Article
Multidisciplinary Sciences
Sudheer Gupta, Ashvini Yadav, Sam Stubbs, Simon Frost, Kudsia Ansari, Ram Kumar Nema, Shashwati Nema, Debasis Biswas
Summary: This study validates the previous findings on the mutations associated with the Chikungunya outbreak and identifies key mutations throughout the entire genome. The analysis shows a close relation between the outbreak strains and the Singapore 2015 strain, and also reveals previously non-existent mutations in the C and E2 genes, as well as in the nsP3 gene.
Article
Microbiology
Hon S. Ip, Sarah Uhm, Mary Lea Killian, Mia K. Torchetti
Summary: As shown by the response to the SARS-CoV-2 pandemic, whole-genome sequencing is crucial for monitoring viral evolution and guiding antiviral treatments. With the rapid spread of highly pathogenic avian influenza virus, there is a need for rapid sequencing to aid in response and mitigation efforts. This study evaluates a portable nanopore sequencing platform for routine use in a diagnostic laboratory, finding that limited amplification and rapid procedures are the most effective approaches.
Article
Biochemistry & Molecular Biology
Paul A. P. Atkins, Maria Elena S. Gamo, Daniel F. Voytas
Summary: Researchers overcame the limitations posed by donor molecules in gene targeting events by utilizing ONAS technology and developing the PANGEA bioinformatic pipeline, allowing them to collect a large number of plant somatic GT events and conversion tracts in a short period of time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biology
Vahid Akbari, Jean-Michel Garant, Kieran O'Neill, Pawan Pandoh, Richard Moore, Marco A. Marra, Martin Hirst, Steven J. M. Jones
Summary: This study used nanopore sequencing data to map the imprinted intervals in the human genome. It successfully phased the human methylome and detected both known and novel imprinted DMRs. The study also found several conserved imprinted DMRs in mouse, rhesus monkey, and chimpanzee. These findings expand our understanding of imprinting and demonstrate the potential of nanopore sequencing in identifying imprinting regions.
Article
Multidisciplinary Sciences
Ruslan Kalendar, Ulykbek Kairov, Daniyar Karabayev, Akbota Aitkulova, Nuray Tynyshtykbayeva, Asset Daniyarov, Zhenis Otarbay, Saule Rakhimova, Ainur Akilzhanova, Dos Sarbassov
Summary: We have developed a comprehensive set of multiplexed primers for universal SARS-CoV-2 genome sequencing using the Oxford Nanopore Rapid Barcoding library kit. These primers can be used to set up any variant of primer pools for whole-genome sequencing of SARS-CoV-2 with the Oxford Nanopore, using single- or double-tiled amplicons ranging from 1.2 to 4.8 kb. Additionally, this primer set is also applicable for targeted SARS-CoV-2 genome sequencing. We propose an optimized protocol for cDNA synthesis using Maxima H Minus Reverse Transcriptase and a set of SARS-CoV-2 specific primers, which allows efficient cDNA synthesis from a wide range of RNA amounts and quality, and enables whole-genome sequencing of SARS-CoV-2 with long tiled amplicons up to 4.8 kb, even in low-titer virus samples and degraded RNA.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Ryan R. R. Wick, Louise M. M. Judd, Kathryn E. E. Holt
Summary: A perfect bacterial genome assembly requires improved long-read sequencing, assemblers, and polishers. By combining Oxford Nanopore Technologies long reads and Illumina short reads, we suggest using Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, and additional short-read polishing tools and manual curation. We also discuss potential challenges and provide an online tutorial for reference.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Immunology
Laura T. Phillips, Adam A. Witney, Martina Furegato, Ken G. Laing, Liqing Zhou, S. Tariq Sadiq
Summary: Early versions of nanopore technology show promise as a real-time surveillance tool, capable of accurately identifying closely related Neisseria gonorrhoeae strains and important antimicrobial resistance markers from cultured isolates, with very short sequencing times.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Biotechnology & Applied Microbiology
Jidong Lang, Yanju Li, Wenjuan Yang, Ruyi Dong, Yuebin Liang, Jia Liu, Lanyou Chen, Weiwei Wang, Binbin Ji, Geng Tian, Nanying Che, Bo Meng
Summary: This study identified and annotated the genome sequence and ARGs of the newly isolated bacterium A. faecalis PGB1.
