre, Reunion Island
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Hadrich I, Khemakhem N, Ilahi A, Trabelsi H, Sellami H, Makni F, Neji S, Ayadi A. Genotypic Analysis of the Population Structure in Malassezia globosa and Malassezia restricta. J Fungi (Basel) 2023; 9:jof9020263. [PMID: 36836377 PMCID: PMC9963534 DOI: 10.3390/jof9020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 02/18/2023] Open
Abstract
The molecular characterization of Malassezia spp. isolates from animals and humans has not been thoroughly studied. Although a range of molecular methods has been developed for diagnosing Malassezia species, they have several drawbacks, such as inefficiency in differentiating all the species, high cost and questionable reproducibility. The present study aimed to develop VNTR markers for genotyping Malassezia isolated from clinical and animal samples. A total of 44 M. globosa and 24 M. restricta isolates were analyzed. Twelve VNTR markers were selected on seven different chromosomes (I, II, III, IV, V, VII and IX), six for each Malassezia species. The highest discriminatory power for a single locus was obtained with the STR-MG1 marker (0.829) and STR-MR2 marker (0.818) for M. globosa and M. restricta, respectively. After the analysis of multiple loci, 24 genotypes were noted among 44 isolates in M. globosa, with a discrimination index D of 0.943 and 15 genotypes were noted among 24 isolates in M. restricta, with a discrimination index D of 0.967. An endogenous infection was detected in two patients. Different genotypes of M. globosa strains colonized one patient. Interestingly, VNTR markers analysis revealed a carriage between a breeder and his dog in three cases for M. globosa and two for M. restricta. The FST (0.018 to 0.057) values indicate a low differentiation between the three populations of M. globosa. These results suggest a dominant clonal mode of reproduction in M. globosa. The typing of M. restricta showed a genotypic diversity of the strains, which can cause various skin pathologies. However, patient five was colonized with strains having the same genotype collected from different body parts (back, shoulder). VNTR analysis was capable of identifying species with high accuracy and reliability. More importantly, the method would facilitate monitoring Malassezia colonization in domestic animals and humans. It was shown that the patterns are stable and the method is discriminant, making it a powerful tool for epidemiological purposes.
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Affiliation(s)
- Ines Hadrich
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax 3029, Tunisia
- Faculty of Science, University of Gabes, Gabes 6029, Tunisia
- Correspondence: ; Tel./Fax: +216-74-247-130
| | - Nahed Khemakhem
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax 3029, Tunisia
- Laboratory of Parasitology—Mycology, UH Habib Bourguiba, Sfax 3029, Tunisia
| | - Amin Ilahi
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax 3029, Tunisia
| | - Houaida Trabelsi
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax 3029, Tunisia
- Laboratory of Parasitology—Mycology, UH Habib Bourguiba, Sfax 3029, Tunisia
| | - Hayet Sellami
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax 3029, Tunisia
- Laboratory of Parasitology—Mycology, UH Habib Bourguiba, Sfax 3029, Tunisia
| | - Fattouma Makni
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax 3029, Tunisia
- Laboratory of Parasitology—Mycology, UH Habib Bourguiba, Sfax 3029, Tunisia
| | - Sourour Neji
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax 3029, Tunisia
- Laboratory of Parasitology—Mycology, UH Habib Bourguiba, Sfax 3029, Tunisia
| | - Ali Ayadi
- Laboratory of Fungal and Parasitic Molecular Biology, School of Medicine, University of Sfax, Sfax 3029, Tunisia
- Laboratory of Parasitology—Mycology, UH Habib Bourguiba, Sfax 3029, Tunisia
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Kerry RG, Montalbo FJP, Das R, Patra S, Mahapatra GP, Maurya GK, Nayak V, Jena AB, Ukhurebor KE, Jena RC, Gouda S, Majhi S, Rout JR. An overview of remote monitoring methods in biodiversity conservation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80179-80221. [PMID: 36197618 PMCID: PMC9534007 DOI: 10.1007/s11356-022-23242-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.
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Affiliation(s)
- Rout George Kerry
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | | | - Rajeswari Das
- Department of Soil Science and Agricultural Chemistry, School of Agriculture, GIET University, Gunupur, Rayagada, Odisha 765022 India
| | - Sushmita Patra
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | | | - Ganesh Kumar Maurya
- Zoology Section, Mahila MahaVidyalya, Banaras Hindu University, Varanasi, 221005 India
| | - Vinayak Nayak
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | - Atala Bihari Jena
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Ram Chandra Jena
- Department of Pharmaceutical Sciences, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Sushanto Gouda
- Department of Zoology, Mizoram University, Aizawl, 796009 India
| | - Sanatan Majhi
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Jyoti Ranjan Rout
- School of Biological Sciences, AIPH University, Bhubaneswar, Odisha 752101 India
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Descorps-Declère S, Richard GF. Megasatellite formation and evolution in vertebrate genes. Cell Rep 2022; 40:111347. [PMID: 36103826 DOI: 10.1016/j.celrep.2022.111347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/28/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022] Open
Abstract
Since formation of the first proto-eukaryotes, gene repertoire and genome complexity have significantly increased. Among genetic elements responsible for this increase are tandem repeats. Here we describe a genome-wide analysis of large tandem repeats, called megasatellites, in 58 vertebrate genomes. Two bursts occurred, one after the radiation between Agnatha and Gnathostomata fishes and the second one in therian mammals. Megasatellites are enriched in subtelomeric regions and frequently encoded in genes involved in transcription regulation, intracellular trafficking, and cell membrane metabolism, reminiscent of what is observed in fungus genomes. The presence of many introns within young megasatellites suggests that an exon-intron DNA segment is first duplicated and amplified before accumulation of mutations in intronic parts partially erases the megasatellite in such a way that it becomes detectable only in exons. Our results suggest that megasatellite formation and evolution is a dynamic and still ongoing process in vertebrate genomes.
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Affiliation(s)
- Stéphane Descorps-Declère
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 25 rue du Dr Roux, 75015 Paris, France.
| | - Guy-Franck Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Natural & Synthetic Genome Instabilities, 25 rue du Dr Roux, 75015 Paris, France.
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6
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Korotkov EV, Kamionskya AM, Korotkova MA. Detection of Highly Divergent Tandem Repeats in the Rice Genome. Genes (Basel) 2021; 12:genes12040473. [PMID: 33806152 PMCID: PMC8064497 DOI: 10.3390/genes12040473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/11/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022] Open
Abstract
Currently, there is a lack of bioinformatics approaches to identify highly divergent tandem repeats (TRs) in eukaryotic genomes. Here, we developed a new mathematical method to search for TRs, which uses a novel algorithm for constructing multiple alignments based on the generation of random position weight matrices (RPWMs), and applied it to detect TRs of 2 to 50 nucleotides long in the rice genome. The RPWM method could find highly divergent TRs in the presence of insertions or deletions. Comparison of the RPWM algorithm with the other methods of TR identification showed that RPWM could detect TRs in which the average number of base substitutions per nucleotide (x) was between 1.5 and 3.2, whereas T-REKS and TRF methods could not detect divergent TRs with x > 1.5. Applied to the search of TRs in the rice genome, the RPWM method revealed that TRs occupied 5% of the genome and that most of them were 2 and 3 bases long. Using RPWM, we also revealed the correlation of TRs with dispersed repeats and transposons, suggesting that some transposons originated from TRs. Thus, the novel RPWM algorithm is an effective tool to search for highly divergent TRs in the genomes.
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Affiliation(s)
- Eugene V Korotkov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld.2, 33 Leninsky Ave., 119071 Moscow, Russia
- MEPhI (Moscow Engineering Physics Institute), National Research Nuclear University, 31 Kashirskoye Shosse, 115409 Moscow, Russia
| | - Anastasiya M Kamionskya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld.2, 33 Leninsky Ave., 119071 Moscow, Russia
| | - Maria A Korotkova
- MEPhI (Moscow Engineering Physics Institute), National Research Nuclear University, 31 Kashirskoye Shosse, 115409 Moscow, Russia
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Liehr T. Repetitive Elements in Humans. Int J Mol Sci 2021; 22:ijms22042072. [PMID: 33669810 PMCID: PMC7922087 DOI: 10.3390/ijms22042072] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
Repetitive DNA in humans is still widely considered to be meaningless, and variations within this part of the genome are generally considered to be harmless to the carrier. In contrast, for euchromatic variation, one becomes more careful in classifying inter-individual differences as meaningless and rather tends to see them as possible influencers of the so-called 'genetic background', being able to at least potentially influence disease susceptibilities. Here, the known 'bad boys' among repetitive DNAs are reviewed. Variable numbers of tandem repeats (VNTRs = micro- and minisatellites), small-scale repetitive elements (SSREs) and even chromosomal heteromorphisms (CHs) may therefore have direct or indirect influences on human diseases and susceptibilities. Summarizing this specific aspect here for the first time should contribute to stimulating more research on human repetitive DNA. It should also become clear that these kinds of studies must be done at all available levels of resolution, i.e., from the base pair to chromosomal level and, importantly, the epigenetic level, as well.
