NAR Genomics and Bioinformatics最新文献_第9页

Synteruptor: mining genomic islands for non-classical specialized metabolite gene clusters. Synteruptor：挖掘基因组岛屿上的非典型特化代谢物基因簇。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2024-06-19 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae069

Drago Haas, Matthieu Barba, Cláudia M Vicente, Šarká Nezbedová, Amélie Garénaux, Stéphanie Bury-Moné, Jean-Noël Lorenzi, Laurence Hôtel, Luisa Laureti, Annabelle Thibessard, Géraldine Le Goff, Jamal Ouazzani, Pierre Leblond, Bertrand Aigle, Jean-Luc Pernodet, Olivier Lespinet, Sylvie Lautru

{"title":"Synteruptor: mining genomic islands for non-classical specialized metabolite gene clusters.","authors":"Drago Haas, Matthieu Barba, Cláudia M Vicente, Šarká Nezbedová, Amélie Garénaux, Stéphanie Bury-Moné, Jean-Noël Lorenzi, Laurence Hôtel, Luisa Laureti, Annabelle Thibessard, Géraldine Le Goff, Jamal Ouazzani, Pierre Leblond, Bertrand Aigle, Jean-Luc Pernodet, Olivier Lespinet, Sylvie Lautru","doi":"10.1093/nargab/lqae069","DOIUrl":"10.1093/nargab/lqae069","url":null,"abstract":"Microbial specialized metabolite biosynthetic gene clusters (SMBGCs) are a formidable source of natural products of pharmaceutical interest. With the multiplication of genomic data available, very efficient bioinformatic tools for automatic SMBGC detection have been developed. Nevertheless, most of these tools identify SMBGCs based on sequence similarity with enzymes typically involved in specialised metabolism and thus may miss SMBGCs coding for undercharacterised enzymes. Here we present Synteruptor (https://bioi2.i2bc.paris-saclay.fr/synteruptor), a program that identifies genomic islands, known to be enriched in SMBGCs, in the genomes of closely related species. With this tool, we identified a SMBGC in the genome of Streptomyces ambofaciens ATCC23877, undetected by antiSMASH versions prior to antiSMASH 5, and experimentally demonstrated that it directs the biosynthesis of two metabolites, one of which was identified as sphydrofuran. Synteruptor is also a valuable resource for the delineation of individual SMBGCs within antiSMASH regions that may encompass multiple clusters, and for refining the boundaries of these SMBGCs.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae069"},"PeriodicalIF":4.0,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11195616/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141447204","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

Morphological and dietary changes encoded in the genome of Beroe ovata, a ctenophore-eating ctenophore. 食栉水母 Beroe ovata 基因组编码的形态和食物变化。

IF 4.6

NAR Genomics and Bioinformatics Pub Date : 2024-06-18 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae072

Alexandra M Vargas, Melissa B DeBiasse, Lana L Dykes, Allison Edgar, T Danielle Hayes, Daniel J Groso, Leslie S Babonis, Mark Q Martindale, Joseph F Ryan

{"title":"Morphological and dietary changes encoded in the genome of Beroe ovata, a ctenophore-eating ctenophore.","authors":"Alexandra M Vargas, Melissa B DeBiasse, Lana L Dykes, Allison Edgar, T Danielle Hayes, Daniel J Groso, Leslie S Babonis, Mark Q Martindale, Joseph F Ryan","doi":"10.1093/nargab/lqae072","DOIUrl":"10.1093/nargab/lqae072","url":null,"abstract":"As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata. Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata. Despite the gene losses in B. ovata, our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata. This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http://ryanlab.whitney.ufl.edu/bovadb/), a portal for the B. ovata genome.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae072"},"PeriodicalIF":4.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11184263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141421206","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

Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability. 基于基因间间隔（IGS）变异性对高度分化的小鼠 rDNA 单元进行比较分析和分类。

IF 4.6

NAR Genomics and Bioinformatics Pub Date : 2024-06-14 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae070

Jung-Hyun Kim, Ramaiah Nagaraja, Alexey Y Ogurtsov, Vladimir N Noskov, Mikhail Liskovykh, Hee-Sheung Lee, Yutaro Hori, Takehiko Kobayashi, Kent Hunter, David Schlessinger, Natalay Kouprina, Svetlana A Shabalina, Vladimir Larionov

