RNA modifications in physiology and pathology: Progressing towards application in clinical settings

Cellular Signalling, Journal Year: 2024, Volume and Issue: 121, P. 111242 - 111242

Published: June 6, 2024

Language: Английский

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Detecting a wide range of epitranscriptomic modifications using a nanopore-sequencing-based computational approach with 1D score-clustering

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 10, 2024

To date, over 40 epigenetic and 300 epitranscriptomic modifications have been identified. However, current short-read sequencing-based experimental methods can detect <10% of these modifications. Integrating long-read sequencing technologies with advanced computational approaches, including statistical analysis machine learning, offers a promising new frontier to address this challenge. While supervised learning achieved some success, their usefulness is restricted limited number well-characterized Here, we introduce Modena, an innovative unsupervised approach utilizing nanopore capable detecting broad range Modena outperformed other in five out six benchmark datasets, cases by wide margin, while being equally competitive the second best method on one dataset. Uniquely, also demonstrates consistent accuracy DNA dataset, distinguishing it from approaches. A key feature its use 'dynamic thresholding', based 1D score-clustering. This methodology differs substantially traditional statistics-based 'hard-thresholds.' We show that not but has broader applicability. Specifically, when combined two existing algorithms, thresholding' significantly enhances performance, resulting up threefold improvement F1-scores.

Language: Английский

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Application of Biological Nanopore Sequencing Technology in the Detection of Microorganisms^†

Chinese Journal of Chemistry, Journal Year: 2023, Volume and Issue: 41(23), P. 3473 - 3483

Published: July 19, 2023

Comprehensive Summary Environmental pollution and the spread of pathogenic microorganisms pose a significant threat to health humans planet. Thus, understanding detecting is crucial for maintaining healthy living environment. Nanopore sequencing single‐molecule detection method developed in 1990s that has revolutionized various research fields. It offers several advantages over traditional methods, including low cost, label‐free, time‐saving speed, long reading, real‐time monitoring, convenient carrying, other advantages. In this review, we summarize technical principles characteristics nanopore discuss its applications amplicon sequencing, metagenome whole‐genome environmental microorganisms, as well situ application under some special circumstances. We also analyze challenges microbiology research. Overall, potential greatly enhance research, but further developments are needed overcome current challenges.

Language: Английский

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Identification and perturbation of pseudouridine modifications in human mRNAs

Published: Jan. 1, 2023

Pseudouridine (Ψ) is one of the most prevalent modifications in RNA, with its presence detected across various RNA types, including mRNA. The association Ψ different diseases, particularly cancers, and critical role tRNA structure underscores biological significance. However, robust detection this modification remains a formidable challenge, specific function within mRNA sequences unknown. In initial segment thesis, semi-quantitative method developed that leverages direct long-read nanopore sequencing for identifying pseudouridylated sites on human mRNAs. This approach capitalizes U-to-C basecalling error observed at positions. A comparative analysis involving modification-free transcriptome reveals depth coverage k-mer are pivotal parameters accurately detecting pseudouridine modifications.By fine-tuning these to account errors, our successfully identifies well-established pseudouridylation previously unreported uridine-modified sites. Many newly identified align k-mers targeted by synthases. Our workflow enables native molecules from data, showcasing capability discern multiple same strand. Expanding investigation, we introduce concepts type I II hypermodifications. Type hypermodifications denote instances high occupancy (>40%) single position, providing insights into extent On other hand, signify scenarios where more than occurs transcript. nuanced categorization adds understanding pseudouridine's influence, paving way comprehensive exploration processes. second part explore dynamics as cellular state. We use cultured SH-SY5Y neuroblastoma cells model system investigate impact cell state changes differentiating neuron-like assess alterations pseudouridine-modified patterns upon exposure lead, an environmental neurotoxin implicated developmental disorders. assign positions their cognate synthase performing siRNA knockdown experiments PUS7 TRUB1 validating targets using algorithm, Mod-p ID. find many fall coding sequences. also modified three categories: 1. Modification level all states (static), 2. levels differ (plastic), 3. depends change (condition-dependent plastic). Interestingly, motif tend be static, while can either static or plastic depending These studies provide exciting candidates future individual modifications. --Author's abstract

Language: Английский

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