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Affiliation(s)
- Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany
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Ahmad SF, Singchat W, Jehangir M, Suntronpong A, Panthum T, Malaivijitnond S, Srikulnath K. Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics. Cells 2020; 9:E2714. [PMID: 33352976 PMCID: PMC7767330 DOI: 10.3390/cells9122714] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
A substantial portion of the primate genome is composed of non-coding regions, so-called "dark matter", which includes an abundance of tandemly repeated sequences called satellite DNA. Collectively known as the satellitome, this genomic component offers exciting evolutionary insights into aspects of primate genome biology that raise new questions and challenge existing paradigms. A complete human reference genome was recently reported with telomere-to-telomere human X chromosome assembly that resolved hundreds of dark regions, encompassing a 3.1 Mb centromeric satellite array that had not been identified previously. With the recent exponential increase in the availability of primate genomes, and the development of modern genomic and bioinformatics tools, extensive growth in our knowledge concerning the structure, function, and evolution of satellite elements is expected. The current state of knowledge on this topic is summarized, highlighting various types of primate-specific satellite repeats to compare their proportions across diverse lineages. Inter- and intraspecific variation of satellite repeats in the primate genome are reviewed. The functional significance of these sequences is discussed by describing how the transcriptional activity of satellite repeats can affect gene expression during different cellular processes. Sex-linked satellites are outlined, together with their respective genomic organization. Mechanisms are proposed whereby satellite repeats might have emerged as novel sequences during different evolutionary phases. Finally, the main challenges that hinder the detection of satellite DNA are outlined and an overview of the latest methodologies to address technological limitations is presented.
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Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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9
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Suchkova IO, Borisova EV, Patkin EL. Length Polymorphism and Methylation Status of UPS29 Minisatellite of the ACAP3 Gene as Molecular Biomarker of Epilepsy. Sex Differences in Seizure Types and Symptoms. Int J Mol Sci 2020; 21:E9206. [PMID: 33276684 PMCID: PMC7730309 DOI: 10.3390/ijms21239206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/24/2020] [Accepted: 11/27/2020] [Indexed: 01/10/2023] Open
Abstract
Epilepsy is a neurological disease with different clinical forms and inter-individuals heterogeneity, which may be associated with genetic and/or epigenetic polymorphisms of tandem-repeated noncoding DNA. These polymorphisms may serve as predictive biomarkers of various forms of epilepsy. ACAP3 is the protein regulating morphogenesis of neurons and neuronal migration and is an integral component of important signaling pathways. This study aimed to carry out an association analysis of the length polymorphism and DNA methylation of the UPS29 minisatellite of the ACAP3 gene in patients with epilepsy. We revealed an association of short UPS29 alleles with increased risk of development of symptomatic and cryptogenic epilepsy in women, and also with cerebrovascular pathologies, structural changes in the brain, neurological status, and the clinical pattern of seizures in both women and men. The increase of frequency of hypomethylated UPS29 alleles in men with symptomatic epilepsy, and in women with both symptomatic and cryptogenic epilepsy was observed. For patients with hypomethylated UPS29 alleles, we also observed structural changes in the brain, neurological status, and the clinical pattern of seizures. These associations had sex-specific nature similar to a genetic association. In contrast with length polymorphism epigenetic changes affected predominantly the long UPS29 allele. We suppose that genetic and epigenetic alterations UPS29 can modify ACAP3 expression and thereby affect the development and clinical course of epilepsy.
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Affiliation(s)
- Irina O. Suchkova
- Laboratory of Molecular Cytogenetics of Mammalian Development, Department of Molecular Genetics, Institute of Experimental Medicine of the Russian Academy of Sciences, St. Petersburg 197376, Russia;
| | - Elena V. Borisova
- Department of Neurology, Clinic of Institute of Experimental Medicine, St. Petersburg 197376, Russia;
| | - Eugene L. Patkin
- Laboratory of Molecular Cytogenetics of Mammalian Development, Department of Molecular Genetics, Institute of Experimental Medicine of the Russian Academy of Sciences, St. Petersburg 197376, Russia;
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10
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Burgueño-Rodríguez G, Méndez Y, Olano N, Dabezies A, Bertoni B, Souto J, Castillo L, da Luz J, Soler AM. Ancestry and TPMT-VNTR Polymorphism: Relationship with Hematological Toxicity in Uruguayan Patients with Acute Lymphoblastic Leukemia. Front Pharmacol 2020; 11:594262. [PMID: 33424606 PMCID: PMC7789872 DOI: 10.3389/fphar.2020.594262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/24/2020] [Indexed: 12/14/2022] Open
Abstract
6-Mercaptopurine (6-MP) is a thiopurine drug widely used in childhood acute lymphoblastic leukemia (ALL) therapy. Genes such as TPMT and NUDT15 have an outstanding role in 6-MP metabolism. Mutations in both genes explain a significant portion of hematological toxicities suffered by ALL Uruguayan pediatric patients. A variable number tandem repeat in the TPMT promoter (TPMT-VNTR) has been associated with TPMT expression. This VNTR has a conservative architecture (AnBmC). To explore new causes of hematological toxicities related to ALL therapy, we genotyped the TPMT-VNTR of 130 Uruguayan pediatric patients. Additionally, individual genetic ancestry was estimated by 45 ancestry-informative markers (AIMs). Hematological toxicity was measured as the number of leukopenia events and 6-MP dose along the maintenance phase. As previously reported, we found TPMT*2 and TPMT*3C alleles were associated to TPMT-VNTR A2BC and AB2C, respectively. However, contrasting with other reports, TPMT*3A allele was found in a heterogeneous genetic background in linkage equilibrium. Patients carrying more than 5 A repeats present a significant higher number of leukopenia events among patients without TPMT and/or NUDT15 variants. Native American ancestry and the number of A repeats were significantly correlated with the number of leukopenia events. However, the correlation between Native American ancestry and the number of leukopenia events was lost when the number of A repeats was considered as covariate. This suggests that TPMT-VNTR alleles are more relevant than Native American ancestry in the hematological toxicity. Our results emphasize that TPMT-VNTR may be used as a pharmacogenetic biomarker to predict 6-MP-related hematological toxicity in ALL childhood therapy.
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Affiliation(s)
- Gabriela Burgueño-Rodríguez
- Laboratorio de Genética Molecular Humana, Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad de la República (UdelaR), Salto, Uruguay
| | - Yessika Méndez
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Natalia Olano
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Agustín Dabezies
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Jorge Souto
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Luis Castillo
- Servicio Hemato Oncológico Pediátrico (SHOP), Centro Hospitalario Pereira Rossell (CHPR), Montevideo, Uruguay
| | - Julio da Luz
- Laboratorio de Genética Molecular Humana, Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad de la República (UdelaR), Salto, Uruguay
| | - Ana María Soler
- Laboratorio de Genética Molecular Humana, Centro Universitario Regional (CENUR) Litoral Norte-Sede Salto, Universidad de la República (UdelaR), Salto, Uruguay
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11
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Linthorst J, Meert W, Hestand MS, Korlach J, Vermeesch JR, Reinders MJT, Holstege H. Extreme enrichment of VNTR-associated polymorphicity in human subtelomeres: genes with most VNTRs are predominantly expressed in the brain. Transl Psychiatry 2020; 10:369. [PMID: 33139705 PMCID: PMC7608644 DOI: 10.1038/s41398-020-01060-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/27/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
The human genome harbors numerous structural variants (SVs) which, due to their repetitive nature, are currently underexplored in short-read whole-genome sequencing approaches. Using single-molecule, real-time (SMRT) long-read sequencing technology in combination with FALCON-Unzip, we generated a de novo assembly of the diploid genome of a 115-year-old Dutch cognitively healthy woman. We combined this assembly with two previously published haploid assemblies (CHM1 and CHM13) and the GRCh38 reference genome to create a compendium of SVs that occur across five independent human haplotypes using the graph-based multi-genome aligner REVEAL. Across these five haplotypes, we detected 31,680 euchromatic SVs (>50 bp). Of these, ~62% were comprised of repetitive sequences with 'variable number tandem repeats' (VNTRs), ~10% were mobile elements (Alu, L1, and SVA), while the remaining variants were inversions and indels. We observed that VNTRs with GC-content >60% and repeat patterns longer than 15 bp were 21-fold enriched in the subtelomeric regions (within 5 Mb of the ends of chromosome arms). VNTR lengths can expand to exceed a critical length which is associated with impaired gene transcription. The genes that contained most VNTRs, of which PTPRN2 and DLGAP2 are the most prominent examples, were found to be predominantly expressed in the brain and associated with a wide variety of neurological disorders. Repeat-induced variation represents a sizeable fraction of the genetic variation in human genomes and should be included in investigations of genetic factors associated with phenotypic traits, specifically those associated with neurological disorders. We make available the long and short-read sequence data of the supercentenarian genome, and a compendium of SVs as identified across 5 human haplotypes.
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Affiliation(s)
- Jasper Linthorst
- grid.484519.5Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands ,grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Wim Meert
- grid.5596.f0000 0001 0668 7884Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Matthew S. Hestand
- grid.5596.f0000 0001 0668 7884Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jonas Korlach
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | | | - Marcel J. T. Reinders
- grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Henne Holstege
- Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands. .,Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands. .,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.
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12
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Heitkam T, Weber B, Walter I, Liedtke S, Ost C, Schmidt T. Satellite DNA landscapes after allotetraploidization of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:32-52. [PMID: 31981259 DOI: 10.1111/tpj.14705] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/10/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
If two related plant species hybridize, their genomes may be combined and duplicated within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co-evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn-over sequence class in eukaryotes, aiming to trace its emergence, amplification, and loss during plant speciation and allopolyploidization. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n = 4x = 36 chromosomes. Quinoa originated by hybridization of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3-6.3 million years. Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterized seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic, and fluorescent in situ hybridization. Whereas the satDNA distributions support C. suecicum as possible parental species, we were able to exclude C. pallidicaule as progenitor due to unique repeat profiles. Using quinoa long reads and scaffolds, we detected only limited evidence of intergenomic homogenization of satDNA after allopolyploidization, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidization, and may provide sequence targets for the identification of quinoa's progenitors.
