NAR Genomics and Bioinformatics最新文献_第7页

A four eigen-phase model of multi-omics unveils new insights into yeast metabolic cycle. 多组学的四特征相模型揭示了酵母代谢周期的新见解。

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NAR Genomics and Bioinformatics Pub Date : 2025-03-19 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf022

Linting Wang, Xiaojie Li, Jianhui Shi, Lei M Li

{"title":"A four eigen-phase model of multi-omics unveils new insights into yeast metabolic cycle.","authors":"Linting Wang, Xiaojie Li, Jianhui Shi, Lei M Li","doi":"10.1093/nargab/lqaf022","DOIUrl":"10.1093/nargab/lqaf022","url":null,"abstract":"The yeast metabolic cycle (YMC), characterized by cyclic oscillations in transcripts and metabolites, is an ideal model for studying biological rhythms. Although multiple omics datasets on the YMC are available, a unified landscape for this process is missing. To address this gap, we integrated multi-omics datasets by singular value decompositions (SVDs), which stratify each dataset into two levels and define four eigen-phases: primary 1A/1B and secondary 2A/2B. The eigen-phases occur cyclically in the order 1B, 2A, 1A, and 2B, demonstrating an interplay of induction and repression: one eigen-phase induces the next one at a different level, while represses the other one at the same level. Distinct molecular characteristics were identified for each eigen-phase. Novel ones include the production and consumption of glycerol in eigen-phases 2A/2B, and the opposite regulation of ribosome biogenesis and aerobic respiration between 2A/2B. Moreover, we estimated the timing of multi-omics: histone modifications H3K9ac/H3K18ac precede mRNA transcription in ∼3 min, followed by metabolomic changes in ∼13 min. The transition to the next eigen-phase occurs roughly 38 min later. From epigenome H3K9ac/H3K18ac to metabolome, the eigen-entropy increases. This work provides a computational framework applicable to multi-omics data integration.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf022"},"PeriodicalIF":4.0,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11920873/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143664830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Expansion of the tmRNA sequence database and new tools for search and visualization. 扩充 tmRNA 序列数据库以及用于搜索和可视化的新工具。

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NAR Genomics and Bioinformatics Pub Date : 2025-03-18 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf019

Eric P Nawrocki, Anton I Petrov, Kelly P Williams

{"title":"Expansion of the tmRNA sequence database and new tools for search and visualization.","authors":"Eric P Nawrocki, Anton I Petrov, Kelly P Williams","doi":"10.1093/nargab/lqaf019","DOIUrl":"10.1093/nargab/lqaf019","url":null,"abstract":"Transfer-messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf019"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11915505/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

SeArcH schemes for Approximate stRing mAtching. 近似环形蚀刻的序列方案。

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NAR Genomics and Bioinformatics Pub Date : 2025-03-18 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf025

Simon Gene Gottlieb, Knut Reinert

{"title":"SeArcH schemes for Approximate stRing mAtching.","authors":"Simon Gene Gottlieb, Knut Reinert","doi":"10.1093/nargab/lqaf025","DOIUrl":"10.1093/nargab/lqaf025","url":null,"abstract":"Finding approximate occurrences of a query in a text using a full-text index is a central problem in stringology with many applications, especially in bioinformatics. The recent work has shown significant speed-ups by combining bidirectional indices and employing variations of search schemes. Search schemes partition a query and describe how to search the resulting parts with a given error bound. The performance of search schemes can be approximated by the node count, which represents an upper bound of the number of search steps. Finding optimum search schemes is a difficult combinatorial optimization problem that becomes hard to solve for four and more errors. This paper improves on a few topics important to search scheme based searches: First, we show how search schemes can be used to model previously published approximate search strategies such as suffix filters, 01*0-seeds, or the pigeonhole principle. This unifies these strategies in the search scheme framework, makes them easily comparable and results in novel search schemes that allow for any number of errors. Second, we present a search scheme construction heuristic, which is on par with optimum search schemes and has a better node count than any known search scheme for equal or above four errors. Finally, using the different search schemes, we show that the node count measure is not an ideal performance metric and therefore propose an improved performance metric called the weighted node count, which approximates a search algorithm's run time much more accurately.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf025"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11915513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

NucleoSeeker-precision filtering of RNA databases to curate high-quality datasets. 核搜索器-精确过滤RNA数据库，以策划高质量的数据集。

