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1.
Planta Med ; 90(7-08): 534-545, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38843793

RESUMO

Chamomile (Matricaria chamomilla) is an important medicinal plant whose beneficial activities partly rely on certain flavonoids. The first dedicated step in flavonoid biosynthesis is chalcone synthase (CHS, EC 2.3.1.74). The genomic DNA of CHS was studied in six chamomile specimens from different genotypes to describe interspecimen, as well as interspecific, variability. One specimen of M. discoidea was included as an outgroup. The two exons of CHS of M. chamomilla (McCHS) and M. discoidea (MdCHS) were 188 bp and 1,011 bp long, separated by an intron of variable length between 192 and 199 bp in McCHS and 201 bp in MdCHS, respectively. The two exons with 5.3 and 6.2 mutations per 100 bp, respectively, were more conserved than the intron with 11.5 mutations per 100 bp. In total, 96 SNPs were detected in both species, of which 12 SNPs were only present in MdCHS and 80 SNPs only in McCHS. Overall, 70 haplotypes (multilocus genotypes, MLGs) were detected. The samples could be classified into two groups, a 'compact' group of a low number and diversity of haplotypes and a 'variable' group of a high number and diversity of haplotypes. Of the 74 SNPs in McCHS, only six SNPs were non-synonymous. However, the amino acid changes did not affect critical areas of the enzyme. The combination of the six SNPs resulted in nine translated amino acid MLGs. The CHS network located MdCHS, due to the crossing barrier, quite distant from chamomile. MdCHS docked to McCHS at a position from where McCHS divergently evolved into two directions.


Assuntos
Aciltransferases , Matricaria , Aciltransferases/genética , Aciltransferases/metabolismo , Matricaria/genética , Matricaria/enzimologia , Polimorfismo de Nucleotídeo Único , Haplótipos , Variação Genética , DNA de Plantas/genética , Genótipo , Filogenia , Íntrons
2.
Nat Commun ; 15(1): 5130, 2024 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-38879536

RESUMO

Intron retention (IR) is the most common alternative splicing event in Arabidopsis. An increasing number of studies have demonstrated the major role of IR in gene expression regulation. The impacts of IR on plant growth and development and response to environments remain underexplored. Here, we found that IR functions directly in gene expression regulation on a genome-wide scale through the detainment of intron-retained transcripts (IRTs) in the nucleus. Nuclear-retained IRTs can be kept away from translation through this mechanism. COP1-dependent light modulation of the IRTs of light signaling genes, such as PIF4, RVE1, and ABA3, contribute to seedling morphological development in response to changing light conditions. Furthermore, light-induced IR changes are under the control of the spliceosome, and in part through COP1-dependent ubiquitination and degradation of DCS1, a plant-specific spliceosomal component. Our data suggest that light regulates the activity of the spliceosome and the consequent IRT nucleus detainment to modulate photomorphogenesis through COP1.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Núcleo Celular , Regulação da Expressão Gênica de Plantas , Íntrons , Luz , Spliceossomos , Ubiquitina-Proteína Ligases , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Arabidopsis/efeitos da radiação , Arabidopsis/metabolismo , Íntrons/genética , Regulação da Expressão Gênica de Plantas/efeitos da radiação , Spliceossomos/metabolismo , Ubiquitina-Proteína Ligases/metabolismo , Ubiquitina-Proteína Ligases/genética , Núcleo Celular/metabolismo , Plântula/crescimento & desenvolvimento , Plântula/genética , Plântula/efeitos da radiação , Plântula/metabolismo , Processamento Alternativo , Ubiquitinação
3.
PLoS Genet ; 20(6): e1011316, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38833506