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Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Ines Walter
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Susan Liedtke
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
| | - Charlotte Ost
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
- Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany
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13
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Functional and Structural Analysis of Predicted Proteins Obtained from Homo sapiens' Minisatellite 33.15-Tagged Transcript pAKT-45 Variants. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2562950. [PMID: 32566673 PMCID: PMC7273396 DOI: 10.1155/2020/2562950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/20/2020] [Accepted: 03/06/2020] [Indexed: 11/18/2022]
Abstract
The spermatozoa are transcriptionally dormant entities which have been recognized to be an archive of mRNA, coding for a variety of functionally crucial cellular proteins. This significant repository of mRNA is predicted to be associated with early embryogenesis and postfertilization. The mRNA transcripts which are tagged with minisatellites have been involved in the regulation of the gene functions as well as their organization. However, very little information is available regarding the expression of the transcripts tagged with minisatellites in spermatozoa. Therefore, in order to understand the functions and the conformational behavior of the proteins expressed from these minisatellite-tagged transcripts, we have performed a detailed in silico analysis using the sequences of the transcripts. The protein predicted from KF274549 showed the functionalities similar to uncharacterized C4orf26 proteins, while that obtained from KF274557 predicted to be a metallophosphoesterase. Furthermore, the structural folds in the structure of these predicted proteins were analyzed by using the homology modeling and their conformational behaviors in the explicit water conditions were analyzed by using the techniques of Molecular Dynamics (MD) simulations. This detailed analysis will facilitate the understanding of these proteins in the spermatozoon region and can be used for uncovering other attributes of the metabolic network.
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14
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DNA methylation in satellite repeats disorders. Essays Biochem 2020; 63:757-771. [PMID: 31387943 DOI: 10.1042/ebc20190028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.
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15
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Li Y, Chen X, Wu K, Pan J, Long H, Yan Y. Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics. Microorganisms 2020; 8:microorganisms8050662. [PMID: 32370063 PMCID: PMC7285179 DOI: 10.3390/microorganisms8050662] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 01/02/2023] Open
Abstract
Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large group of unicellular eukaryotes with extremely long evolutionary history and genome diversity. With recent publications of multiple ciliate genomes, we start to get a chance to explore perfect SSRs with motif size 1-100 bp and at least three motif repeats in nine species of two ciliate classes, Oligohymenophorea and Spirotrichea. We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in Tetrahymena. Micronuclear SSRs are universally more abundant than the macronuclear ones of the same motif-size, except for the 8-bp-motif SSRs in extensively fragmented chromosomes. Both the abundance and A/T content of SSRs decrease as motif-size increases, while the abundance is positively correlated with the A/T content of the genome. Also, smaller genomes have lower proportions of coding SSRs out of all SSRs in Paramecium species. This genome-wide and cross-species analysis reveals the high diversity of SSRs and reflects the rapid evolution of these simple repetitive elements in ciliate genomes.
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16
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Sayour AE, Elbauomy E, Abdel-Hamid NH, Mahrous A, Carychao D, Cooley MB, Elhadidy M. MLVA fingerprinting of Brucella melitensis circulating among livestock and cases of sporadic human illness in Egypt. Transbound Emerg Dis 2020; 67:2435-2445. [PMID: 32304280 DOI: 10.1111/tbed.13581] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 11/26/2022]
Abstract
Brucella melitensis is a serious public health threat, with human infection exhibiting acute febrile illness and chronic health problems. The present study investigated the genetic diversity and epidemiological links of the important zoonotic bacterium B. melitensis in Egypt using multilocus variable-number tandem repeat analysis (MLVA-16) including eight minisatellite (panel 1) and eight microsatellite (panel 2, subdivided into 2A and 2B) markers. A total of 118 isolates were identified as B. melitensis biovar 3 by classical biotyping and Bruce-ladder assay. Although B. melitensis is primarily associated with infection in sheep and goats, most of B. melitensis isolates in this study were obtained from secondary hosts (cattle, buffaloes, humans and a camel) suggesting cross-species adaptation of B. melitensis to large ruminants in Egypt. The MLVA-16 scheme competently discriminated 70 genotypes, with 51 genotypes represented by single isolates, and the remaining 19 genotypes were shared among 67 isolates, suggesting both sporadic and epidemiologically related characteristics of B. melitensis infection. Matching of local genotypes with representatives of global genotypes revealed that the majority of Egyptian isolates analysed had a West Mediterranean descendance. As this study represents the first comprehensive genotyping and genetic analysis of B. melitensis from different sources in Egypt, the information generated from this study will augment knowledge about the main epidemiological links associated with this bacterium and will allow a better understanding of the current epidemiological situation of brucellosis in Egypt. Ultimately, this will help to adopt effective brucellosis intervention strategies in Egypt and other developing nations.
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Affiliation(s)
- Ashraf E Sayour
- Department of Brucellosis Research, Animal Health Research Institute, Agricultural Research Center, Giza, Egypt
| | - Essam Elbauomy
- Department of Brucellosis Research, Animal Health Research Institute, Agricultural Research Center, Giza, Egypt
| | - Nour H Abdel-Hamid
- Department of Brucellosis Research, Animal Health Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ayman Mahrous
- Department of Zoonoses, General Organization for Veterinary Services (GOVS), Giza, Egypt
| | - Diana Carychao
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center, U.S. Department of Agriculture, Albany, CA, USA
| | - Michael B Cooley
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, Western Regional Research Center, U.S. Department of Agriculture, Albany, CA, USA
| | - Mohamed Elhadidy
- Zewail City of Science and Technology, University of Science and Technology, Giza, Egypt.,Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
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17
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Lansing F, Paszkowski-Rogacz M, Schmitt LT, Schneider PM, Rojo Romanos T, Sonntag J, Buchholz F. A heterodimer of evolved designer-recombinases precisely excises a human genomic DNA locus. Nucleic Acids Res 2020; 48:472-485. [PMID: 31745551 PMCID: PMC7107906 DOI: 10.1093/nar/gkz1078] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/04/2023] Open
Abstract
Site-specific recombinases (SSRs) such as the Cre/loxP system are useful genome engineering tools that can be repurposed by altering their DNA-binding specificity. However, SSRs that delete a natural sequence from the human genome have not been reported thus far. Here, we describe the generation of an SSR system that precisely excises a 1.4 kb fragment from the human genome. Through a streamlined process of substrate-linked directed evolution we generated two separate recombinases that, when expressed together, act as a heterodimer to delete a human genomic sequence from chromosome 7. Our data indicates that designer-recombinases can be generated in a manageable timeframe for precision genome editing. A large-scale bioinformatics analysis suggests that around 13% of all human protein-coding genes could be targetable by dual designer-recombinase induced genomic deletion (dDRiGD). We propose that heterospecific designer-recombinases, which work independently of the host DNA repair machinery, represent an efficient and safe alternative to nuclease-based genome editing technologies.
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Affiliation(s)
- Felix Lansing
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Lukas Theo Schmitt
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Paul Martin Schneider
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Teresa Rojo Romanos
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Jan Sonntag
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
| | - Frank Buchholz
- Medical Faculty and University Hospital Carl Gustav Carus, UCC Section Medical Systems Biology, TU Dresden, 01307 Dresden, Germany
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18
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Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 2019; 47:10994-11006. [PMID: 31584084 PMCID: PMC6868369 DOI: 10.1093/nar/gkz841] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/03/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022] Open
Abstract
The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with 'ready-to-use' deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.
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Affiliation(s)
- Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Pablo Mier
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Husch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Husch-Weg 15, 55128 Mainz, Germany
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton. CB10 1SD, UK
| | - Patryk Jarnot
- Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Aleksandra Gruca
- Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Universite Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
- Institut de Biologie Computationnelle, 34095 Montpellier, France
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, PO Box 20537, CY 1678 Nicosia, Cyprus
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
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19
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Dubrova Y. Mutation Induction in Humans and Mice: Where Are We Now? Cancers (Basel) 2019; 11:cancers11111708. [PMID: 31683966 PMCID: PMC6895811 DOI: 10.3390/cancers11111708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 10/21/2019] [Accepted: 10/30/2019] [Indexed: 01/09/2023] Open
Abstract
The analysis of mutation induction in human families exposed to mutagens provides the only source of reliable estimates of factors contributing to the genetic risk of human exposure to mutagens. In this paper, I briefly summarize the results of recent studies on the pattern of mutation induction in the human and mouse germline. The results of recent studies on the genome-wide effects of exposure to mutagens on mutation induction in the mammalian germline are presented and discussed. Lastly, this review also addresses the issue of transgenerational effects of parental exposure to mutagens on mutation rates in their non-exposed offspring, which are known as transgenerational instability. The possible contribution of transgenerational instability to the genetic risk of human exposure to mutagens is discussed.
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Affiliation(s)
- Yuri Dubrova
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
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20
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Bernardo LP, Mombach DM, Loreto ELS. Characterization of Herves-like transposable elements (hATs) in Drosophila species and their evolutionary scenario. INSECT MOLECULAR BIOLOGY 2019; 28:616-627. [PMID: 30793407 DOI: 10.1111/imb.12577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A monophyletic group of Drosophila hAT transposable elements, referred to as Herves-like, was characterized and found to be present in 46% of 57 screened Drosophila species. A remarkable characteristic of these elements is the presence of a long array of minisatellite repeats (MnRs) in both subterminal extremities of the elements. The copy number of these minisatellites was highly variable between and within populations. Twenty-three strains of Drosophila willistoni, covering its geographic distribution, were screened for polymorphism in the copy number of 5' MnRs, showing a variation from 7 to 20 repeat copies. These MnRs are well conserved among Drosophila species and probably function as transposase binding sequences, as provided by short subterminal repeats in other hAT elements. Miniature inverted repeat transposable elements were found in 27% of species carrying Herves-like elements. Phylogenetic analysis showed incongruences between transposable elements and species phylogenies, suggesting that at least four horizontal transfer events have occurred.
