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1.
BMC Bioinformatics ; 25(1): 235, 2024 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-38992593

RESUMO

BACKGROUND: SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It takes a guide gene tree as input and generates a gene sequence with its transcripts for each node of the tree, from the root to the leaves. However, the sets of transcripts simulated at different nodes of the guide gene tree lack evolutionary connections. Consequently, SimSpliceEvol is not suitable for evaluating methods for transcript phylogeny inference or gene phylogeny inference that rely on transcript conservation. RESULTS: Here, we introduce SimSpliceEvol2, which, compared to the first version, incorporates an explicit model of transcript evolution for simulating alternative transcripts along the branches of a guide gene tree, as well as the transcript phylogenies inferred. We offer a comprehensive software with a graphical user interface and an updated version of the web server, ensuring easy and user-friendly access to the tool. CONCLUSION: SimSpliceEvol2 generates synthetic datasets that are useful for evaluating methods and tools for spliced RNA sequence analysis, such as spliced alignment methods, methods for identifying conserved transcripts, and transcript phylogeny reconstruction methods. The web server is accessible at https://simspliceevol.cobius.usherbrooke.ca , where you can also download the standalone software. Comprehensive documentation for the software is available at the same address. For developers interested in the source code, which requires the installation of all prerequisites to run, it is provided at  https://github.com/UdeS-CoBIUS/SimSpliceEvol .


Assuntos
Processamento Alternativo , Evolução Molecular , Filogenia , Software , Processamento Alternativo/genética , Éxons/genética , Análise de Sequência de RNA/métodos , Simulação por Computador
6.
PLoS One ; 19(7): e0305012, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38980892

RESUMO

Pre-messenger RNA (pre-mRNA) splicing modulation is an attractive approach for investigating the mechanisms of genetic disorders caused by mis-splicing. Previous reports have indicated that a modified U7 small nuclear RNA (U7 snRNA) is a prospective tool for modulating splicing both in vitro and in vivo. To date, very few studies have investigated the role of antisense sequence length in modified U7 snRNA. In this study, we designed a series of antisense sequences with various lengths and evaluated their efficiency in inducing splicing modulation. To express modified U7 snRNAs, we constructed a series of plasmid DNA sequences which codes cytomegalovirus (CMV) enhancer, human U1 promoter, and modified mouse U7 snRNAs with antisense sequences of different lengths. We evaluated in vitro splicing modulation efficiency using a luciferase reporter system for simple and precise evaluation as well as reverse transcription-polymerase chain reaction to monitor splicing patterns. Our in vitro assay findings suggest that antisense sequences of modified mouse U7 snRNAs have an optimal length for efficient splicing modulation, which depends on the target exon. In addition, antisense sequences that were either too long or too short decreased splicing modulation efficiency. To confirm reproducibility, we performed an in vitro assay using two target genes, mouse Fas and mouse Dmd. Together, our data suggests that the antisense sequence length should be optimized for modified mouse U7 snRNAs to induce efficient splicing modulation.


Assuntos
Precursores de RNA , Splicing de RNA , RNA Nuclear Pequeno , RNA Nuclear Pequeno/genética , Animais , Camundongos , Humanos , Precursores de RNA/genética , Precursores de RNA/metabolismo , Sequência de Bases , Éxons/genética , RNA Antissenso/genética
7.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 41(7): 849-852, 2024 Jul 10.
Artigo em Chinês | MEDLINE | ID: mdl-38946371

RESUMO

OBJECTIVE: To investigate the clinical and genetic features of a child with Dyschromatosis symmetrica hereditaria (DSH) and variant of the ADAR1 gene. METHODS: A child who was admitted to the Department of Dermatology of the First Affiliated Hospital of Zhengzhou University in June 2020 due to irregular pigmented maculopapular rash on the dorsum of hands was selected as the study subject. Whole exome sequencing (WES) was carried out for the child and his similarly affected father, and Sanger sequencing was used to verify the candidate variant. SWISS-MODEL was used to predict the secondary and tertiary structures of the wild-type and mutant ADAR1 proteins. RESULTS: The child, a 13-year-old boy, had symmetrical hyperpigmented and depigmented spots on the back of his hands and was clinically diagnosed with DSH. WES and Sanger sequencing results showed that he and his father had both harbored a heterozygous c.2858dup (p.T954Dfs*20) truncating variant in exon 10 of the ADAR1 gene. Based on the guidelines from the American College of Medical Genetics and Genomics, the variant was predicted as pathogenic (PVS1+PM2_Supporting+PM1+PP3). CONCLUSION: The c.2858dup (p.T954Dfs*20) variant of the ADAR1 gene probably underlay the DSH in this pedigree.