{"title":"Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability.","authors":"Jung-Hyun Kim, Ramaiah Nagaraja, Alexey Y Ogurtsov, Vladimir N Noskov, Mikhail Liskovykh, Hee-Sheung Lee, Yutaro Hori, Takehiko Kobayashi, Kent Hunter, David Schlessinger, Natalay Kouprina, Svetlana A Shabalina, Vladimir Larionov","doi":"10.1093/nargab/lqae070","DOIUrl":"10.1093/nargab/lqae070","url":null,"abstract":"Ribosomal DNA (rDNA) repeat units are organized into tandem clusters in eukaryotic cells. In mice, these clusters are located on at least eight chromosomes and show extensive variation in the number of repeats between mouse genomes. To analyze intra- and inter-genomic variation of mouse rDNA repeats, we selectively isolated 25 individual rDNA units using Transformation-Associated Recombination (TAR) cloning. Long-read sequencing and subsequent comparative sequence analysis revealed that each full-length unit comprises an intergenic spacer (IGS) and a ∼13.4 kb long transcribed region encoding the three rRNAs, but with substantial variability in rDNA unit size, ranging from ∼35 to ∼46 kb. Within the transcribed regions of rDNA units, we found 209 variants, 70 of which are in external transcribed spacers (ETSs); but the rDNA size differences are driven primarily by IGS size heterogeneity, due to indels containing repetitive elements and some functional signals such as enhancers. Further evolutionary analysis categorized rDNA units into distinct clusters with characteristic IGS lengths; numbers of enhancers; and presence/absence of two common SNPs in promoter regions, one of which is located within promoter (p)RNA and may influence pRNA folding stability. These characteristic features of IGSs also correlated significantly with 5'ETS variant patterns described previously and associated with differential expression of rDNA units. Our results suggest that variant rDNA units are differentially regulated and open a route to investigate the role of rDNA variation on nucleolar formation and possible associations with pathology.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae070"},"PeriodicalIF":4.6,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11177557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141331907","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

omicsMIC: a comprehensive benchmarking platform for robust comparison of imputation methods in mass spectrometry-based omics data. omicsMIC：一个综合基准平台，用于对基于质谱的整体组学数据中的估算方法进行稳健比较。

IF 4

NAR Genomics and Bioinformatics Pub Date : 2024-06-14 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae071

Weiqiang Lin, Jiadong Ji, Kuan-Jui Su, Chuan Qiu, Qing Tian, Lan-Juan Zhao, Zhe Luo, Chong Wu, Hui Shen, Hongwen Deng

{"title":"omicsMIC: a comprehensive benchmarking platform for robust comparison of imputation methods in mass spectrometry-based omics data.","authors":"Weiqiang Lin, Jiadong Ji, Kuan-Jui Su, Chuan Qiu, Qing Tian, Lan-Juan Zhao, Zhe Luo, Chong Wu, Hui Shen, Hongwen Deng","doi":"10.1093/nargab/lqae071","DOIUrl":"10.1093/nargab/lqae071","url":null,"abstract":"Mass spectrometry is a powerful and widely used tool for generating proteomics, lipidomics and metabolomics profiles, which is pivotal for elucidating biological processes and identifying biomarkers. However, missing values in mass spectrometry-based omics data may pose a critical challenge for the comprehensive identification of biomarkers and elucidation of the biological processes underlying human complex disorders. To alleviate this issue, various imputation methods for mass spectrometry-based omics data have been developed. However, a comprehensive comparison of these imputation methods is still lacking, and researchers are frequently confronted with a multitude of options without a clear rationale for method selection. To address this pressing need, we developed omicsMIC (mass spectrometry-based omics with Missing values Imputation methods Comparison platform), an interactive platform that provides researchers with a versatile framework to evaluate the performance of 28 diverse imputation methods. omicsMIC offers a nuanced perspective, acknowledging the inherent heterogeneity in biological data and the unique attributes of each dataset. Our platform empowers researchers to make data-driven decisions in imputation method selection based on real-time visualizations of the outcomes associated with different imputation strategies. The comprehensive benchmarking and versatility of omicsMIC make it a valuable tool for the scientific community engaged in mass spectrometry-based omics research. omicsMIC is freely available at https://github.com/WQLin8/omicsMIC.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae071"},"PeriodicalIF":4.0,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11177553/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141331908","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

GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes. GTDrift：用于探索真核生物中遗传漂变、基因组和转录组特征之间相互作用的资源。

IF 4.6

NAR Genomics and Bioinformatics Pub Date : 2024-06-12 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae064

Florian Bénitière, Laurent Duret, Anamaria Necsulea

{"title":"GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes.","authors":"Florian Bénitière, Laurent Duret, Anamaria Necsulea","doi":"10.1093/nargab/lqae064","DOIUrl":"10.1093/nargab/lqae064","url":null,"abstract":"We present GTDrift, a comprehensive data resource that enables explorations of genomic and transcriptomic characteristics alongside proxies of the intensity of genetic drift in individual species. This resource encompasses data for 1506 eukaryotic species, including 1413 animals and 93 green plants, and is organized in three components. The first two components contain approximations of the effective population size, which serve as indicators of the extent of random genetic drift within each species. In the first component, we meticulously investigated public databases to assemble data on life history traits such as longevity, adult body length and body mass for a set of 979 species. The second component includes estimations of the ratio between the rate of non-synonymous substitutions and the rate of synonymous substitutions (dN/dS) in protein-coding sequences for 1324 species. This ratio provides an estimate of the efficiency of natural selection in purging deleterious substitutions. Additionally, we present polymorphism-derived N e estimates for 66 species. The third component encompasses various genomic and transcriptomic characteristics. With this component, we aim to facilitate comparative transcriptomics analyses across species, by providing easy-to-use processed data for more than 16 000 RNA-seq samples across 491 species. These data include intron-centered alternative splicing frequencies, gene expression levels and sequencing depth statistics for each species, obtained with a homogeneous analysis protocol. To enable cross-species comparisons, we provide orthology predictions for conserved single-copy genes based on BUSCO gene sets. To illustrate the possible uses of this database, we identify the most frequently used introns for each gene and we assess how the sequencing depth available for each species affects our power to identify major and minor splice variants.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae064"},"PeriodicalIF":4.6,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11167491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141311879","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

Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements. 基于结构的学习，预测和模拟顺式调控元件中蛋白质与 DNA 的相互作用以及转录因子的协同作用。

IF 4.6

NAR Genomics and Bioinformatics Pub Date : 2024-06-12 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae068

Fornes Oriol, Meseguer Alberto, Aguirre-Plans Joachim, Gohl Patrick, Bota Patricia M, Molina-Fernández Ruben, Bonet Jaume, Chinchilla-Hernandez Altair, Pegenaute Ferran, Gallego Oriol, Fernandez-Fuentes Narcis, Oliva Baldo

{"title":"Structure-based learning to predict and model protein-DNA interactions and transcription-factor co-operativity in cis-regulatory elements.","authors":"Fornes Oriol, Meseguer Alberto, Aguirre-Plans Joachim, Gohl Patrick, Bota Patricia M, Molina-Fernández Ruben, Bonet Jaume, Chinchilla-Hernandez Altair, Pegenaute Ferran, Gallego Oriol, Fernandez-Fuentes Narcis, Oliva Baldo","doi":"10.1093/nargab/lqae068","DOIUrl":"10.1093/nargab/lqae068","url":null,"abstract":"Transcription factor (TF) binding is a key component of genomic regulation. There are numerous high-throughput experimental methods to characterize TF-DNA binding specificities. Their application, however, is both laborious and expensive, which makes profiling all TFs challenging. For instance, the binding preferences of ∼25% human TFs remain unknown; they neither have been determined experimentally nor inferred computationally. We introduce a structure-based learning approach to predict the binding preferences of TFs and the automated modelling of TF regulatory complexes. We show the advantage of using our approach over the classical nearest-neighbor prediction in the limits of remote homology. Starting from a TF sequence or structure, we predict binding preferences in the form of motifs that are then used to scan a DNA sequence for occurrences. The best matches are either profiled with a binding score or collected for their subsequent modeling into a higher-order regulatory complex with DNA. Co-operativity is modelled by: (i) the co-localization of TFs and (ii) the structural modeling of protein-protein interactions between TFs and with co-factors. We have applied our approach to automatically model the interferon-β enhanceosome and the pioneering complexes of OCT4, SOX2 (or SOX11) and KLF4 with a nucleosome, which are compared with the experimentally known structures.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae068"},"PeriodicalIF":4.6,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11167492/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141311880","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