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Affiliation(s)
- L P Bernardo
- PPG Biodiverdade Animal, Universidade Federal de Santa Maria (UFSM), Santa Maria, Brazil
| | - D M Mombach
- Department of Biochemistry and Molecular Biology, CCNE, Univeridade Federal de Santa Maria, Santa Maria, Brazil
| | - E L S Loreto
- Department of Biochemistry and Molecular Biology, CCNE, Univeridade Federal de Santa Maria, Santa Maria, Brazil
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21
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De novo emergence and potential function of human-specific tandem repeats in brain-related loci. Hum Genet 2019; 138:661-672. [PMID: 31069507 DOI: 10.1007/s00439-019-02017-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/16/2019] [Indexed: 01/02/2023]
Abstract
Tandem repeats (TRs) are widespread in the genomes of all living organisms. In eukaryotes, they are found in both coding and noncoding regions and have potential roles in the regulation of cellular processes such as transcription, translation and in the modification of protein structure. Recent studies have highlighted TRs as a key regulator of gene expression and a potential contributor to human evolution. Thus, TRs are emerging as an important source of variation that can result in differential gene expression at intra- and inter-species levels. In this study, we performed a genome-wide survey to identify TRs that have emerged in the human lineage. We further examined these loci to explore their potential functional significance for human evolution. We identified 152 human-specific TR (HSTR) loci containing a repeat unit of more than ten bases, with most of them showing a repeat count of two. Gene set enrichment analysis showed that HSTR-associated genes were associated with biological functions in brain development and synapse function. In addition, we compared gene expression of human HSTR loci with orthologues from non-human primates (NHP) in seven different tissues. Strikingly, the expression level of HSTR-associated genes in brain tissues was significantly higher in human than in NHP. These results suggest the possibility that de novo emergence of TRs could have resulted in altered gene expression in humans within a short-time frame and contributed to the rapid evolution of human brain function.
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22
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Urbančič D, Šmid A, Stocco G, Decorti G, Mlinarič-Raščan I, Karas Kuželički N. Novel motif of variable number of tandem repeats in TPMT promoter region and evolutionary association of variable number of tandem repeats with TPMT*3 alleles. Pharmacogenomics 2018; 19:1311-1322. [PMID: 30345902 DOI: 10.2217/pgs-2018-0123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM SNPs in the gene for TPMT exemplify one of the most successful translations of pharmacogenomics into clinical practice. This study explains the correlation between common SNPs and variable number of tandem repeats (VNTR) in promoter of the gene. MATERIALS & METHODS We determined VNTR polymorphisms, as well as TPMT*2 and TPMT*3 SNPs and TPMT activity in Slovenian and Italian individuals and lymphoblastoid cell lines. RESULTS We observed a previously unreported VNTR allele, AB7C, in a TPMT*3A heterozygous individual. VNTRs with two (AB2C) and three or more (ABnC, n ≥ 3) B motifs were statistically significant in complete linkage disequilibrium (D' = 1, r2 = 1, p < 0.0001) with the TPMT*3C and TPMT*3A alleles, respectively. CONCLUSION The study provides insights into the stepwise evolution of TPMT*3 alleles from *3C to *3A, with increasing number of B motifs in the VNTR region.
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Affiliation(s)
- Dunja Urbančič
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Alenka Šmid
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Giuliana Decorti
- Laboratorio di Diagnostica Avanzata Traslazionale, Institute for Maternal & Child Health - IRCCS 'Burlo Garofolo', 34127 Trieste, Italy.,Department of Medicine, Surgery & Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Irena Mlinarič-Raščan
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Nataša Karas Kuželički
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
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23
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Qi WH, Jiang XM, Yan CC, Zhang WQ, Xiao GS, Yue BS, Zhou CQ. Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes. Sci Rep 2018; 8:14407. [PMID: 30258087 PMCID: PMC6158176 DOI: 10.1038/s41598-018-32286-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/04/2018] [Indexed: 01/23/2023] Open
Abstract
As the first examination of distribution, guanine-cytosine (GC) pattern, and variation analysis of microsatellites (SSRs) in different genomic regions of six bovid species, SSRs displayed nonrandomly distribution in different regions. SSR abundances are much higher in the introns, transposable elements (TEs), and intergenic regions compared to the 3′-untranslated regions (3′UTRs), 5′UTRs and coding regions. Trinucleotide perfect SSRs (P-SSRs) were the most frequent in the coding regions, whereas, mononucleotide P-SSRs were the most in the introns, 3′UTRs, TEs, and intergenic regions. Trifold P-SSRs had more GC-contents in the 5′UTRs and coding regions than that in the introns, 3′UTRs, TEs, and intergenic regions, whereas mononucleotide P-SSRs had the least GC-contents in all genomic regions. The repeat copy numbers (RCN) of the same mono- to hexanucleotide P-SSRs showed significantly different distributions in different regions (P < 0.01). Except for the coding regions, mononucleotide P-SSRs had the most RCNs, followed by the pattern: di- > tri- > tetra- > penta- > hexanucleotide P-SSRs in the same regions. The analysis of coefficient of variability (CV) of SSRs showed that the CV variations of RCN of the same mono- to hexanucleotide SSRs were relative higher in the intronic and intergenic regions, followed by the CV variation of RCN in the TEs, and the relative lower was in the 5′UTRs, 3′UTRs, and coding regions. Wide SSR analysis of different genomic regions has helped to reveal biological significances of their distributions.
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Affiliation(s)
- Wen-Hua Qi
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, 404100, P. R. China
| | - Xue-Mei Jiang
- College of Environmental and Chemistry Engineering, Chongqing Three Gorges University, Chongqing, 404100, P. R. China
| | - Chao-Chao Yan
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
| | - Wan-Qing Zhang
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan Province, 625014, P. R. China
| | - Guo-Sheng Xiao
- College of Biology and Food Engineering, Chongqing Three Gorges University, Chongqing, 404100, P. R. China
| | - Bi-Song Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, P. R. China
| | - Cai-Quan Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, P. R. China.
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24
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Krüger J, Schleinitz D. Genetic Fingerprinting Using Microsatellite Markers in a Multiplex PCR Reaction: A Compilation of Methodological Approaches from Primer Design to Detection Systems. Methods Mol Biol 2018; 1492:1-15. [PMID: 27822853 DOI: 10.1007/978-1-4939-6442-0_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Microsatellites are polymorphic DNA loci comprising repeated sequence motifs of two to five base pairs which are dispersed throughout the genome. Genotyping of microsatellites is a widely accepted tool for diagnostic and research purposes such as forensic investigations and parentage testing, but also in clinics (e.g. monitoring of bone marrow transplantation), as well as for the agriculture and food industries. The co-amplification of several short tandem repeat (STR) systems in a multiplex reaction with simultaneous detection helps to obtain more information from a DNA sample where its availability may be limited. Here, we introduce and describe this commonly used genotyping technique, providing an overview on available resources on STRs, multiplex design, and analysis.
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Affiliation(s)
- Jacqueline Krüger
- Department of Medicine, Dermatology and Neurology, University of Leipzig, Leipzig, Germany.,Leipzig University Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Dorit Schleinitz
- Department of Medicine, Dermatology and Neurology, University of Leipzig, Leipzig, Germany. .,Leipzig University Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany.
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25
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Oliveira MS, Dorneles EMS, Soares PMF, Fonseca AA, Orzil L, de Souza PG, Lage AP. Molecular epidemiology of Brucella abortus isolated from cattle in Brazil, 2009-2013. Acta Trop 2017; 166:106-113. [PMID: 27816477 DOI: 10.1016/j.actatropica.2016.10.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 01/20/2023]
Abstract
The aims of the present study were to genotype Brucella abortus strains isolated from cattle in Brazil between 2009 and 2013, and to analyze their distribution to support the Programa Nacional de Controle e Erradicação de Brucelose e Tuberculose (PNCEBT) (National Brucellosis and Tuberculosis Control and Eradication Program). One hundred forty B. abortus strains isolated from cattle in Brazil between 2009 and 2013 were genotyped using a set of 18 variable number of tandem repeats (VNTR) (MLVA16+HOOF-Print 3 and 4). The multiple locus VNTR analysis (MLVA) composed by eight markers (MLVA8) revealed eight different genotypes among B. abortus strains, including five previously described and three new ones. Analysis of the MLVA16 loci revealed fifty-eight distinct genotypes, from which three were identical, thirty-eight were considered very close, and seventeen were considered distant compared to those previously described and deposited in MLVAbank. Analysis of the HOOF-Prints 3 and 4 revealed the larger number of different alleles among all VNTR assessed, exhibiting maximum resolution when associated with MLVA16 markers. This study also provides insights on the genotypes of B. abortus circulating in Brazil, which certainly contribute for the better understanding of the epidemiology and control of bovine brucellosis in the country. Moreover, our data showed a high genetic diversity among the B. abortus strains isolated between 2009 and 2013, and a close relationship among these strains and Brazilian B. abortus deposited by MLVAbank.
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Affiliation(s)
- Mayra Silva Oliveira
- Laboratório de Bacteriologia Aplicada, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 567, 31270-901, Belo Horizonte, MG, Brazil.
| | - Elaine Maria Seles Dorneles
- Laboratório de Bacteriologia Aplicada, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 567, 31270-901, Belo Horizonte, MG, Brazil; Departamento de Medicina Veterinária, Universidade Federal de Lavras, Av. Dr. Sylvio Menicucci, 1001, Caixa Posta 3037, 37200-000, Lavras, MG, Brazil.
| | - Paulo Martins Filho Soares
- Laboratório Nacional Agropecuário, Ministério da Agricultura, Pecuária e Abastecimento, Av. Rômulo Joviano, 33600-000, Pedro Leopoldo, MG, Brazil.
| | - Antônio Augusto Fonseca
- Laboratório Nacional Agropecuário, Ministério da Agricultura, Pecuária e Abastecimento, Av. Rômulo Joviano, 33600-000, Pedro Leopoldo, MG, Brazil.
| | - Lívia Orzil
- Laboratório Nacional Agropecuário, Ministério da Agricultura, Pecuária e Abastecimento, Av. Rômulo Joviano, 33600-000, Pedro Leopoldo, MG, Brazil
| | - Patrícia Gomes de Souza
- Laboratório Nacional Agropecuário, Ministério da Agricultura, Pecuária e Abastecimento, Av. Rômulo Joviano, 33600-000, Pedro Leopoldo, MG, Brazil
| | - Andrey Pereira Lage
- Laboratório de Bacteriologia Aplicada, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Caixa Postal 567, 31270-901, Belo Horizonte, MG, Brazil.
