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Nikolaeva OV, Beregova AM, Efeykin BD, Miroliubova TS, Zhuravlev AY, Ivantsov AY, Mikhailov KV, Spiridonov SE, Aleoshin VV. Expression of Hairpin-Enriched Mitochondrial DNA in Two Hairworm Species (Nematomorpha). Int J Mol Sci 2023; 24:11411. [PMID: 37511167 PMCID: PMC10380579 DOI: 10.3390/ijms241411411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Nematomorpha (hairworms) is a phylum of parasitic ecdysozoans, best known for infecting arthropods and guiding their hosts toward water, where the parasite can complete its life cycle. Over 350 species of nematomorphs have been described, yet molecular data for the group remain scarce. The few available mitochondrial genomes of nematomorphs are enriched with long inverted repeats, which are embedded in the coding sequences of their genes-a remarkably unusual feature exclusive to this phylum. Here, we obtain and annotate the repeats in the mitochondrial genome of another nematomorph species-Parachordodes pustulosus. Using genomic and transcriptomic libraries, we investigate the impact of inverted repeats on the read coverage of the mitochondrial genome. Pronounced drops in the read coverage coincide with regions containing long inverted repeats, denoting the 'blind spots' of short-fragment sequencing libraries. Phylogenetic inference with the novel data reveals multiple disagreements between the traditional system of Nematomorpha and molecular data, rendering several genera paraphyletic, including Parachordodes.
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Affiliation(s)
- Olga V. Nikolaeva
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 40, Moscow 119991, Russia
| | - Aleksandra M. Beregova
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 40, Moscow 119991, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 73, Moscow 119991, Russia
| | - Boris D. Efeykin
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskiy Ave., 33, Moscow 119071, Russia (S.E.S.)
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Per., 19, Bld. 1, Moscow 127051, Russia
| | - Tatiana S. Miroliubova
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskiy Ave., 33, Moscow 119071, Russia (S.E.S.)
| | - Andrey Yu. Zhuravlev
- Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 12, Moscow 119991, Russia
| | - Andrey Yu. Ivantsov
- Borissiak Palaeontological Institute, Russian Academy of Sciences, Profsoyuznaya Str., 123, Moscow 117647, Russia
| | - Kirill V. Mikhailov
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 40, Moscow 119991, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Per., 19, Bld. 1, Moscow 127051, Russia
| | - Sergei E. Spiridonov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskiy Ave., 33, Moscow 119071, Russia (S.E.S.)
| | - Vladimir V. Aleoshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Leninskie Gory Str., 1, Bld. 40, Moscow 119991, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoy Karetny Per., 19, Bld. 1, Moscow 127051, Russia
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2
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Shamanskiy V, Mikhailova AA, Tretiakov EO, Ushakova K, Mikhailova AG, Oreshkov S, Knorre DA, Ree N, Overdevest JB, Lukowski SW, Gostimskaya I, Yurov V, Liou CW, Lin TK, Kunz WS, Reymond A, Mazunin I, Bazykin GA, Fellay J, Tanaka M, Khrapko K, Gunbin K, Popadin K. Secondary structure of the human mitochondrial genome affects formation of deletions. BMC Biol 2023; 21:103. [PMID: 37158879 PMCID: PMC10166460 DOI: 10.1186/s12915-023-01606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Aging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain their distribution. Here, we hypothesized that the close proximity of direct repeats on single-stranded mitochondrial DNA (mtDNA) might play a role in the formation of deletions. RESULTS By analyzing human mtDNA deletions in the major arc of mtDNA, which is single-stranded during replication and is characterized by a high number of deletions, we found a non-uniform distribution with a "hot spot" where one deletion breakpoint occurred within the region of 6-9 kb and another within 13-16 kb of the mtDNA. This distribution was not explained by the presence of direct repeats, suggesting that other factors, such as the spatial proximity of these two regions, can be the cause. In silico analyses revealed that the single-stranded major arc may be organized as a large-scale hairpin-like loop with a center close to 11 kb and contacting regions between 6-9 kb and 13-16 kb, which would explain the high deletion activity in this contact zone. The direct repeats located within the contact zone, such as the well-known common repeat with a first arm at 8470-8482 bp (base pair) and a second arm at 13,447-13,459 bp, are three times more likely to cause deletions compared to direct repeats located outside of the contact zone. A comparison of age- and disease-associated deletions demonstrated that the contact zone plays a crucial role in explaining the age-associated deletions, emphasizing its importance in the rate of healthy aging. CONCLUSIONS Overall, we provide topological insights into the mechanism of age-associated deletion formation in human mtDNA, which could be used to predict somatic deletion burden and maximum lifespan in different human haplogroups and mammalian species.