RESUMO

Splicing is an important step of gene expression regulation in eukaryotes, as there are many mRNA precursors that can be alternatively spliced in different tissues, at different cell cycle phases or under different external stimuli. We have developed several integrated fluorescence-based in vivo splicing reporter constructs that allow the quantification of fission yeast splicing in vivo on intact cells, and we have compared their splicing efficiency in a wild type strain and in a prp2-1 (U2AF65) genetic background, showing a clear dependency between Prp2 and a consensus signal at 5' splicing site (5'SS). To isolate novel genes involved in regulated splicing, we have crossed the reporter showing more intron retention with the Schizosaccharomyces pombe knock out collection. Among the candidate genes involved in the regulation of splicing, we have detected strong splicing defects in two of the mutants -Δcwf12, a member of the NineTeen Complex (NTC) and Δsaf5, a methylosome subunit that acts together with the survival motor neuron (SMN) complex in small nuclear ribonucleoproteins (snRNP) biogenesis. We have identified that strains with mutations in cwf12 have inefficient splicing, mainly when the 5'SS differs from the consensus. However, although Δsaf5 cells also have some dependency on 5'SS sequence, we noticed that when one intron of a given pre-mRNA was affected, the rest of the introns of the same pre-mRNA had high probabilities of being also affected. This observation points Saf5 as a link between transcription rate and splicing.


Assuntos
Splicing de RNA , Proteínas de Schizosaccharomyces pombe , Schizosaccharomyces , Transcrição Gênica , Schizosaccharomyces/genética , Schizosaccharomyces/metabolismo , Proteínas de Schizosaccharomyces pombe/genética , Proteínas de Schizosaccharomyces pombe/metabolismo , Regulação Fúngica da Expressão Gênica , Íntrons/genética , Mutação , Processamento Alternativo/genética , Ribonucleoproteínas Nucleares Pequenas/genética , Ribonucleoproteínas Nucleares Pequenas/metabolismo , Precursores de RNA/genética , Precursores de RNA/metabolismo , Sítios de Splice de RNA/genética , Fator de Processamento U2AF/genética , Fator de Processamento U2AF/metabolismo
4.
BMC Genomics ; 25(1): 595, 2024 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-38872102

RESUMO

BACKGROUND: Nuclear introns in Euglenida have been understudied. This study aimed to investigate nuclear introns in Euglenida by identifying a large number of introns in Euglena gracilis (E. gracilis), including cis-spliced conventional and nonconventional introns, as well as trans-spliced outrons. We also examined the sequence characteristics of these introns. RESULTS: A total of 28,337 introns and 11,921 outrons were identified. Conventional and nonconventional introns have distinct splice site features; the former harbour canonical GT/C-AG splice sites, whereas the latter are capable of forming structured motifs with their terminal sequences. We observed that short introns had a preference for canonical GT-AG introns. Notably, conventional introns and outrons in E. gracilis exhibited a distinct cytidine-rich polypyrimidine tract, in contrast to the thymidine-rich tracts observed in other organisms. Furthermore, the SL-RNAs in E. gracilis, as well as in other trans-splicing species, can form a recently discovered motif called the extended U6/5' ss duplex with the respective U6s. We also describe a novel type of alternative splicing pattern in E. gracilis. The tandem repeat sequences of introns in this protist were determined, and their contents were comparable to those in humans. CONCLUSIONS: Our findings highlight the unique features of E. gracilis introns and provide insights into the splicing mechanism of these introns, as well as the genomics and evolution of Euglenida.


Assuntos
Euglena gracilis , Íntrons , Euglena gracilis/genética , Sítios de Splice de RNA , Processamento Alternativo , Splicing de RNA
5.
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
6.
BMC Genomics ; 25(1): 600, 2024 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-38877417

RESUMO

BACKGROUND: Splicing variants are a major class of pathogenic mutations, with their severity equivalent to nonsense mutations. However, redundant and degenerate splicing signals hinder functional assessments of sequence variations within introns, particularly at branch sites. We have established a massively parallel splicing assay to assess the impact on splicing of 11,191 disease-relevant variants. Based on the experimental results, we then applied regression-based methods to identify factors determining splicing decisions and their respective weights. RESULTS: Our statistical modeling is highly sensitive, accurately annotating the splicing defects of near-exon intronic variants, outperforming state-of-the-art predictive tools. We have incorporated the algorithm and branchpoint information into a web-based tool, SpliceAPP, to provide an interactive application. This user-friendly website allows users to upload any genetic variants with genome coordinates (e.g., chr15 74,687,208 A G), and the tool will output predictions for splicing error scores and evaluate the impact on nearby splice sites. Additionally, users can query branch site information within the region of interest. CONCLUSIONS: In summary, SpliceAPP represents a pioneering approach to screening pathogenic intronic variants, contributing to the development of precision medicine. It also facilitates the annotation of splicing motifs. SpliceAPP is freely accessible using the link https://bc.imb.sinica.edu.tw/SpliceAPP . Source code can be downloaded at https://github.com/hsinnan75/SpliceAPP .