Assuntos
Adenosina Desaminase , Transtornos da Pigmentação , Proteínas de Ligação a RNA , Humanos , Masculino , Adenosina Desaminase/genética , Transtornos da Pigmentação/genética , Transtornos da Pigmentação/congênito , Proteínas de Ligação a RNA/genética , Adolescente , Mutação , Sequenciamento do Exoma , Éxons , Testes Genéticos , Linhagem
11.
Proc Natl Acad Sci U S A ; 121(28): e2400151121, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38954548

RESUMO

Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across a set of 38 abundant and conserved protein families. Taking advantage of genomic exon-intron organization and extensive protein sequence data, we explore exon boundary conservation and assess the foldon-like behavior of exons using energy landscape theoretic measurements. We found deviations in the exon size distribution from exponential decay indicating selection in evolution. We show that when taken together there is a pronounced tendency to independent foldability for segments corresponding to the more conserved exons, supporting the idea of exon-foldon correspondence. While 45% of the families follow this general trend when analyzed individually, there are some families for which other stronger functional determinants, such as preserving frustrated active sites, may be acting. We further develop a systematic partitioning of protein domains using exon boundary hotspots, showing that minimal common exons correspond with uninterrupted alpha and/or beta elements for the majority of the families but not for all of them.


Assuntos
Éxons , Dobramento de Proteína , Éxons/genética , Humanos , Proteínas/genética , Proteínas/química , Evolução Molecular , Íntrons/genética
12.
RNA Biol ; 21(1): 52-74, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38989833

RESUMO

The aim of this study was to compare the circular transcriptome of divergent tissues in order to understand: i) the presence of circular RNAs (circRNAs) that are not exonic circRNAs, i.e. originated from backsplicing involving known exons and, ii) the origin of artificial circRNA (artif_circRNA), i.e. circRNA not generated in-vivo. CircRNA identification is mostly an in-silico process, and the analysis of data from the BovReg project (https://www.bovreg.eu/) provided an opportunity to explore new ways to identify reliable circRNAs. By considering 117 tissue samples, we characterized 23,926 exonic circRNAs, 337 circRNAs from 273 introns (191 ciRNAs, 146 intron circles), 108 circRNAs from small non-coding genes and nearly 36.6K circRNAs classified as other_circRNAs. Furthermore, for 63 of those samples we analysed in parallel data from total-RNAseq (ribosomal RNAs depleted prior to library preparation) with paired mRNAseq (library prepared with poly(A)-selected RNAs). The high number of circRNAs detected in mRNAseq, and the significant number of novel circRNAs, mainly other_circRNAs, led us to consider all circRNAs detected in mRNAseq as artificial. This study provided evidence of 189 false entries in the list of exonic circRNAs: 103 artif_circRNAs identified by total RNAseq/mRNAseq comparison using two circRNA tools, 26 probable artif_circRNAs, and 65 identified by deep annotation analysis. Extensive benchmarking was performed (including analyses with CIRI2 and CIRCexplorer-2) and confirmed 94% of the 23,737 reliable exonic circRNAs. Moreover, this study demonstrates the effectiveness of a panel of highly expressed exonic circRNAs (5-8%) in analysing the tissue specificity of the bovine circular transcriptome.


Assuntos
Éxons , RNA Circular , RNA Circular/genética , Animais , Bovinos , Íntrons , Biologia Computacional/métodos , Transcriptoma , Perfilação da Expressão Gênica/métodos , Análise de Sequência de RNA/métodos
13.
Nat Commun ; 15(1): 4932, 2024 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-38858365

RESUMO

This study investigates the role of circular RNAs (circRNAs) in the context of Varicella-Zoster Virus (VZV) lytic infection. We employ two sequencing technologies, short-read sequencing and long-read sequencing, following RNase R treatment on VZV-infected neuroblastoma cells to identify and characterize both cellular and viral circRNAs. Our large scanning analysis identifies and subsequent experiments confirm 200 VZV circRNAs. Moreover, we discover numerous VZV latency-associated transcripts (VLTs)-like circRNAs (circVLTslytic), which contain multiple exons and different isoforms within the same back-splicing breakpoint. To understand the functional significance of these circVLTslytic, we utilize the Bacteria Artificial Chromosome system to disrupt the expression of viral circRNAs in genomic DNA location. We reveal that the sequence flanking circVLTs' 5' splice donor plays a pivotal role as a cis-acting element in the formation of circVLTslytic. The circVLTslytic is dispensable for VZV replication, but the mutation downstream of circVLTslytic exon 5 leads to increased acyclovir sensitivity in VZV infection models. This suggests that circVLTslytic may have a role in modulating the sensitivity to antiviral treatment. The findings shed new insight into the regulation of cellular and viral transcription during VZV lytic infection, emphasizing the intricate interplay between circRNAs and viral processes.