Article
Virology
Kathy K. Li, Betty Lau, Nicolas M. Suarez, Salvatore Camiolo, Rory Gunson, Andrew J. Davison, Richard J. Orton
Summary: Nanopore sequencing is increasingly used in clinical settings due to its portability, cost-effectiveness, and real-time operation. Despite initial challenges, improvements in sequencing hardware and software have mitigated high sequencing error rates. In this study, we evaluated the feasibility of using nanopore sequencing to determine the complete genomes of human cytomegalovirus (HCMV) directly from high-viral-load clinical samples without viral DNA enrichment, PCR amplification, or prior sequence knowledge. Our hybrid bioinformatic approach achieved highly accurate HCMV genomes from urine and lung samples, demonstrating the capability of nanopore sequencing for clinical diagnostics.
Article
Virology
Yi Yan, Ke Wu, Jun Chen, Haizhou Liu, Yi Huang, Yong Zhang, Jin Xiong, Weipeng Quan, Xin Wu, Yu Liang, Kunlun He, Zhilong Jia, Depeng Wang, Di Liu, Hongping Wei, Jianjun Chen
Summary: Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic, with the ability to identify pathogens and trace virus genetics. Modifications to the approach using specific amplicon amplification and the Oxford Nanopore PromethION platform have enabled rapid and stable acquisition of high-quality SARS-CoV-2 genomes, as well as the detection of genetic mutations.
Article
Biochemistry & Molecular Biology
Ying Ni, Xudong Liu, Zemenu Mengistie Simeneh, Mengsu Yang, Runsheng Li
Summary: This study evaluates the application of the recently released R10.4 flow cell from Oxford Nanopore Technologies in human cancer genomics and epigenomic research. The results show that R10.4 performs better than R9.4.1 in terms of read accuracy, variant detection, methylation calling, and genome recovery rate. In addition, the study proposes a promising method for high-yield single-cell whole-genome amplification sequencing and provides a possible solution for filtering false positive sites using R10.4 data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Igor Filipovic, Gordana Rasic, James Hereward, Maria Gharuka, Gregor J. Devine, Michael J. Furlong, Kayvan Etebari
Summary: This study presents a de novo genome assembly and structural annotation for the coconut rhinoceros beetle, providing a foundation for further genetic research and management programs. The assembly process resulted in a high-quality assembly with high contiguity and accuracy, surpassing previously published coleopteran genomes. The study also identified potential targets for RNAi-based control of beetles.
Article
Virology
Kevin Groen, Stefan van Nieuwkoop, Theo M. Bestebroer, Pieter L. Fraaij, Ron A. M. Fouchier, Bernadette G. van den Hoogen
Summary: HMPV, a causative agent of respiratory illness, circulates globally in two main genetic lineages, A and B. Whole genome sequencing using MinION Nanopore technology provides a robust method for studying HMPV genetics, epidemiology, and evolutionary dynamics.
Article
Microbiology
Maria T. Arevalo, Mark A. Karavis, Sarah E. Katoski, Jacquelyn V. Harris, Jessica M. Hill, Samir V. Deshpande, Pierce A. Roth, Alvin T. Liem, R. Cory Bernhards
Summary: This article describes a method for rapid identification of the novel coronavirus, which includes sequencing analysis and mutational analysis to provide important information about the virus. The method is accurate and efficient, and can be used for the characterization of viral outbreaks.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Shuaibing Yang, Qianqian Zhao, Lihua Tang, Zejia Chen, Zhaoting Wu, Kaixin Li, Ruoru Lin, Yang Chen, Danlin Ou, Li Zhou, Jianzhen Xu, Qingsong Qin
Summary: This study used Oxford nanopore sequencing technology to complete whole-genome sequencing of cervical cancer tissue and CaSki cell line, successfully assembling HPV35 and HPV16 genomic sequences. Nanopore sequencing also revealed integration breakpoints and concatemeric genomic sequences.