Assuntos
Internet , Mutação , Splicing de RNA , Software , Humanos , Algoritmos , Íntrons/genética , Sítios de Splice de RNA/genética , Biologia Computacional/métodos
7.
Nat Commun ; 15(1): 4963, 2024 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-38862535

RESUMO

Image-based lineage tracing enables tissue turnover kinetics and lineage potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco, which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion kinetics and neighboring effects of oncogenic clones to be dissected. We now report Red2Flpe-SCON: a mosaic knockout system that uses multicolor reporters to label both mutant and wild-type cells. We develop the Red2Flpe mouse line for red clone-specific Flpe expression, as well as the FRT-based SCON (Short Conditional IntrON) method to facilitate tunable conditional mosaic knockouts in mice. We use the Red2Flpe-SCON method to study Sox2 mutant clonal analysis in the esophageal epithelium of adult mice which reveal that the stem cell gene, Sox2, is less essential for adult stem cell maintenance itself, but rather for stem cell proliferation and differentiation.


Assuntos
Proteínas Luminescentes , Camundongos Knockout , Proteína Vermelha Fluorescente , Fatores de Transcrição SOXB1 , Animais , Fatores de Transcrição SOXB1/genética , Fatores de Transcrição SOXB1/metabolismo , Camundongos , Proteínas Luminescentes/genética , Proteínas Luminescentes/metabolismo , Mosaicismo , Diferenciação Celular , Proliferação de Células/genética , Esôfago/metabolismo , Esôfago/patologia , Linhagem da Célula/genética , Íntrons/genética , Feminino , Masculino
10.
Int J Mol Sci ; 25(11)2024 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-38892127

RESUMO

ABCA4 is the most frequently mutated gene leading to inherited retinal disease (IRD) with over 2200 pathogenic variants reported to date. Of these, ~1% are copy number variants (CNVs) involving the deletion or duplication of genomic regions, typically >50 nucleotides in length. An in-depth assessment of the current literature based on the public database LOVD, regarding the presence of known CNVs and structural variants in ABCA4, and additional sequencing analysis of ABCA4 using single-molecule Molecular Inversion Probes (smMIPs) for 148 probands highlighted recurrent and novel CNVs associated with ABCA4-associated retinopathies. An analysis of the coverage depth in the sequencing data led to the identification of eleven deletions (six novel and five recurrent), three duplications (one novel and two recurrent) and one complex CNV. Of particular interest was the identification of a complex defect, i.e., a 15.3 kb duplicated segment encompassing exon 31 through intron 41 that was inserted at the junction of a downstream 2.7 kb deletion encompassing intron 44 through intron 47. In addition, we identified a 7.0 kb tandem duplication of intron 1 in three cases. The identification of CNVs in ABCA4 can provide patients and their families with a genetic diagnosis whilst expanding our understanding of the complexity of diseases caused by ABCA4 variants.


Assuntos
Transportadores de Cassetes de Ligação de ATP , Variações do Número de Cópias de DNA , Doenças Retinianas , Humanos , Transportadores de Cassetes de Ligação de ATP/genética , Doenças Retinianas/genética , Feminino , Masculino , Linhagem , Íntrons/genética , Éxons/genética , Duplicação Gênica
11.
J Genet ; 1032024.
Artigo em Inglês | MEDLINE | ID: mdl-38831649

RESUMO

The mitogenome is an important tool for taxonomic and evolutionary investigation. Here, a few complete mitogenomes of red algae have been reported. We have reported the complete mitogenome sequences of Grateloupia cornea Okamura, 1913 (Rhodophyta, Halymeniales). The genome is 30,595 bp in circumference, and has a strongly biased [AT] = 66.9%. Like most other Grateloupia species, it has a group II intron in the cox1 gene. Maximum likelihood and maximum parsimony analyses showed that G. cornea is more closely related to G. asiatica. This shows that the group II intron in the cox1 ORF present in most species of Grateloupia was present in their common ancestor, and uniquely lost in G. asiatica. The seven Grateloupia species with known mitogenome sequences remain monophyletic, with the genus Polyopes as sister taxon. The complete mitochondrial genome data will be valuable for future research on comparative mitochondrial genome analysis, an extensive understanding of gene content and organization, evolution of the cox1 intron in Rhodophyta as well as phylogenetic analysis.