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NAR Genomics and Bioinformatics Pub Date : 2025-03-18 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf021

Utkarsh Upadhyay, Fabrizio Pucci, Julian Herold, Alexander Schug

{"title":"NucleoSeeker-precision filtering of RNA databases to curate high-quality datasets.","authors":"Utkarsh Upadhyay, Fabrizio Pucci, Julian Herold, Alexander Schug","doi":"10.1093/nargab/lqaf021","DOIUrl":"10.1093/nargab/lqaf021","url":null,"abstract":"The structural prediction of biomolecules via computational methods complements the often involved wet-lab experiments. Unlike protein structure prediction, RNA structure prediction remains a significant challenge in bioinformatics, primarily due to the scarcity of annotated RNA structure data and its varying quality. Many methods have used this limited data to train deep learning models but redundancy, data leakage and bad data quality hampers their performance. In this work, we present NucleoSeeker, a tool designed to curate high-quality, tailored datasets from the Protein Data Bank (PDB) database. It is a unified framework that combines multiple tools and streamlines an otherwise complicated process of data curation. It offers multiple filters at structure, sequence, and annotation levels, giving researchers full control over data curation. Further, we present several use cases. In particular, we demonstrate how NucleoSeeker allows the creation of a nonredundant RNA structure dataset to assess AlphaFold3's performance for RNA structure prediction. This demonstrates NucleoSeeker's effectiveness in curating valuable nonredundant tailored datasets to both train novel and judge existing methods. NucleoSeeker is very easy to use, highly flexible, and can significantly increase the quality of RNA structure datasets.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf021"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11915511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Determinant-based grouping of SNPs and its application for detecting disease-associated genomic loci. 基于决定因子的snp分组及其在疾病相关基因组位点检测中的应用

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NAR Genomics and Bioinformatics Pub Date : 2025-03-18 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf024

Gennady Khvorykh, Andrey Khrunin

{"title":"Determinant-based grouping of SNPs and its application for detecting disease-associated genomic loci.","authors":"Gennady Khvorykh, Andrey Khrunin","doi":"10.1093/nargab/lqaf024","DOIUrl":"10.1093/nargab/lqaf024","url":null,"abstract":"Groups of single nucleotide polymorphisms (SNPs) are more effective than individual SNPs in identifying genetic loci associated with diseases. However, an optimal method for grouping SNPs remains an open question. Here, we introduce a novel approach for SNP grouping, leveraging the determinant of linkage disequilibrium (LD) matrices as a comprehensive metric of multicollinearity. This method builds on the established use of determinants in regression analysis as an aggregate measure of variable interdependence. We proposed that SNPs be grouped by evaluating the determinant of their LD matrices, with the approach validated using both synthetic genotype-phenotype data and real-world data from genome-wide association studies (GWAS) of ischemic stroke. Application of this method identified two previously known and five novel candidate genes associated with the onset of disease. Additionally, we developed a straightforward procedure to estimate a critical parameter for the model: the minimal determinant value for an LD matrix to be considered singular. In summary, the determinant of the LD matrix serves as a robust integrative measure for assessing SNP group quality. This metric underpins a bioinformatics workflow capable of identifying genomic loci associated with disease onset, offering a valuable tool for advancing genetic association studies.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf024"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11915498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658839","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble. BacTermFinder：一个全面和通用的细菌终结者发现者使用CNN集合。

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NAR Genomics and Bioinformatics Pub Date : 2025-03-08 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf016