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26
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Chalhoub H, Pletzer D, Weingart H, Braun Y, Tunney MM, Elborn JS, Rodriguez-Villalobos H, Plésiat P, Kahl BC, Denis O, Winterhalter M, Tulkens PM, Van Bambeke F. Mechanisms of intrinsic resistance and acquired susceptibility of Pseudomonas aeruginosa isolated from cystic fibrosis patients to temocillin, a revived antibiotic. Sci Rep 2017; 7:40208. [PMID: 28091521 PMCID: PMC5238406 DOI: 10.1038/srep40208] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/01/2016] [Indexed: 12/29/2022] Open
Abstract
The β-lactam antibiotic temocillin (6-α-methoxy-ticarcillin) shows stability to most extended spectrum β-lactamases, but is considered inactive against Pseudomonas aeruginosa. Mutations in the MexAB-OprM efflux system, naturally occurring in cystic fibrosis (CF) isolates, have been previously shown to reverse this intrinsic resistance. In the present study, we measured temocillin activity in a large collection (n = 333) of P. aeruginosa CF isolates. 29% of the isolates had MICs ≤ 16 mg/L (proposed clinical breakpoint for temocillin). Mutations were observed in mexA or mexB in isolates for which temocillin MIC was ≤512 mg/L (nucleotide insertions or deletions, premature termination, tandem repeat, nonstop, and missense mutations). A correlation was observed between temocillin MICs and efflux rate of N-phenyl-1-naphthylamine (MexAB-OprM fluorescent substrate) and extracellular exopolysaccharide abundance (contributing to a mucoid phenotype). OpdK or OpdF anion-specific porins expression decreased temocillin MIC by ~1 two-fold dilution only. Contrarily to the common assumption that temocillin is inactive on P. aeruginosa, we show here clinically-exploitable MICs on a non-negligible proportion of CF isolates, explained by a wide diversity of mutations in mexA and/or mexB. In a broader context, this work contributes to increase our understanding of MexAB-OprM functionality and help delineating how antibiotics interact with MexA and MexB.
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Affiliation(s)
- Hussein Chalhoub
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Daniel Pletzer
- Life Sciences, School of Engineering and Science, Jacobs University, Bremen, Germany
| | - Helge Weingart
- Life Sciences, School of Engineering and Science, Jacobs University, Bremen, Germany
| | - Yvonne Braun
- Life Sciences, School of Engineering and Science, Jacobs University, Bremen, Germany
| | - Michael M Tunney
- CF &Airways Microbiology Research Group, Queen's University Belfast, Belfast, UK
| | - J Stuart Elborn
- CF &Airways Microbiology Research Group, Queen's University Belfast, Belfast, UK
| | - Hector Rodriguez-Villalobos
- Laboratoire de microbiologie, Cliniques Universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Patrick Plésiat
- Laboratoire de bactériologie, Hôpital Jean Minjoz, Besançon, France
| | | | - Olivier Denis
- Laboratoire de microbiologie, Hôpital Erasme, Université libre de Bruxelles, Brussels, Belgium
| | - Mathias Winterhalter
- Life Sciences, School of Engineering and Science, Jacobs University, Bremen, Germany
| | - Paul M Tulkens
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Françoise Van Bambeke
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
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27
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Martínez-García PJ, Crepeau MW, Puiu D, Gonzalez-Ibeas D, Whalen J, Stevens KA, Paul R, Butterfield TS, Britton MT, Reagan RL, Chakraborty S, Walawage SL, Vasquez-Gross HA, Cardeno C, Famula RA, Pratt K, Kuruganti S, Aradhya MK, Leslie CA, Dandekar AM, Salzberg SL, Wegrzyn JL, Langley CH, Neale DB. The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:507-32. [PMID: 27145194 DOI: 10.1111/tpj.13207] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 04/22/2016] [Accepted: 04/27/2016] [Indexed: 05/18/2023]
Abstract
The Persian walnut (Juglans regia L.), a diploid species native to the mountainous regions of Central Asia, is the major walnut species cultivated for nut production and is one of the most widespread tree nut species in the world. The high nutritional value of J. regia nuts is associated with a rich array of polyphenolic compounds, whose complete biosynthetic pathways are still unknown. A J. regia genome sequence was obtained from the cultivar 'Chandler' to discover target genes and additional unknown genes. The 667-Mbp genome was assembled using two different methods (SOAPdenovo2 and MaSuRCA), with an N50 scaffold size of 464 955 bp (based on a genome size of 606 Mbp), 221 640 contigs and a GC content of 37%. Annotation with MAKER-P and other genomic resources yielded 32 498 gene models. Previous studies in walnut relying on tissue-specific methods have only identified a single polyphenol oxidase (PPO) gene (JrPPO1). Enabled by the J. regia genome sequence, a second homolog of PPO (JrPPO2) was discovered. In addition, about 130 genes in the large gallate 1-β-glucosyltransferase (GGT) superfamily were detected. Specifically, two genes, JrGGT1 and JrGGT2, were significantly homologous to the GGT from Quercus robur (QrGGT), which is involved in the synthesis of 1-O-galloyl-β-d-glucose, a precursor for the synthesis of hydrolysable tannins. The reference genome for J. regia provides meaningful insight into the complex pathways required for the synthesis of polyphenols. The walnut genome sequence provides important tools and methods to accelerate breeding and to facilitate the genetic dissection of complex traits.
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Affiliation(s)
| | - Marc W Crepeau
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Daniela Puiu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Daniel Gonzalez-Ibeas
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Jeanne Whalen
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Robin Paul
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | | | | | - Russell L Reagan
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Sandeep Chakraborty
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Sriema L Walawage
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Charis Cardeno
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kevin Pratt
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Sowmya Kuruganti
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | | | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269-3043, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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28
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Misawa K. Short tandem repeats in the human, cow, mouse, chicken, and lizard genomes are concentrated in the terminal regions of chromosomes. GENE REPORTS 2016. [DOI: 10.1016/j.genrep.2016.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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29
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30
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Heitkam T, Petrasch S, Zakrzewski F, Kögler A, Wenke T, Wanke S, Schmidt T. Next-generation sequencing reveals differentially amplified tandem repeats as a major genome component of Northern Europe’s oldest Camellia japonica. Chromosome Res 2015; 23:791-806. [DOI: 10.1007/s10577-015-9500-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 11/30/2022]
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31
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Wasik K, Gurtowski J, Zhou X, Ramos OM, Delás MJ, Battistoni G, El Demerdash O, Falciatori I, Vizoso DB, Smith AD, Ladurner P, Schärer L, McCombie WR, Hannon GJ, Schatz M. Genome and transcriptome of the regeneration-competent flatworm, Macrostomum lignano. Proc Natl Acad Sci U S A 2015; 112:12462-7. [PMID: 26392545 PMCID: PMC4603488 DOI: 10.1073/pnas.1516718112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The free-living flatworm, Macrostomum lignano has an impressive regenerative capacity. Following injury, it can regenerate almost an entirely new organism because of the presence of an abundant somatic stem cell population, the neoblasts. This set of unique properties makes many flatworms attractive organisms for studying the evolution of pathways involved in tissue self-renewal, cell-fate specification, and regeneration. The use of these organisms as models, however, is hampered by the lack of a well-assembled and annotated genome sequences, fundamental to modern genetic and molecular studies. Here we report the genomic sequence of M. lignano and an accompanying characterization of its transcriptome. The genome structure of M. lignano is remarkably complex, with ∼75% of its sequence being comprised of simple repeats and transposon sequences. This has made high-quality assembly from Illumina reads alone impossible (N50=222 bp). We therefore generated 130× coverage by long sequencing reads from the Pacific Biosciences platform to create a substantially improved assembly with an N50 of 64 Kbp. We complemented the reference genome with an assembled and annotated transcriptome, and used both of these datasets in combination to probe gene-expression patterns during regeneration, examining pathways important to stem cell function.
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Affiliation(s)
- Kaja Wasik
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - James Gurtowski
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Xin Zhou
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Molecular and Cellular Biology Graduate Program, Stony Brook University, NY 11794
| | - Olivia Mendivil Ramos
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - M Joaquina Delás
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Giorgia Battistoni
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Osama El Demerdash
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Ilaria Falciatori
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Dita B Vizoso
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - Andrew D Smith
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089
| | - Peter Ladurner
- Department of Evolutionary Biology, Institute of Zoology and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Lukas Schärer
- Department of Evolutionary Biology, Zoological Institute, University of Basel, 4051 Basel, Switzerland
| | - W Richard McCombie
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Gregory J Hannon
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom;
| | - Michael Schatz
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724;
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32
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Oliveira GAF, Dantas JLL, Oliveira EJ. Informativeness of minisatellite and microsatellite markers for genetic analysis in papaya. Genetica 2015; 143:613-31. [PMID: 26280323 DOI: 10.1007/s10709-015-9860-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/12/2015] [Indexed: 10/23/2022]
Abstract
The objective of this study was to evaluate information on minisatellite and microsatellite markers in papaya (Carica papaya L.). Forty minisatellites and 91 microsatellites were used for genotyping 24 papaya accessions. Estimates of genetic diversity, genetic linkage and analyses of population structure were compared. A lower average number of alleles per locus was observed in minisatellites (3.10) compared with microsatellites (3.57), although the minisatellites showed rarer alleles (18.54 %) compared with microsatellite (13.85 %). Greater expected (He = 0.52) and observed (Ho = 0.16) heterozygosity was observed in the microsatellites compared with minisatellites (He = 0.42 and Ho = 0.11), possibly due to the high number of hermaphroditic accessions, resulting in high rates of self-fertilization. The polymorphic information content and Shannon-Wiener diversity were also higher for microsatellites (from 0.47 to 1.10, respectively) compared with minisatellite (0.38 and 0.85, respectively). The probability of paternity exclusion was high for both markers (>0.999), and the combined probability of identity was from 1.65(-13) to 4.33(-38) for mini- and micro-satellites, respectively, which indicates that both types of markers are ideal for genetic analysis. The Bayesian analysis indicated the formation of two groups (K = 2) for both markers, although the minisatellites indicated a substructure (K = 4). A greater number of accessions with a low probability of assignment to specific groups were observed for microsatellites. Collectively, the results indicated higher informativeness of microsatellites. However, the lower informative power of minisatellites may be offset by the use of larger number of loci. Furthermore, minisatellites are subject to less error in genotyping because there is greater power to detect genotyping systems when larger motifs are used.