Assuntos
Genoma Mitocondrial , Filogenia , Rodófitas , Rodófitas/genética , Rodófitas/classificação , Íntrons/genética , Evolução Molecular
12.
Nat Commun ; 15(1): 4980, 2024 Jun 19.
Artigo em Inglês | MEDLINE | ID: mdl-38898052

RESUMO

The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work provides a solid basis for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers.


Assuntos
Domínio Catalítico , Íntrons , Splicing de RNA , Spliceossomos , Splicing de RNA/efeitos dos fármacos , Spliceossomos/metabolismo , Spliceossomos/efeitos dos fármacos , Humanos , Íntrons/genética , Bibliotecas de Moléculas Pequenas/farmacologia , Bibliotecas de Moléculas Pequenas/química
13.
Nat Commun ; 15(1): 4697, 2024 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-38824128

RESUMO

Differentiation of male gametocytes into flagellated fertile male gametes relies on the assembly of axoneme, a major component of male development for mosquito transmission of the malaria parasite. RNA-binding protein (RBP)-mediated post-transcriptional regulation of mRNA plays important roles in eukaryotic sexual development, including the development of female Plasmodium. However, the role of RBP in defining the Plasmodium male transcriptome and its function in male gametogenesis remains incompletely understood. Here, we performed genome-wide screening for gender-specific RBPs and identified an undescribed male-specific RBP gene Rbpm1 in the Plasmodium. RBPm1 is localized in the nucleus of male gametocytes. RBPm1-deficient parasites fail to assemble the axoneme for male gametogenesis and thus mosquito transmission. RBPm1 interacts with the spliceosome E complex and regulates the splicing initiation of certain introns in a group of 26 axonemal genes. RBPm1 deficiency results in intron retention and protein loss of these axonemal genes. Intron deletion restores axonemal protein expression and partially rectifies axonemal defects in RBPm1-null gametocytes. Further splicing assays in both reporter and endogenous genes exhibit stringent recognition of the axonemal introns by RBPm1. The splicing activator RBPm1 and its target introns constitute an axonemal intron splicing program in the post-transcriptional regulation essential for Plasmodium male development.


Assuntos
Axonema , Íntrons , Proteínas de Protozoários , Splicing de RNA , Proteínas de Ligação a RNA , Íntrons/genética , Proteínas de Ligação a RNA/metabolismo , Proteínas de Ligação a RNA/genética , Animais , Proteínas de Protozoários/genética , Proteínas de Protozoários/metabolismo , Masculino , Axonema/metabolismo , Feminino , Gametogênese/genética , Spliceossomos/metabolismo , Spliceossomos/genética , Plasmodium berghei/genética , Plasmodium berghei/crescimento & desenvolvimento , Plasmodium berghei/metabolismo , Malária/parasitologia , Plasmodium/genética , Plasmodium/metabolismo
14.
Nat Commun ; 15(1): 4617, 2024 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-38816363

RESUMO

The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover. Through generation of a viable DBR1 knockout cell line, we find the predominantly nuclear Dbr1 enzyme to encode the sole debranching activity in human cells. Dbr1 preferentially debranches substrates that contain canonical U2 binding motifs, suggesting that branchsites discovered through sequencing do not necessarily represent those favored by the spliceosome. We find that Dbr1 also exhibits specificity for particular 5' splice site sequences. We identify Dbr1 interactors through co-immunoprecipitation mass spectrometry. We present a mechanistic model for Dbr1 recruitment to the branchpoint through the intron-binding protein AQR. In addition to a 20-fold increase in lariats, Dbr1 depletion increases exon skipping. Using ADAR fusions to timestamp lariats, we demonstrate a defect in spliceosome recycling. In the absence of Dbr1, spliceosomal components remain associated with the lariat for a longer period of time. As splicing is co-transcriptional, slower recycling increases the likelihood that downstream exons will be available for exon skipping.