Critical cis-parameters influence STructure assisted RNA translation (START) initiation on non-AUG codons in eukaryotes. 影响真核生物非 AUG 密码子上结构辅助 RNA 翻译（START）启动的关键顺式参数。

IF 4.6

NAR Genomics and Bioinformatics Pub Date : 2024-06-11 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae065

Antonin Tidu, Fatima Alghoul, Laurence Despons, Gilbert Eriani, Franck Martin

{"title":"Critical cis-parameters influence STructure assisted RNA translation (START) initiation on non-AUG codons in eukaryotes.","authors":"Antonin Tidu, Fatima Alghoul, Laurence Despons, Gilbert Eriani, Franck Martin","doi":"10.1093/nargab/lqae065","DOIUrl":"10.1093/nargab/lqae065","url":null,"abstract":"In eukaryotes, translation initiation is a highly regulated process, which combines cis-regulatory sequences located on the messenger RNA along with trans-acting factors like eukaryotic initiation factors (eIF). One critical step of translation initiation is the start codon recognition by the scanning 43S particle, which leads to ribosome assembly and protein synthesis. In this study, we investigated the involvement of secondary structures downstream the initiation codon in the so-called START (STructure-Assisted RNA translation) mechanism on AUG and non-AUG translation initiation. The results demonstrate that downstream secondary structures can efficiently promote non-AUG translation initiation if they are sufficiently stable to stall a scanning 43S particle and if they are located at an optimal distance from non-AUG codons to stabilize the codon-anticodon base pairing in the P site. The required stability of the downstream structure for efficient translation initiation varies in distinct cell types. We extended this study to genome-wide analysis of functionally characterized alternative translation initiation sites in Homo sapiens. This analysis revealed that about 25% of these sites have an optimally located downstream secondary structure of adequate stability which could elicit START, regardless of the start codon. We validated the impact of these structures on translation initiation for several selected uORFs.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae065"},"PeriodicalIF":4.6,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307012","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

Improved selection of canonical proteins for reference proteomes. 改进参考蛋白质组的典型蛋白质选择。

IF 4.6

NAR Genomics and Bioinformatics Pub Date : 2024-06-08 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae066

Giuseppe Insana, Maria J Martin, William R Pearson

{"title":"Improved selection of canonical proteins for reference proteomes.","authors":"Giuseppe Insana, Maria J Martin, William R Pearson","doi":"10.1093/nargab/lqae066","DOIUrl":"10.1093/nargab/lqae066","url":null,"abstract":"The 'canonical' protein sets distributed by UniProt are widely used for similarity searching, and functional and structural annotation. For many investigators, canonical sequences are the only version of a protein examined. However, higher eukaryotes often encode multiple isoforms of a protein from a single gene. For unreviewed (UniProtKB/TrEMBL) protein sequences, the longest sequence in a Gene-Centric group is chosen as canonical. This choice can create inconsistencies, selecting >95% identical orthologs with dramatically different lengths, which is biologically unlikely. We describe the ortho2tree pipeline, which examines Reference Proteome canonical and isoform sequences from sets of orthologous proteins, builds multiple alignments, constructs gap-distance trees, and identifies low-cost clades of isoforms with similar lengths. After examining 140 000 proteins from eight mammals in UniProtKB release 2022_05, ortho2tree proposed 7804 canonical changes for release 2023_01, while confirming 53 434 canonicals. Gap distributions for isoforms selected by ortho2tree are similar to those in bacterial and yeast alignments, organisms unaffected by isoform selection, suggesting ortho2tree canonicals more accurately reflect genuine biological variation. 82% of ortho2tree proposed-changes agreed with MANE; for confirmed canonicals, 92% agreed with MANE. Ortho2tree can improve canonical assignment among orthologous sequences that are >60% identical, a group that includes vertebrates and higher plants.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae066"},"PeriodicalIF":4.6,"publicationDate":"2024-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165316/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307793","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