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Affiliation(s)
- G A F Oliveira
- Universidade Federal do Recôncavo da Bahia (UFRB), Cruz das Almas, BA, Brazil
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33
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Tawn EJ, Curwen GB, Rees GS, Jonas P. Germline minisatellite mutations in workers occupationally exposed to radiation at the Sellafield nuclear facility. JOURNAL OF RADIOLOGICAL PROTECTION : OFFICIAL JOURNAL OF THE SOCIETY FOR RADIOLOGICAL PROTECTION 2015; 35:21-36. [PMID: 25485533 DOI: 10.1088/0952-4746/35/1/21] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Germline minisatellite mutation rates were investigated in male workers occupationally exposed to radiation at the Sellafield nuclear facility. DNA samples from 160 families with 255 offspring were analysed for mutations at eight hypervariable minisatellite loci (B6.7, CEB1, CEB15, CEB25, CEB36, MS1, MS31, MS32) by Southern hybridisation. No significant difference was observed between the paternal mutation rate of 5.0% (37 mutations in 736 alleles) for control fathers with a mean preconceptional testicular dose of 9 mSv and that of 5.8% (66 in 1137 alleles) for exposed fathers with a mean preconceptional testicular dose of 194 mSv. Subgrouping the exposed fathers into two dose groups with means of 111 mSv and 274 mSv revealed paternal mutation rates of 6.0% (32 mutations in 536 alleles) and 5.7% (34 mutations in 601 alleles), respectively, neither of which was significantly different in comparisons with the rate for the control fathers. Maternal mutation rates of 1.6% (12 mutations in 742 alleles) for the partners of control fathers and 1.7% (19 mutations in 1133 alleles) for partners of exposed fathers were not significantly different. This study provides evidence that paternal preconceptional occupational radiation exposure does not increase the germline minisatellite mutation rate and therefore refutes suggestions that such exposure could result in a destabilisation of the germline that can be passed on to future generations.
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Affiliation(s)
- E Janet Tawn
- Centre for Integrated Genomic Medical Research (CIGMR), Centre for Epidemiology, Institute of Population Health, The University of Manchester, Manchester, M13 9PT, UK. Formerly of Westlakes Research Institute4Westlakes Research Institute closed in 2010., Westlakes Science and Technology Park, Moor Row, Cumbria, CA24 3LN, UK
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34
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Affiliation(s)
- J. Rich
- CNRS UMR 8126, Universit Paris-Sud 11, Institut Gustave Roussy
| | - V. V. Ogryzko
- CNRS UMR 8126, Universit Paris-Sud 11, Institut Gustave Roussy
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35
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Mick V, Le Carrou G, Corde Y, Game Y, Jay M, Garin-Bastuji B. Brucella melitensis in France: persistence in wildlife and probable spillover from Alpine ibex to domestic animals. PLoS One 2014; 9:e94168. [PMID: 24732322 PMCID: PMC3986073 DOI: 10.1371/journal.pone.0094168] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/12/2014] [Indexed: 11/19/2022] Open
Abstract
Bovine brucellosis is a major zoonosis, mainly caused by Brucella abortus, more rarely by Brucella melitensis. France has been bovine brucellosis officially-free since 2005 with no cases reported in domestic/wild ruminants since 2003. In 2012, bovine and autochthonous human cases due to B. melitensis biovar 3 (Bmel3) occurred in the French Alps. Epidemiological investigations implemented in wild and domestic ruminants evidenced a high seroprevalence (>45%) in Alpine ibex (Capra ibex); no cases were disclosed in other domestic or wild ruminants, except for one isolated case in a chamois (Rupicapra rupicapra). These results raised the question of a possible persistence/emergence of Brucella in wildlife. The purpose of this study was to assess genetic relationships among the Bmel3 strains historically isolated in humans, domestic and wild ruminants in Southeastern France, over two decades, by the MLVA-panel2B assay, and to propose a possible explanation for the origin of the recent bovine and human infections. Indeed, this genotyping strategy proved to be efficient for this microepidemiological investigation using an interpretation cut-off established for a fine-scale setting. The isolates, from the 2012 domestic/human outbreak harbored an identical genotype, confirming a recent and direct contamination from cattle to human. Interestingly, they clustered not only with isolates from wildlife in 2012, but also with local historical domestic isolates, in particular with the 1999 last bovine case in the same massif. Altogether, our results suggest that the recent bovine outbreak could have originated from the Alpine ibex population. This is the first report of a B. melitensis spillover from wildlife to domestic ruminants and the sustainability of the infection in Alpine ibex. However, this wild population, reintroduced in the 1970s in an almost closed massif, might be considered as a semi-domestic free-ranging herd. Anthropogenic factors could therefore account with the high observed intra-species prevalence.
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Affiliation(s)
- Virginie Mick
- Paris-Est University/Anses, EU/OIE/FAO & National Reference Laboratory for Brucellosis, Animal Health Laboratory, Maisons-Alfort, France
| | - Gilles Le Carrou
- Paris-Est University/Anses, EU/OIE/FAO & National Reference Laboratory for Brucellosis, Animal Health Laboratory, Maisons-Alfort, France
| | - Yannick Corde
- Paris-Est University/Anses, EU/OIE/FAO & National Reference Laboratory for Brucellosis, Animal Health Laboratory, Maisons-Alfort, France
| | - Yvette Game
- Departmental Veterinary Laboratory of Savoie (LDAV 73), Chambery, France
| | - Maryne Jay
- Paris-Est University/Anses, EU/OIE/FAO & National Reference Laboratory for Brucellosis, Animal Health Laboratory, Maisons-Alfort, France
| | - Bruno Garin-Bastuji
- Paris-Est University/Anses, EU/OIE/FAO & National Reference Laboratory for Brucellosis, Animal Health Laboratory, Maisons-Alfort, France
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Alam CM, Singh AK, Sharfuddin C, Ali S. Incidence, complexity and diversity of simple sequence repeats across potexvirus genomes. Gene 2014; 537:189-96. [DOI: 10.1016/j.gene.2014.01.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/15/2013] [Accepted: 01/04/2014] [Indexed: 01/18/2023]
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Schaper E, Gascuel O, Anisimova M. Deep conservation of human protein tandem repeats within the eukaryotes. Mol Biol Evol 2014; 31:1132-48. [PMID: 24497029 PMCID: PMC3995336 DOI: 10.1093/molbev/msu062] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Tandem repeats (TRs) are a major element of protein sequences in all domains of life. They are particularly abundant in mammals, where by conservative estimates one in three proteins contain a TR. High generation-scale duplication and deletion rates were reported for nucleic TR units. However, it is not known whether protein TR units can also be frequently lost or gained providing a source of variation for rapid adaptation of protein function, or alternatively, tend to have conserved TR unit configurations over long evolutionary times. To obtain a systematic picture, we performed a proteome-wide analysis of the mode of evolution for human protein TRs. For this purpose, we propose a novel method for the detection of orthologous TRs based on circular profile hidden Markov models. For all detected TRs, we reconstructed bispecies TR unit phylogenies across 61 eukaryotes ranging from human to yeast. Moreover, we performed additional analyses to correlate functional and structural annotations of human TRs with their mode of evolution. Surprisingly, we find that the vast majority of human TRs are ancient, with TR unit number and order preserved intact since distant speciation events. For example, ≥61% of all human TRs have been strongly conserved at least since the root of all mammals, approximately 300 Ma. Further, we find no human protein TR that shows evidence for strong recent duplications and deletions. The results are in contrast to the high generation-scale mutability of nucleic TRs. Presumably, most protein TRs fold into stable and conserved structures that are indispensable for the function of the TR-containing protein. All of our data and results are available for download from http://www.atgc-montpellier.fr/TRE.
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Affiliation(s)
- Elke Schaper
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
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38
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In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes. Gene 2013; 530:193-200. [DOI: 10.1016/j.gene.2013.08.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/10/2013] [Accepted: 08/13/2013] [Indexed: 11/20/2022]
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Abstract
Microsatellites are DNA sequences of tandem repeats of one to six nucleotides, which are highly polymorphic, and thus the molecular markers of choice in many kinship, population genetic, and conservation studies. There have been significant technical improvements since the early methods for microsatellite isolation were developed, and today the most common procedures take advantage of the hybrid capture methods of enriched-targeted microsatellite DNA. Furthermore, recent advents in sequencing technologies (i.e., next-generation sequencing, NGS) have fostered the mining of microsatellite markers in non-model organisms, affording a cost-effective way of obtaining a large amount of sequence data potentially useful for loci characterization. The rapid improvements of NGS platforms together with the increase in available microsatellite information open new avenues to the understanding of the evolutionary forces that shape genetic structuring in wild populations. Here, we provide detailed methodological procedures for microsatellite isolation based on the screening of GT microsatellite-enriched libraries, either by cloning and Sanger sequencing of positive clones or by direct NGS. Guides for designing new species-specific primers and basic genotyping are also given.