Assuntos
Íntrons , Splicing de RNA , Spliceossomos , Humanos , Íntrons/genética , Spliceossomos/metabolismo , Células HEK293 , RNA Nucleotidiltransferases/metabolismo , RNA Nucleotidiltransferases/genética , Éxons/genética , Proteínas de Ligação a RNA/metabolismo , Proteínas de Ligação a RNA/genética , Células HeLa , Sítios de Splice de RNA
15.
Am J Hum Genet ; 111(6): 1100-1113, 2024 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-38733992

RESUMO

Splicing-based transcriptome-wide association studies (splicing-TWASs) of breast cancer have the potential to identify susceptibility genes. However, existing splicing-TWASs test the association of individual excised introns in breast tissue only and thus have limited power to detect susceptibility genes. In this study, we performed a multi-tissue joint splicing-TWAS that integrated splicing-TWAS signals of multiple excised introns in each gene across 11 tissues that are potentially relevant to breast cancer risk. We utilized summary statistics from a meta-analysis that combined genome-wide association study (GWAS) results of 424,650 women of European ancestry. Splicing-level prediction models were trained in GTEx (v.8) data. We identified 240 genes by the multi-tissue joint splicing-TWAS at the Bonferroni-corrected significance level; in the tissue-specific splicing-TWAS that combined TWAS signals of excised introns in genes in breast tissue only, we identified nine additional significant genes. Of these 249 genes, 88 genes in 62 loci have not been reported by previous TWASs, and 17 genes in seven loci are at least 1 Mb away from published GWAS index variants. By comparing the results of our splicing-TWASs with previous gene-expression-based TWASs that used the same summary statistics and expression prediction models trained in the same reference panel, we found that 110 genes in 70 loci that are identified only by the splicing-TWASs. Our results showed that for many genes, expression quantitative trait loci (eQTL) did not show a significant impact on breast cancer risk, whereas splicing quantitative trait loci (sQTL) showed a strong impact through intron excision events.


Assuntos
Neoplasias da Mama , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Splicing de RNA , Transcriptoma , Humanos , Neoplasias da Mama/genética , Feminino , Splicing de RNA/genética , Íntrons/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Perfilação da Expressão Gênica
16.
Mol Cell ; 84(11): 2070-2086.e20, 2024 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-38703770

RESUMO

The MYCN oncoprotein binds active promoters in a heterodimer with its partner protein MAX. MYCN also interacts with the nuclear exosome, a 3'-5' exoribonuclease complex, suggesting a function in RNA metabolism. Here, we show that MYCN forms stable high-molecular-weight complexes with the exosome and multiple RNA-binding proteins. MYCN binds RNA in vitro and in cells via a conserved sequence termed MYCBoxI. In cells, MYCN associates with thousands of intronic transcripts together with the ZCCHC8 subunit of the nuclear exosome targeting complex and enhances their processing. Perturbing exosome function results in global re-localization of MYCN from promoters to intronic RNAs. On chromatin, MYCN is then replaced by the MNT(MXD6) repressor protein, inhibiting MYCN-dependent transcription. RNA-binding-deficient alleles show that RNA-binding limits MYCN's ability to activate cell growth-related genes but is required for MYCN's ability to promote progression through S phase and enhance the stress resilience of neuroblastoma cells.