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Affiliation(s)
- Victor Shamanskiy
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina A Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Evgenii O Tretiakov
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Kristina Ushakova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina G Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Sergei Oreshkov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Natalia Ree
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Jonathan B Overdevest
- Department of Otolaryngology, Columbia University Irving Medical Center, New York, USA
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Australia
| | - Irina Gostimskaya
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Valerian Yurov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang-Gung Memorial Hospital and Chang-Gung University, Kaohsiung, Taiwan
| | - Tsu-Kung Lin
- Department of Neurology, Kaohsiung Chang-Gung Memorial Hospital and Chang-Gung University, Kaohsiung, Taiwan
| | - Wolfram S Kunz
- Division of Neurochemistry, Department of Experimental Epileptology and Cognition Research, University Bonn, Bonn, Germany
- Department of Epileptology, University Hospital of Bonn, Bonn, Germany
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Georgii A Bazykin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Laboratory of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia
| | - Jacques Fellay
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Masashi Tanaka
- Department for Health and Longevity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku-Ku, Tokyo, 162-8636, Japan
- Department of Neurology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Department of Clinical Laboratory, IMS Miyoshi General Hospital, Fujikubo, Miyoshi-Machi, Iruma, Saitama Prefecture, 974-3354-0041, Japan
| | | | - Konstantin Gunbin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Konstantin Popadin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
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Yuan R, Tang W, Zhang H, You W, Hu X, Zhang H, Chen L, Nian W, Ding S, Luo Y. Palindromic-assisted self-annealing transcription amplification for reliable genotyping of epidermal growth factor receptor exon mutations. Biosens Bioelectron 2021; 194:113633. [PMID: 34543825 DOI: 10.1016/j.bios.2021.113633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 01/25/2023]
Abstract
Reliable discrimination of specific epidermal growth factor receptor (EGFR) gene mutations plays a critical role in guiding lung cancer therapeutics. Until now, convenient and accurate recognition of the specific deletion of EGFR exons has remained particularly challenging. Herein, we propose a palindromic-assisted self-annealing transcription amplification (PASTA) strategy for the reliable detection of circulating EGFR exon mutations. We designed a palindromic DNA hairpin nanorobot consisting of a palindromic tail, a T7 promoter, a target recognition region, and a transcription template. The nanorobot enabled prompt self-assembly into a target-hairpin/hairpin-target dimer in the presence of single-stranded DNA target and further triggered in vitro transcription. In a proof-of-concept experiment for detecting circulating 15n-del EGFR mutation, a detection limit of 0.8 fM and a linear detection range of 1 fM to 100 pM was achieved, and an accuracy of 100% was reached in clinical validation by analyzing 20 samples from clinical lung cancer patients. Empowered by the intrinsic sensitivity and selectivity, the proposed PASTA approach will lead to the development of a universal platform for reliable molecular subtyping.
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Affiliation(s)
- Rui Yuan
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China; Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China; College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Wanyan Tang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China
| | - Hong Zhang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China; College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Wenxin You
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China; Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Xiaolin Hu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Haiwei Zhang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China
| | - Ling Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Weiqi Nian
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China.
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China.
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Smirnov A, Battulin N. Concatenation of Transgenic DNA: Random or Orchestrated? Genes (Basel) 2021; 12:genes12121969. [PMID: 34946918 PMCID: PMC8701086 DOI: 10.3390/genes12121969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022] Open
Abstract
Generation of transgenic organisms by pronuclear microinjection has become a routine procedure. However, while the process of DNA integration in the genome is well understood, we still do not know much about the recombination between transgene molecules that happens in the first moments after DNA injection. Most of the time, injected molecules are joined together in head-to-tail tandem repeats-the so-called concatemers. In this review, we focused on the possible concatenation mechanisms and how they could be studied with genetic reporters tracking individual copies in concatemers. We also discuss various features of concatemers, including palindromic junctions and repeat-induced gene silencing (RIGS). Finally, we speculate how cooperation of DNA repair pathways creates a multicopy concatenated insert.
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Affiliation(s)
- Alexander Smirnov
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Nariman Battulin
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Institute of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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Smirnov A, Fishman V, Yunusova A, Korablev A, Serova I, Skryabin BV, Rozhdestvensky TS, Battulin N. DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote. Nucleic Acids Res 2020; 48:719-735. [PMID: 31740957 PMCID: PMC7145541 DOI: 10.1093/nar/gkz1085] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
Mechanisms that ensure repair of double-strand DNA breaks (DSBs) are instrumental in the integration of foreign DNA into the genome of transgenic organisms. After pronuclear microinjection, exogenous DNA is usually found as a concatemer comprising multiple co-integrated transgene copies. Here, we investigated the contribution of various DSB repair pathways to the concatemer formation. We injected mouse zygotes with a pool of linear DNA molecules carrying unique barcodes at both ends and obtained 10 transgenic embryos with 1–300 transgene copies. Sequencing the barcodes allowed us to assign relative positions to the copies in concatemers and detect recombination events that occurred during integration. Cumulative analysis of approximately 1,000 integrated copies reveals that over 80% of them underwent recombination when their linear ends were processed by synthesis-dependent strand annealing (SDSA) or double-strand break repair (DSBR). We also observed evidence of double Holliday junction (dHJ) formation and crossing over during the concatemer formations. Sequencing indels at the junctions between copies shows that at least 10% of DNA molecules introduced into the zygotes are ligated by non-homologous end joining (NHEJ). Our barcoding approach, verified with Pacific Biosciences Single Molecule Real-Time (SMRT) long-range sequencing, documents high activity of homologous recombination after DNA microinjection.
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Affiliation(s)
| | - Veniamin Fishman
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | | | - Alexey Korablev
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Irina Serova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Boris V Skryabin
- Medical Faculty, Core Facility Transgenic animal and genetic engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Timofey S Rozhdestvensky
- Medical Faculty, Core Facility Transgenic animal and genetic engineering Models (TRAM), University of Muenster, Muenster, Germany
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
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