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Affiliation(s)
- Elena G Gonzalez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, Madrid, Spain
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40
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Sankaranarayanan K, Taleei R, Rahmanian S, Nikjoo H. Ionizing radiation and genetic risks. XVII. Formation mechanisms underlying naturally occurring DNA deletions in the human genome and their potential relevance for bridging the gap between induced DNA double-strand breaks and deletions in irradiated germ cells. Mutat Res 2013; 753:114-130. [PMID: 23948232 DOI: 10.1016/j.mrrev.2013.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/27/2013] [Accepted: 07/22/2013] [Indexed: 12/21/2022]
Abstract
While much is known about radiation-induced DNA double-strand breaks (DSBs) and their repair, the question of how deletions of different sizes arise as a result of the processing of DSBs by the cell's repair systems has not been fully answered. In order to bridge this gap between DSBs and deletions, we critically reviewed published data on mechanisms pertaining to: (a) repair of DNA DSBs (from basic studies in this area); (b) formation of naturally occurring structural variation (SV) - especially of deletions - in the human genome (from genomic studies) and (c) radiation-induced mutations and structural chromosomal aberrations in mammalian somatic cells (from radiation mutagenesis and radiation cytogenetic studies). The specific aim was to assess the relative importance of the postulated mechanisms in generating deletions in the human genome and examine whether empirical data on radiation-induced deletions in mouse germ cells are consistent with predictions of these mechanisms. The mechanisms include (a) NHEJ, a DSB repair process that does not require any homology and which functions in all stages of the cell cycle (and is of particular relevance in G0/G1); (b) MMEJ, also a DSB repair process but which requires microhomology and which presumably functions in all cell cycle stages; (c) NAHR, a recombination-based DSB repair mechanism which operates in prophase I of meiosis in germ cells; (d) MMBIR, a microhomology-mediated, replication-based mechanism which operates in the S phase of the cell cycle, and (e) strand slippage during replication (involved in the origin of small insertions and deletions (INDELs). Our analysis permits the inference that, between them, these five mechanisms can explain nearly all naturally occurring deletions of different sizes identified in the human genome, NAHR and MMBIR being potentially more versatile in this regard. With respect to radiation-induced deletions, the basic studies suggest that those arising as a result of the operation of NHEJ/MMEJ processes, as currently formulated, are expected to be relatively small. However, data on induced mutations in mouse spermatogonial stem cells (irradiation in G0/G1 phase of the cell cycle and DSB repair presumed to be via NHEJ predominantly) show that most are associated with deletions of different sizes, some in the megabase range. There is thus a 'discrepancy' between what the basic studies suggest and the empirical observations in mutagenesis studies. This discrepancy, however, is only an apparent but not a real one. It can be resolved by considering the issue of deletions in the broader context of and in conjunction with the organization of chromatin in chromosomes and nuclear architecture, the conceptual framework for which already exists in studies carried out during the past fifteen years or so. In this paper, we specifically hypothesize that repair of DSBs induced in chromatin loops may offer a basis to explain the induction of deletions of different sizes and suggest an approach to test the hypothesis. We emphasize that the bridging of the gap between induced DSB and resulting deletions of different sizes is critical for current efforts in computational modeling of genetic risks.
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Affiliation(s)
- Krishnaswami Sankaranarayanan
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Instituet, Box 260, Stockholm SE 17176, Sweden
| | - Reza Taleei
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Instituet, Box 260, Stockholm SE 17176, Sweden
| | - Shirin Rahmanian
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Instituet, Box 260, Stockholm SE 17176, Sweden
| | - Hooshang Nikjoo
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Instituet, Box 260, Stockholm SE 17176, Sweden.
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A Whole Genome Screen for Minisatellite Stability Genes in Stationary-Phase Yeast Cells. G3-GENES GENOMES GENETICS 2013; 3:741-756. [PMID: 23550123 PMCID: PMC3618361 DOI: 10.1534/g3.112.005397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Repetitive elements comprise a significant portion of most eukaryotic genomes. Minisatellites, a type of repetitive element composed of repeat units 15−100 bp in length, are stable in actively dividing cells but change in composition during meiosis and in stationary-phase cells. Alterations within minisatellite tracts have been correlated with the onset of a variety of diseases, including diabetes mellitus, myoclonus epilepsy, and several types of cancer. However, little is known about the factors preventing minisatellite alterations. Previously, our laboratory developed a color segregation assay in which a minisatellite was inserted into the ADE2 gene in the yeast Saccharomyces cerevisiae to monitor alteration events. We demonstrated that minisatellite alterations that occur in stationary-phase cells give rise to a specific colony morphology phenotype known as blebbing. Here, we performed a modified version of the synthetic genetic array analysis to screen for mutants that produce a blebbing phenotype. Screens were conducted using two distinctly different minisatellite tracts: the ade2-min3 construct consisting of three identical 20-bp repeats, and the ade2-h7.5 construct, consisting of seven-and-a-half 28-bp variable repeats. Mutations in 102 and 157 genes affect the stability of the ade2-min3 and ade2-h7.5 alleles, respectively. Only seven hits overlapped both screens, indicating that different factors regulate repeat stability depending upon minisatellite size and composition. Importantly, we demonstrate that mismatch repair influences the stability of the ade2-h7.5 allele, indicating that this type of DNA repair stabilizes complex minisatellites in stationary phase cells. Our work provides insight into the factors regulating minisatellite stability.
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Detection and characterization of megasatellites in orthologous and nonorthologous genes of 21 fungal genomes. EUKARYOTIC CELL 2013; 12:794-803. [PMID: 23543670 DOI: 10.1128/ec.00001-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Megasatellites are large DNA tandem repeats, originally described in Candida glabrata, in protein-coding genes. Most of the genes in which megasatellites are found are of unknown function. In this work, we extended the search for megasatellites to 20 additional completely sequenced fungal genomes and extracted 216 megasatellites in 203 out of 142,121 genes, corresponding to the most exhaustive description of such genetic elements available today. We show that half of the megasatellites detected encode threonine-rich peptides predicted to be intrinsically disordered, suggesting that they may interact with several partners or serve as flexible linkers. Megasatellite motifs were clustered into several families. Their distribution in fungal genes shows that different motifs are found in orthologous genes and similar motifs are found in unrelated genes, suggesting that megasatellite formation or spreading does not necessarily track the evolution of their host genes. Altogether, these results suggest that megasatellites are created and lost during evolution of fungal genomes, probably sharing similar functions, although their primary sequences are not necessarily conserved.
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43
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Linschooten JO, Verhofstad N, Gutzkow K, Olsen AK, Yauk C, Oligschläger Y, Brunborg G, van Schooten FJ, Godschalk RWL. Paternal lifestyle as a potential source of germline mutations transmitted to offspring. FASEB J 2013; 27:2873-9. [PMID: 23538710 DOI: 10.1096/fj.13-227694] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Paternal exposure to high levels of radioactivity causes heritable germline minisatellite mutations. However, the effect of more general paternal exposures, such as cigarette smoking, on germline mutations remains unexplored. We analyzed two of the most commonly used minisatellite loci (CEB1 and B6.7) to identify germline mutations in blood samples of complete mother-father-child triads from the Norwegian Mother and Child Cohort Study (MoBa). The presence of mutations was subsequently related to general lifestyle factors, including paternal smoking before the partner became pregnant. Paternally derived mutations at the B6.7 locus (mutation frequency 0.07) were not affected by lifestyle. In contrast, high gross yearly income as a general measure of a healthy lifestyle coincided with low-mutation frequencies at the CEB1 locus (P=0.047). Income was inversely related to smoking behavior, and paternally derived CEB1 mutations were dose dependently increased when the father smoked in the 6 mo before pregnancy, 0.21 vs. 0.05 in smoking and nonsmoking fathers, respectively (P=0.061). These results suggest that paternal lifestyle can affect the chance of heritable mutations in unstable repetitive DNA sequences. To our knowledge, this is the first study reporting an effect of lifestyle on germline minisatellite mutation frequencies in a human population with moderate paternal exposures.
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Affiliation(s)
- Joost O Linschooten
- Department of Toxicology, School for Nutrition, Toxicology and Metabolism, Maastricht University, 6200MD Maastricht, The Netherlands
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44
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Abstract
First discovered as a structure-specific endonuclease that evolved to cut at the base of single-stranded flaps, flap endonuclease (FEN1) is now recognized as a central component of cellular DNA metabolism. Substrate specificity allows FEN1 to process intermediates of Okazaki fragment maturation, long-patch base excision repair, telomere maintenance, and stalled replication fork rescue. For Okazaki fragments, the RNA primer is displaced into a 5' flap and then cleaved off. FEN1 binds to the flap base and then threads the 5' end of the flap through its helical arch and active site to create a configuration for cleavage. The threading requirement prevents this active nuclease from cutting the single-stranded template between Okazaki fragments. FEN1 efficiency and specificity are critical to the maintenance of genome fidelity. Overall, recent advances in our knowledge of FEN1 suggest that it was an ancient protein that has been fine-tuned over eons to coordinate many essential DNA transactions.
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Affiliation(s)
- Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA.