NFixDB (Nitrogen Fixation DataBase)-a comprehensive integrated database for robust 'omics analysis of diazotrophs. NFixDB（固氮数据库）--一个全面的综合数据库，用于对重氮营养体进行强大的 "omics "分析。

IF 4.6

NAR Genomics and Bioinformatics Pub Date : 2024-06-06 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae063

Madeline Bellanger, Jose L Figueroa, Lisa Tiemann, Maren L Friesen, Richard Allen White Iii

{"title":"NFixDB (Nitrogen Fixation DataBase)-a comprehensive integrated database for robust 'omics analysis of diazotrophs.","authors":"Madeline Bellanger, Jose L Figueroa, Lisa Tiemann, Maren L Friesen, Richard Allen White Iii","doi":"10.1093/nargab/lqae063","DOIUrl":"10.1093/nargab/lqae063","url":null,"abstract":"Biological nitrogen fixation is a fundamental biogeochemical process that transforms molecular nitrogen into biologically available nitrogen via diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which is arranged in three different gene clusters: (i) molybdenum nitrogenase (nifHDK) is the most abundant, followed by it's alternatives, (ii) vanadium nitrogenase (vnfHDK) and (iii) iron nitrogenase (anfHDK). Multiple databases have been constructed as resources for diazotrophic 'omics analysis; however, an integrated database based on whole genome references does not exist. Here, we present NFixDB (Nitrogen Fixation DataBase), a comprehensive integrated whole genome based database for diazotrophs, which includes all nitrogenases (nifHDK, vnfHDK, anfHDK) and nitrogenase-like enzymes (e.g. nflHD) linked to ribosomal RNA operons (16S-5S-23S). NFixDB was computed using Hidden Markov Models (HMMs) against the entire whole genome based Genome Taxonomy Database (GTDB R214), providing searchable reference HMMs for all nitrogenase and nitrogenase-like genes, complete ribosomal RNA operons, both GTDB and NCBI/RefSeq taxonomy, and an SQL database for querying matches. We compared NFixDB to nifH databases from Buckley, Zehr, Mise and FunGene finding extensive evidence of nifH, in addition to vnfH and nflH. NFixDB contains >4000 verified nifHDK sequences contained on 50 unique phyla of bacteria and archaea. NFixDB provides the first comprehensive nitrogenase database available to researchers unlocking diazotrophic microbial potential.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae063"},"PeriodicalIF":4.6,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11155484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141284891","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

Characterization of trans-spliced chimeric RNAs: insights into the mechanism of trans-splicing. 反式拼接嵌合 RNA 的特征：反式拼接机制的启示。

IF 4.6

NAR Genomics and Bioinformatics Pub Date : 2024-06-06 eCollection Date: 2024-06-01 DOI: 10.1093/nargab/lqae067

Rui Yokomori, Takehiro G Kusakabe, Kenta Nakai

{"title":"Characterization of trans-spliced chimeric RNAs: insights into the mechanism of trans-splicing.","authors":"Rui Yokomori, Takehiro G Kusakabe, Kenta Nakai","doi":"10.1093/nargab/lqae067","DOIUrl":"10.1093/nargab/lqae067","url":null,"abstract":"Trans-splicing is a post-transcriptional processing event that joins exons from separate RNAs to produce a chimeric RNA. However, the detailed mechanism of trans-splicing remains poorly understood. Here, we characterize trans-spliced genes and provide insights into the mechanism of trans-splicing in the tunicate Ciona. Tunicates are the closest invertebrates to humans, and their genes frequently undergo trans-splicing. Our analysis revealed that, in genes that give rise to both trans-spliced and non-trans-spliced messenger RNAs, trans-splice acceptor sites were preferentially located at the first functional acceptor site, and their paired donor sites were weak in both Ciona and humans. Additionally, we found that Ciona trans-spliced genes had GU- and AU-rich 5' transcribed regions. Our data and findings not only are useful for Ciona research community, but may also aid in a better understanding of the trans-splicing mechanism, potentially advancing the development of gene therapy based on trans-splicing.","PeriodicalId":33994,"journal":{"name":"NAR Genomics and Bioinformatics","volume":"6 2","pages":"lqae067"},"PeriodicalIF":4.6,"publicationDate":"2024-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11155486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141284889","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