FRONTIERS IN GENETICS
(2022)
Review
Biochemistry & Molecular Biology
Sandro Baldi
DNA PACKAGING: NUCLEOSOME AND CHROMATIN
(2019)
Article
Biochemistry & Molecular Biology
Pravin Kumar Ankush Jagtap, Marisa Mueller, Pawel Masiewicz, Soeren von Buloew, Nele Merret Hollmann, Po-Chia Chen, Bernd Simon, Andreas W. Thomae, Peter B. Becker, Janosch Hennig
NUCLEIC ACIDS RESEARCH
(2019)
Article
Biochemistry & Molecular Biology
Khairunnadiya Prayitno, Tamas Schauer, Catherine Regnard, Peter B. Becker
Article
Biochemistry & Molecular Biology
Lisa Harpprecht, Sandro Baldi, Tamas Schauer, Andreas Schmidt, Tanja Bange, Maria S. Robles, Elisabeth Kremmer, Axel Imhof, Peter B. Becker
NUCLEIC ACIDS RESEARCH
(2019)
Article
Multidisciplinary Sciences
Christian Albig, Chao Wang, Geoffrey P. Dann, Felix Wojcik, Tamas Schauer, Silke Krause, Sylvain Maenner, Weili Cai, Yeran Li, Jack Girton, Tom W. Muir, Jorgen Johansen, Kristen M. Johansen, Peter B. Becker, Catherine Regnard
NATURE COMMUNICATIONS
(2019)
Review
Biochemistry & Molecular Biology
Sandro Baldi, Philipp Korber, Peter B. Becker
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
Article
Biology
Alessandro Scacchetti, Tamas Schauer, Alexander Reim, Zivkos Apostolou, Aline Campos Sparr, Silke Krause, Patrick Heun, Michael Wierer, Peter B. Becker
Article
Biochemistry & Molecular Biology
Marisa Mueller, Tamas Schauer, Silke Krause, Raffaella Villa, Andreas W. Thomae, Peter B. Becker
NUCLEIC ACIDS RESEARCH
(2020)
Review
Cell Biology
Alessandro Scacchetti, Peter B. Becker
Summary: Histone variant H2A.Z, incorporated into chromatin by SWR1-type remodelers, plays a key role in transcriptional regulation. Tight transcriptional control by H2A.Z nucleosomes relies on other histone variants or chromatin modifications, such as histone acetylation. Functional cooperation between SWR1-type remodelers and NuA4 histone acetyltransferase complexes is structurally implemented through species-specific strategies, a recurring theme in evolution.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Article
Cell Biology
Raffaella Villa, Pravin Kumar Ankush Jagtap, Andreas W. Thomae, Aline Campos Sparr, Ignasi Forne, Janosch Hennig, Tobias Straub, Peter B. Becker
Summary: The dosage compensation complex (DCC) in Drosophila shows different evolutionary processes in recognizing X-chromosomal binding sites between D. melanogaster and D. virilis, with the roX2 RNA playing a more instructive role in the latter species. This study highlights the divergent evolution of protein, DNA, and RNA components in achieving X-specific regulation.
GENES & DEVELOPMENT
(2021)
Article
Biochemistry & Molecular Biology
Nikolas Eggers, Peter B. Becker
Summary: Using a unique experimental system, this study explored the principles of DNA shape recognition and factor cooperativity in chromatin. By reconstituting chromatin on Drosophila genomes, the researchers identified the physiological binding profile of MSL2 through interaction with other factors and competition with non-functional sites. The results revealed novel aspects of target selection in a complex chromatin environment.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Marius F. Schneider, Veronika Mueller, Stephan A. Mueller, Stefan F. Lichtenthaler, Peter B. Becker, Johanna C. Scheuermann
Summary: The evolution of brain complexity is correlated with the increased expression of long noncoding RNAs in neural tissues. In this study, the functional characterization of the lncRNA LINC01322, also known as RUS, was presented. RUS is exclusively expressed in neural cells and plays a role in neuronal differentiation. Depletion of RUS results in arrest of neuronal precursors and changes in the expression of genes involved in neurogenesis. This suggests that RUS may mediate gene activation and repression in a context-dependent manner.
LIFE SCIENCE ALLIANCE
(2022)
Article
Biochemistry & Molecular Biology
Nikolas Eggers, Fotios Gkountromichos, Silke Krause, Aline Campos-Sparr, Peter B. Becker
Summary: MSL2, a subunit of the Drosophila dosage compensation complex, cooperates with CLAMP to bind MSL recognition elements on the X chromosome. This cooperative binding requires physical interaction between the two proteins and prevents competition. The cooperation largely occurs at the level of individual binding elements and is limited to a small selection of sites in vivo.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamas Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B. Becker
LIFE SCIENCE ALLIANCE
(2018)