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45
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Evolution of an Ancient Microsatellite Hotspot in the Conifer Mitochondrial Genome and Comparison with Other Plants. J Mol Evol 2013; 76:146-57. [DOI: 10.1007/s00239-013-9547-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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46
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Stimulation of gross chromosomal rearrangements by the human CEB1 and CEB25 minisatellites in Saccharomyces cerevisiae depends on G-quadruplexes or Cdc13. PLoS Genet 2012; 8:e1003033. [PMID: 23133402 PMCID: PMC3486850 DOI: 10.1371/journal.pgen.1003033] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 08/29/2012] [Indexed: 11/19/2022] Open
Abstract
Genomes contain tandem repeats that are at risk of internal rearrangements and a threat to genome integrity. Here, we investigated the behavior of the human subtelomeric minisatellites HRAS1, CEB1, and CEB25 in Saccharomyces cerevisiae. In mitotically growing wild-type cells, these GC-rich tandem arrays stimulate the rate of gross chromosomal rearrangements (GCR) by 20, 1,620, and 276,000-fold, respectively. In the absence of the Pif1 helicase, known to inhibit GCR by telomere addition and to unwind G-quadruplexes, the GCR rate is further increased in the presence of CEB1, by 385-fold compared to the pif1Δ control strain. The behavior of CEB1 is strongly dependent on its capacity to form G-quadruplexes, since the treatment of WT cells with the Phen-DC(3) G-quadruplex ligand has a 52-fold stimulating effect while the mutation of the G-quadruplex-forming motif reduced the GCR rate 30-fold in WT and 100-fold in pif1Δ cells. The GCR events are telomere additions within CEB1. Differently, the extreme stimulation of CEB25 GCR depends on its affinity for Cdc13, which binds the TG-rich ssDNA telomere overhang. This property confers a biased orientation-dependent behavior to CEB25, while CEB1 and HRAS1 increase GCR similarly in either orientation. Furthermore, we analyzed the minisatellites' distribution in the human genome and discuss their potential role to trigger subtelomeric rearrangements.
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47
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Wang DY, Hadj-Henni L, Thierry S, Arné P, Chermette R, Botterel F, Hadrich I, Makni F, Ayadi A, Ranque S, Huang WY, Guillot J. Simple and highly discriminatory VNTR-based multiplex PCR for tracing sources of Aspergillus flavus isolates. PLoS One 2012; 7:e44204. [PMID: 23028503 PMCID: PMC3444452 DOI: 10.1371/journal.pone.0044204] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 07/30/2012] [Indexed: 11/26/2022] Open
Abstract
Aspergillus flavus is second only to A. fumigatus in causing invasive aspergillosis and it is the major agent responsible for fungal sinusitis, keratitis and endophthalmitis in many countries in the Middle East, Africa and Southeast Asia. Despite the growing challenge due to A. flavus, data on the molecular epidemiology of this fungus remain scarce. The objective of the present study was to develop a new typing method based on the detection of VNTR (Variable number tandem repeat) markers. Eight VNTR markers located on 6 different chromosomes (1, 2, 3, 5, 7 and 8) of A. flavus were selected, combined by pairs for multiplex amplifications and tested on 30 unrelated isolates and six reference strains. The Simpson index for individual markers ranged from 0.398 to 0.818. A combined loci index calculated with all the markers yielded an index of 0.998. The MLVA (Multiple Locus VNTR Analysis) technique proved to be specific and reproducible. In a second time, a total of 55 isolates from Chinese avian farms and from a Tunisian hospital have been evaluated. One major cluster of genotypes could be defined by using the graphing algorithm termed Minimum Spanning Tree. This cluster comprised most of the isolates collected in an avian farm in southern China. The MLVA technique should be considered as an excellent and cost-effective typing method that could be used in many laboratories without the need for sophisticated equipment.
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Affiliation(s)
- Dong Ying Wang
- Parasitology Department, College of Animal Science and Technology, Guangxi University, Nanning, China
- ANSES, Laboratoire de Santé Animale, UMR BIPAR, Maisons-Alfort, France
| | - Leila Hadj-Henni
- ANSES, Laboratoire de Santé Animale, UMR BIPAR, Maisons-Alfort, France
| | - Simon Thierry
- ANSES, Laboratoire de Santé Animale, UMR BIPAR, Maisons-Alfort, France
| | - Pascal Arné
- ENVA, Laboratoire de Santé Animale, UMR BIPAR, Maisons-Alfort, France
| | - René Chermette
- ENVA, Laboratoire de Santé Animale, UMR BIPAR, Maisons-Alfort, France
| | | | - Inès Hadrich
- Laboratoire de Biologie Moléculaire Parasitaire et Fongique, Faculté de Médecine de Sfax, Sfax, Tunisia
| | - Fattouma Makni
- Laboratoire de Biologie Moléculaire Parasitaire et Fongique, Faculté de Médecine de Sfax, Sfax, Tunisia
| | - Ali Ayadi
- Laboratoire de Biologie Moléculaire Parasitaire et Fongique, Faculté de Médecine de Sfax, Sfax, Tunisia
| | - Stéphane Ranque
- Aix-Marseille Université, UMR MD3, Marseille, France
- APHM, Timone, Laboratoire de Parasitologie-Mycologie, Marseille, France
| | - Wei Yi Huang
- Parasitology Department, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Jacques Guillot
- ENVA, Laboratoire de Santé Animale, UMR BIPAR, Maisons-Alfort, France
- * E-mail:
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Glunčić M, Paar V. Direct mapping of symbolic DNA sequence into frequency domain in global repeat map algorithm. Nucleic Acids Res 2012; 41:e17. [PMID: 22977183 PMCID: PMC3592446 DOI: 10.1093/nar/gks721] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The main feature of global repeat map (GRM) algorithm (www.hazu.hr/grm/software/win/grm2012.exe) is its ability to identify a broad variety of repeats of unbounded length that can be arbitrarily distant in sequences as large as human chromosomes. The efficacy is due to the use of complete set of a K-string ensemble which enables a new method of direct mapping of symbolic DNA sequence into frequency domain, with straightforward identification of repeats as peaks in GRM diagram. In this way, we obtain very fast, efficient and highly automatized repeat finding tool. The method is robust to substitutions and insertions/deletions, as well as to various complexities of the sequence pattern. We present several case studies of GRM use, in order to illustrate its capabilities: identification of α-satellite tandem repeats and higher order repeats (HORs), identification of Alu dispersed repeats and of Alu tandems, identification of Period 3 pattern in exons, implementation of ‘magnifying glass’ effect, identification of complex HOR pattern, identification of inter-tandem transitional dispersed repeat sequences and identification of long segmental duplications. GRM algorithm is convenient for use, in particular, in cases of large repeat units, of highly mutated and/or complex repeats, and of global repeat maps for large genomic sequences (chromosomes and genomes).
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Affiliation(s)
- Matko Glunčić
- Faculty of Science, University of Zagreb, Bijenička 32 and Croatian Academy of Sciences and Arts, Zrinski trg 11, 10000 Zagreb, Croatia.
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49
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Liu H, Yin J, Xiao M, Gao C, Mason AS, Zhao Z, Liu Y, Li J, Fu D. Characterization and evolution of 5' and 3' untranslated regions in eukaryotes. Gene 2012; 507:106-11. [PMID: 22846368 DOI: 10.1016/j.gene.2012.07.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 06/26/2012] [Accepted: 07/18/2012] [Indexed: 01/21/2023]
Abstract
Untranslated regions (UTRs) in eukaryotes play a significant role in the regulation of translation and mRNA half-life, as well as interacting with specific RNA-binding proteins. However, UTRs receive less attention than more crucial elements such as genes, and the basic structural and evolutionary characteristics of UTRs of different species, and the relationship between these UTRs and the genome size and species gene number is not well understood. To address these questions, we performed a comparative analysis of 5' and 3' untranslated regions of different species by analyzing the basic characteristics of 244,976 UTRs from three eukaryote kingdoms (Plantae, Fungi, and Protista). The results showed that the UTR lengths and SSR frequencies in UTRs increased significantly with increasing species gene number while the length and G+C content in 5' UTRs and different types of repetitive sequences in 3' UTRs increased with the increase of genome size. We also found that the sequence length of 5' UTRs was significantly positively correlated with the presence of transposons and SSRs while the sequence length of 3' UTRs was significantly positively correlated with the presence of tandem repeat sequences. These results suggested that evolution of species complexity from lower organisms to higher organisms is accompanied by an increase in the regulatory complexity of UTRs, mediated by increasing UTR length, increasing G+C content of 5' UTRs, and insertion and expansion of repetitive sequences.
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Affiliation(s)
- Honglei Liu
- Engineering Research Center of South Upland Agriculture of Ministry of Education, PR China, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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50
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Cheng J, Xue H, Zhao X. Variation of serine-aspartate repeats in membrane proteins possibly contributes to staphylococcal microevolution. PLoS One 2012; 7:e34756. [PMID: 22509353 PMCID: PMC3324548 DOI: 10.1371/journal.pone.0034756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2011] [Accepted: 03/05/2012] [Indexed: 11/18/2022] Open
Abstract
Tandem repeats (either as microsatellites or minisatellites) in eukaryotic and prokaryotic organisms are mutation-prone DNA. While minisatellites in prokaryotic genomes are underrepresented, the cell surface adhesins of bacteria often contain the minisatellite SD repeats, encoding the amino acid pair of serine-asparatate, especially in Staphylococcal strains. However, their relationship to biological functions is still elusive. In this study, effort was made to uncover the copy number variations of SD repeats by bioinformatic analysis and to detect changes in SD repeats during a plasmid-based assay, as a first step to understand its biological functions. The SD repeats were found to be mainly present in the cell surface proteins. The SD repeats were genetically unstable and polymorphic in terms of copy numbers and sequence compositions. Unlike SNPs, the change of its copy number was reversible, without frame shifting. More significantly, a rearrangement hot spot, the ATTC/AGRT site, was found to be mainly responsible for the instability and reversibility of SD repeats. These characteristics of SD repeats may facilitate bacteria to respond to environmental changes, with low cost, low risk and high efficiency.
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Affiliation(s)
- Jing Cheng
- Department of Animal Science, McGill University, Montreal, Quebec, Canada
| | - Huping Xue
- Department of Animal Science, McGill University, Montreal, Quebec, Canada
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, Quebec, Canada
- * E-mail:
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