Assuntos
Herpesvirus Humano 3 , RNA Circular , RNA Viral , Replicação Viral , RNA Circular/genética , RNA Circular/metabolismo , Herpesvirus Humano 3/genética , Humanos , RNA Viral/genética , RNA Viral/metabolismo , Replicação Viral/genética , Linhagem Celular Tumoral , Latência Viral/genética , Infecção pelo Vírus da Varicela-Zoster/virologia , Aciclovir/farmacologia , Aciclovir/uso terapêutico , Éxons/genética
14.
BMJ Case Rep ; 17(6)2024 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-38862189

RESUMO

We present a case of a child with congenital thrombotic thrombocytopenic purpura found to have a compound heterozygous variant in the ADAMTS13 gene with a novel variant resulting in a large duplication of exons 9-11 of ADAMTS13 This variant was identified through additional molecular testing via a chromosomal microarray analysis. To our knowledge, this assay had not previously been utilised to identify an ADAMTS13 variant and the additional testing was possible through the involvement of a genetic counsellor.


Assuntos
Proteína ADAMTS13 , Púrpura Trombocitopênica Trombótica , Humanos , Proteína ADAMTS13/genética , Púrpura Trombocitopênica Trombótica/genética , Púrpura Trombocitopênica Trombótica/diagnóstico , Análise em Microsséries/métodos , Duplicação Gênica , Masculino , Feminino , Éxons/genética , Proteínas ADAM/genética
16.
BMC Genomics ; 25(1): 599, 2024 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-38877397

RESUMO

BACKGROUND: Tubulins play crucial roles in numerous fundamental processes of plant development. In flowering plants, tubulins are grouped into α-, ß- and γ-subfamilies, while α- and ß-tubulins possess a large isotype diversity and gene number variations among different species. This circumstance leads to insufficient recognition of orthologous isotypes and significantly complicates extrapolation of obtained experimental results, and brings difficulties for the identification of particular tubulin isotype function. The aim of this research is to identify and characterize tubulins of an emerging biofuel crop Camelina sativa. RESULTS: We report comprehensive identification and characterization of tubulin gene family in C. sativa, including analyses of exon-intron organization, duplicated genes comparison, proper isotype designation, phylogenetic analysis, and expression patterns in different tissues. 17 α-, 34 ß- and 6 γ-tubulin genes were identified and assigned to a particular isotype. Recognition of orthologous tubulin isotypes was cross-referred, involving data of phylogeny, synteny analyses and genes allocation on reconstructed genomic blocks of Ancestral Crucifer Karyotype. An investigation of expression patterns of tubulin homeologs revealed the predominant role of N6 (A) and N7 (B) subgenomes in tubulin expression at various developmental stages, contrarily to general the dominance of transcripts of H7 (C) subgenome. CONCLUSIONS: For the first time a complete set of tubulin gene family members was identified and characterized for allohexaploid C. sativa species. The study demonstrates the comprehensive approach of precise inferring gene orthology. The applied technique allowed not only identifying C. sativa tubulin orthologs in model Arabidopsis species and tracking tubulin gene evolution, but also uncovered that A. thaliana is missing orthologs for several particular isotypes of α- and ß-tubulins.


Assuntos
Evolução Molecular , Genoma de Planta , Família Multigênica , Filogenia , Tubulina (Proteína) , Tubulina (Proteína)/genética , Brassicaceae/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Sintenia , Regulação da Expressão Gênica de Plantas , Duplicação Gênica , Íntrons/genética , Éxons/genética
17.
Sci Rep ; 14(1): 13069, 2024 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-38844820

RESUMO

Insertion mutations in exon 20 of the epidermal growth factor receptor gene (EGFR exon20ins) are rare, heterogeneous alterations observed in non-small cell lung cancer (NSCLC). With a few exceptions, they are associated with primary resistance to established EGFR tyrosine kinase inhibitors (TKIs). As patients carrying EGFR exon20ins may be eligible for treatment with novel therapeutics-the bispecific antibody amivantamab, the TKI mobocertinib, or potential future innovations-they need to be identified reliably in clinical practice for which quality-based routine genetic testing is crucial. Spearheaded by the German Quality Assurance Initiative Pathology two international proficiency tests were run, assessing the performance of 104 participating institutes detecting EGFR exon20ins in tissue and/or plasma samples. EGFR exon20ins were most reliably identified using next-generation sequencing (NGS). Interestingly, success rates of institutes using commercially available mutation-/allele-specific quantitative (q)PCR were below 30% for tissue samples and 0% for plasma samples. Most of these mutation-/allele-specific (q)PCR assays are not designed to detect the whole spectrum of EGFR exon20ins mutations leading to false negative results. These data suggest that NGS is a suitable method to detect EGFR exon20ins in various types of patient samples and is superior to the detection spectrum of commercially available assays.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Receptores ErbB , Éxons , Sequenciamento de Nucleotídeos em Larga Escala , Neoplasias Pulmonares , Humanos , Receptores ErbB/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Carcinoma Pulmonar de Células não Pequenas/genética , Neoplasias Pulmonares/genética , Ensaio de Proficiência Laboratorial , Anticorpos Biespecíficos/uso terapêutico , Mutagênese Insercional , Inibidores de Proteínas Quinases/uso terapêutico
19.
HLA ; 103(6): e15552, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38923200
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