Seyed Mohammad Amin Taheri Ghahfarokhi, Lourdes Peña-Castillo

{"title":"BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.","authors":"Seyed Mohammad Amin Taheri Ghahfarokhi, Lourdes Peña-Castillo","doi":"10.1093/nargab/lqaf016","DOIUrl":"10.1093/nargab/lqaf016","url":null,"abstract":"A terminator is a DNA region that ends the transcription process. Currently, multiple computational tools are available for predicting bacterial terminators. However, these methods are specialized for certain bacteria or terminator type (i.e. intrinsic or factor-dependent). In this work, we developed BacTermFinder using an ensemble of convolutional neural networks (CNNs) receiving as input four different representations of terminator sequences. To develop BacTermFinder, we collected roughly 41 000 bacterial terminators (intrinsic and factor-dependent) of 22 species with varying GC-content (from 28% to 71%) from published studies that used RNA-seq technologies. We evaluated BacTermFinder's performance on terminators of five bacterial species (not used for training BacTermFinder) and two archaeal species. BacTermFinder's performance was compared with that of four other bacterial terminator prediction tools. Based on our results, BacTermFinder outperforms all other four approaches in terms of average recall without increasing the number of false positives. Moreover, BacTermFinder identifies both types of terminators (intrinsic and factor-dependent) and generalizes to archaeal terminators. Additionally, we visualized the saliency map of the CNNs to gain insights on terminator motif per species. BacTermFinder is publicly available at https://github.com/BioinformaticsLabAtMUN/BacTermFinder.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf016"},"PeriodicalIF":4.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11890068/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143587415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Polytect: an automatic clustering and labeling method for multicolor digital PCR data. Polytect：多色数字PCR数据的自动聚类和标记方法。

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NAR Genomics and Bioinformatics Pub Date : 2025-03-08 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf015

Yao Chen, Ward De Spiegelaere, Wim Trypsteen, Jo Vandesompele, Gertjan Wils, David Gleerup, Antoon Lievens, Olivier Thas, Matthijs Vynck

{"title":"Polytect: an automatic clustering and labeling method for multicolor digital PCR data.","authors":"Yao Chen, Ward De Spiegelaere, Wim Trypsteen, Jo Vandesompele, Gertjan Wils, David Gleerup, Antoon Lievens, Olivier Thas, Matthijs Vynck","doi":"10.1093/nargab/lqaf015","DOIUrl":"10.1093/nargab/lqaf015","url":null,"abstract":"Digital polymerase chain reaction (dPCR) is a state-of-the-art targeted quantification method of nucleic acids. The technology is based on massive partitioning of a reaction mixture into individual PCR reactions. The resulting partition-level end-point fluorescence intensities are used to classify partitions as positive or negative, i.e. containing or not containing the target nucleic acid(s). Many automatic dPCR partition classification methods have been proposed, but they are limited to the analysis of single- or dual-color dPCR data. While general-purpose or flow cytometry clustering methods can be directly applied to multicolor dPCR data, these methods do not exploit the approximate prior knowledge on cluster center locations available in dPCR data. We present Polytect, a method that relies on crude cluster results from flowPeaks, previously shown to offer good partition classification performance, and subsequently refines flowPeaks' results by automatic cluster merging and cluster labeling, exploiting the prior knowledge on cluster center locations. Comparative analyses with established methods such as flowPeaks, dpcp, and ddPCRclust reveal that Polytect often surpasses established methods, both on empirical and simulated data. Polytect manages to merge excess clusters, while also successfully identifying empty clusters when fewer than the maximally observable number of clusters are present. On par with recent developments in instruments, Polytect extends beyond two-color data. The method is available as an R package and R Shiny app (https://digpcr.shinyapps.io/Polytect/).","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf015"},"PeriodicalIF":4.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11890064/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143587420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unraveling myriapod evolution: sealion, a novel quartet-based approach for evaluating phylogenetic uncertainty. 揭示多足动物进化：海狮，一种新的基于四重奏的方法来评估系统发育的不确定性。

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NAR Genomics and Bioinformatics Pub Date : 2025-03-07 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf018

Patrick Kück, Mark Wilkinson, Juliane Romahn, Nathan I Seidel, Karen Meusemann, Johann W Wägele

