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Barro-Trastoy D, Köhler C. Helitrons: genomic parasites that generate developmental novelties. Trends Genet 2024; 40:437-448. [PMID: 38429198 DOI: 10.1016/j.tig.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.
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Affiliation(s)
- Daniela Barro-Trastoy
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Claudia Köhler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden.
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Touati R, Elngar AA. Intelligent system based comparative analysis study of SARS-CoV-2 spike protein and antigenic proteins in different types of vaccines. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022; 11:34. [PMID: 35284579 PMCID: PMC8899449 DOI: 10.1186/s43088-022-00216-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/17/2022] [Indexed: 02/08/2023] Open
Abstract
Abstract
Background
Coronaviruses, members of the Coronavirinae subfamily in the Coronaviridae family, are enveloped and positive-stranded RNA viruses that infect animals and humans, causing intestinal and respiratory infections. Coronavirus disease 2019 (COVID-19) is caused by a novel coronavirus, named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). This disease appeared, for the first time (December 2019), in China and has spread quickly worldwide causing a large number of deaths. Considering the global threat, the World Health Organization (WHO) has declared, in March 2020, COVID-19 as a pandemic. Many studies suggest the great effect of the existing vaccines to protect against symptomatic cases of death by the COVID-19 virus. This paper, proposes to compare the main antigenic proteins sequences of the existing vaccines with Spike (S) protein of the SARS-CoV-2 genome. Our choice of S protein is justified by the major role that plays it in the receptor recognition and membrane fusion process based on an intelligent system. Herein, we focus on finding a correlation between S protein and compulsory vaccines in the countries that have a less death number by COVID-19 virus. In this work, we have used a combination of coding methods, signal processing, and bioinformatic techniques with the goal to localize the similar patterns between the S gene of the SARS-Cov-2 genome and 14 investigated vaccines.
Results
A total of 8 similar sequences which have a size more than 6 amino acids were identified. Further, these comparisons propose that these segments can be implicated in the immune response against COVID-19, which may explain the wide variation by country in the severity of this viral threat.
Conclusions
Our in silico study suggests a possible protective effect of Poliovirus, HIB, Hepatitis B, PCV10, Measles, Mumps, and Rubella (MMR) vaccines against COVID-19.
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Touati R, Messaoudi I, Oueslati A, Lachiri Z, Kharrat M. New Intraclass Helitrons Classification Using DNA-Image Sequences and Machine Learning Approaches. Ing Rech Biomed 2021. [DOI: 10.1016/j.irbm.2019.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Touati R, Tajouri A, Mesaoudi I, Oueslati AE, Lachiri Z, Kharrat M. New methodology for repetitive sequences identification in human X and Y chromosomes. Biomed Signal Process Control 2021; 64:102207. [PMID: 33101452 PMCID: PMC7572123 DOI: 10.1016/j.bspc.2020.102207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/23/2020] [Accepted: 09/01/2020] [Indexed: 11/24/2022]
Abstract
Repetitive DNA sequences occupy the major proportion of DNA in the human genome and even in the other species' genomes. The importance of each repetitive DNA type depends on many factors: structural and functional roles, positions, lengths and numbers of these repetitions are clear examples. Conserving such DNA sequences or not in different locations in the chromosome remains a challenge for researchers in biology. Detecting their location despite their great variability and finding novel repetitive sequences remains a challenging task. To side-step this problem, we developed a new method based on signal and image processing tools. In fact, using this method we could find repetitive patterns in DNA images regardless of the repetition length. This new technique seems to be more efficient in detecting new repetitive sequences than bioinformatics tools. In fact, the classical tools present limited performances especially in case of mutations (insertion or deletion). However, modifying one or a few numbers of pixels in the image doesn't affect the global form of the repetitive pattern. As a consequence, we generated a new repetitive patterns database which contains tandem and dispersed repeated sequences. The highly repetitive sequences, we have identified in X and Y chromosomes, are shown to be located in other human chromosomes or in other genomes. The data we have generated is then taken as input to a Convolutional neural network classifier in order to classify them. The system we have constructed is efficient and gives an average of 94.4% as recognition score.
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Affiliation(s)
- Rabeb Touati
- University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), Tunisia
- University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, Le Belvédère, 1002, Tunis, Tunisia
| | - Asma Tajouri
- University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), Tunisia
| | - Imen Mesaoudi
- University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, Le Belvédère, 1002, Tunis, Tunisia
| | - Afef Elloumi Oueslati
- University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, Le Belvédère, 1002, Tunis, Tunisia
| | - Zied Lachiri
- University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, Le Belvédère, 1002, Tunis, Tunisia
| | - Maher Kharrat
- University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis (FMT), Tunisia
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Touati R, Haddad-Boubaker S, Ferchichi I, Messaoudi I, Ouesleti AE, Triki H, Lachiri Z, Kharrat M. Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses. Genomics 2020; 112:4189-4202. [PMID: 32645523 PMCID: PMC7336935 DOI: 10.1016/j.ygeno.2020.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 12/24/2022]
Abstract
Coronaviruses are responsible on respiratory diseases in animal and human. The combination of numerical encoding techniques and digital signal processing methods are becoming increasingly important in handling large genomic data. In this paper, we propose to analyze the SARS-CoV-2 genomic signature using the combination of different nucleotide representations and signal processing tools in the aim to identify its genetic origin. The sequence of SARS-CoV-2 was compared with 21 relevant sequences including Bat, Yak and Pangolin coronavirus sequences. In addition, we developed a new algorithm to locate the nucleotide modifications. The results show that the Bat and Pangolin coronaviruses were the most related to SARS-CoV-2 with 96% and 86% of identity all along the genome. Within the S gene sequence, the Pangolin sequence presents local highest nucleotide identity. Those findings suggest genesis of SARS-Cov-2 through evolution from Bat and Pangolin strains. This study offers new ways to automatically characterize viruses.
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Affiliation(s)
- Rabeb Touati
- University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis, Tunisia; University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie.
| | - Sondes Haddad-Boubaker
- University of Tunis El Manar, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for EMRO region, Institut Pasteur de Tunis, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisie
| | - Imen Ferchichi
- University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis, Tunisia
| | - Imen Messaoudi
- University of Carthage, Higher Institute of Information Technologies and Communications, Industrial Computing Department, Tunisia; University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie
| | - Afef Elloumi Ouesleti
- University of Carthage, National School of Engineers of Carthage, Electrical Engineering Department, Tunisia; University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie
| | - Henda Triki
- University of Tunis El Manar, Laboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for EMRO region, Institut Pasteur de Tunis, 13 place Pasteur, BP74 1002 le Belvédère, Tunis, Tunisie
| | - Zied Lachiri
- University of Tunis El Manar, SITI Laboratory, National School of Engineers of Tunis, BP 37, le Belvédère, 1002 Tunis, Tunisie
| | - Maher Kharrat
- University of Tunis El Manar, LR99ES10 Human Genetics Laboratory, Faculty of Medicine of Tunis, Tunisia
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