{"title":"Unraveling myriapod evolution: sealion, a novel quartet-based approach for evaluating phylogenetic uncertainty.","authors":"Patrick Kück, Mark Wilkinson, Juliane Romahn, Nathan I Seidel, Karen Meusemann, Johann W Wägele","doi":"10.1093/nargab/lqaf018","DOIUrl":"10.1093/nargab/lqaf018","url":null,"abstract":"Myriapods, a diverse group of terrestrial arthropods, comprise four main subgroups: Chilopoda (centipedes), Diplopoda (millipedes), Pauropoda, and Symphyla. Recent phylogenomic studies affirm Myriapoda's monophyly and the monophyletic status of each subgroup but differ in their relationships. To investigate these relationships further, we reanalyzed a transcriptomic dataset of 59 species across 292 single-copy protein-coding genes. Departing from conventional methods, we employed a novel approach that relies on information from polarized quartets (i.e., sets of four orthologous sequences, with one being an outgroup) to evaluate molecular phylogenies. This Hennigian analysis reduces misleading phylogenetic signals in molecular data caused by convergence, plesiomorphy, and rate heterogeneity across sites and across lineages. Our findings reveal that some species, especially those with long root-to-tip distances, disproportionately contribute misleading signals. Analyses using conventional likelihood-based phylogenetic methods suggest that Chilopoda and Diplopoda are sister taxa. By contrast, analyses incorporating novel filters designed to minimize conflict among phylogenetically confounding signals support the monophyly of Progoneata, aligning with morphological evidence. Simulations validate the reliability of our approach, demonstrating its potential to resolve myriapod evolutionary relationships and highlight uncertainty.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf018"},"PeriodicalIF":4.0,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11886814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143587423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cell type-dependent directional transcription at enhancers. 增强子细胞类型依赖的定向转录。

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NAR Genomics and Bioinformatics Pub Date : 2025-03-07 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf007

Saumya Agrawal, Emi Kanamaru, Yoriko Saito, Fumihiko Ishikawa, Michiel de Hoon

{"title":"Cell type-dependent directional transcription at enhancers.","authors":"Saumya Agrawal, Emi Kanamaru, Yoriko Saito, Fumihiko Ishikawa, Michiel de Hoon","doi":"10.1093/nargab/lqaf007","DOIUrl":"10.1093/nargab/lqaf007","url":null,"abstract":"Enhancers are noncoding regulatory regions in the genome that play essential roles in modulating gene expression. Previous work showed that enhancers are not transcriptionally silent but are characterized by bidirectional expression of short capped noncoding RNAs. Balanced bidirectional expression has therefore been used as a key feature for the detection of enhancers from transcriptome data. Instead, by analyzing FANTOM5 and other deep cap analysis gene expression transcriptome datasets, we find enhancer transcription preferentially in one direction in individual cell types. As the preferred direction of transcription of an enhancer can switch between cell types, balanced bidirectional enhancer expression may appear if transcriptome data are aggregated over cell types. 5' single-cell RNA sequencing data showed that enhancers were almost exclusively expressed unidirectionally in a single cell. Reporter assay data demonstrated that the regulatory function of an enhancer does not depend on its preference for unidirectional or bidirectional expression. We conclude that requiring balanced bidirectional transcription for enhancer detection may discard most valid enhancers when applied to transcriptome data of a single cell type.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf007"},"PeriodicalIF":4.0,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11886823/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143587418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The zebrafish (Danio rerio) snoRNAome.

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NAR Genomics and Bioinformatics Pub Date : 2025-03-05 eCollection Date: 2025-03-01 DOI: 10.1093/nargab/lqaf013

Renáta Hamar, Máté Varga

{"title":"The zebrafish (Danio rerio) snoRNAome.","authors":"Renáta Hamar, Máté Varga","doi":"10.1093/nargab/lqaf013","DOIUrl":"10.1093/nargab/lqaf013","url":null,"abstract":"Small nucleolar RNAs (snoRNAs) are one of the most abundant and evolutionary ancient group of functional non-coding RNAs. They were originally described as guides of post-transcriptional rRNA modifications, but emerging evidence suggests that snoRNAs fulfil an impressive variety of cellular functions. To reveal the true complexity of snoRNA-dependent functions, we need to catalogue first the complete repertoire of snoRNAs in a given cellular context. While the systematic mapping and characterization of \"snoRNAomes\" for some species have been described recently, this has not been done hitherto for the zebrafish (Danio rerio). Using size-fractionated RNA sequencing data from adult zebrafish tissues, we created an interactive \"snoRNAome\" database for this species. Our custom-designed analysis pipeline allowed us to identify with high-confidence 67 previously unannotated snoRNAs in the zebrafish genome, resulting in the most complete set of snoRNAs to date in this species. Reanalyzing multiple previously published datasets, we also provide evidence for the dynamic expression of some snoRNAs during the early stages of zebrafish development and tissue-specific expression patterns for others in adults. To facilitate further investigations into the functions of snoRNAs in zebrafish, we created a novel interactive database, snoDanio, which can be used to explore small RNA expression from transcriptomic data.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"7 1","pages":"lqaf013"},"PeriodicalIF":4.0,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11880993/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143567606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0