Assuntos
Proteína Proto-Oncogênica N-Myc , Proteínas Nucleares , Proteínas Oncogênicas , Proteínas de Ligação a RNA , Proteína Proto-Oncogênica N-Myc/metabolismo , Proteína Proto-Oncogênica N-Myc/genética , Humanos , Proteínas de Ligação a RNA/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas Nucleares/metabolismo , Proteínas Nucleares/genética , Proteínas Oncogênicas/metabolismo , Proteínas Oncogênicas/genética , Regiões Promotoras Genéticas , Linhagem Celular Tumoral , Neuroblastoma/metabolismo , Neuroblastoma/genética , Neuroblastoma/patologia , Exossomos/metabolismo , Exossomos/genética , Íntrons , Ligação Proteica , Núcleo Celular/metabolismo , Complexo Multienzimático de Ribonucleases do Exossomo/metabolismo , Complexo Multienzimático de Ribonucleases do Exossomo/genética , Regulação Neoplásica da Expressão Gênica , RNA/metabolismo , RNA/genética , Proteínas Repressoras/metabolismo , Proteínas Repressoras/genética , Proliferação de Células
17.
PLoS One ; 19(5): e0300190, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38814971

RESUMO

Histone variants are paralogs that replace canonical histones in nucleosomes, often imparting novel functions. However, how histone variants arise and evolve is poorly understood. Reconstruction of histone protein evolution is challenging due to large differences in evolutionary rates across gene lineages and sites. Here we used intron position data from 108 nematode genomes in combination with amino acid sequence data to find disparate evolutionary histories of the three H2A variants found in Caenorhabditis elegans: the ancient H2A.ZHTZ-1, the sperm-specific HTAS-1, and HIS-35, which differs from the canonical S-phase H2A by a single glycine-to-alanine C-terminal change. Although the H2A.ZHTZ-1 protein sequence is highly conserved, its gene exhibits recurrent intron gain and loss. This pattern suggests that specific intron sequences or positions may not be important to H2A.Z functionality. For HTAS-1 and HIS-35, we find variant-specific intron positions that are conserved across species. Patterns of intron position conservation indicate that the sperm-specific variant HTAS-1 arose more recently in the ancestor of a subset of Caenorhabditis species, while HIS-35 arose in the ancestor of Caenorhabditis and its sister group, including the genus Diploscapter. HIS-35 exhibits gene retention in some descendent lineages but gene loss in others, suggesting that histone variant use or functionality can be highly flexible. Surprisingly, we find the single amino acid differentiating HIS-35 from core H2A is ancestral and common across canonical Caenorhabditis H2A sequences. Thus, we speculate that the role of HIS-35 lies not in encoding a functionally distinct protein, but instead in enabling H2A expression across the cell cycle or in distinct tissues. This work illustrates how genes encoding such partially-redundant functions may be advantageous yet relatively replaceable over evolutionary timescales, consistent with the patchwork pattern of retention and loss of both genes. Our study shows the utility of intron positions for reconstructing evolutionary histories of gene families, particularly those undergoing idiosyncratic sequence evolution.


Assuntos
Sequência de Aminoácidos , Caenorhabditis elegans , Evolução Molecular , Histonas , Íntrons , Animais , Histonas/genética , Histonas/metabolismo , Íntrons/genética , Caenorhabditis elegans/genética , Filogenia , Sequência Conservada , Proteínas de Caenorhabditis elegans/genética , Masculino
18.
Genes Dev ; 38(7-8): 322-335, 2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38724209

RESUMO

Rare, full-length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envisioned and tested a hypothesis for their formation using Saccharomyces cerevisiae, documenting full-length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron lariat spliceosome (ILS) in which the 3'-OH of the lariat tail (with optional trimming and adenylation by the nuclear 3' processing machinery) attacks the branch, joining the intron 3' end to the 5' splice site in a 3'-5' linked circle. Human U2 and U12 spliceosomes produce analogous full-length and processed circles. Postsplicing catalytic activity of the spliceosome may promote intron transposition during eukaryotic genome evolution.


Assuntos
Íntrons , Splicing de RNA , Saccharomyces cerevisiae , Spliceossomos , Spliceossomos/metabolismo , Spliceossomos/genética , Íntrons/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Humanos , Splicing de RNA/genética , RNA Circular/genética , RNA Circular/metabolismo , RNA/metabolismo , RNA/genética
19.
Eur J Med Genet ; 69: 104949, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38797245

RESUMO

Variation in the non-coding genome is being increasingly recognized to be involved in monogenic disease etiology. However, the interpretation of non-coding variation is complicated by a lack of understanding of how non-coding genetic elements function. Additional lines of evidence are therefore needed to recognize non-coding variants as pathogenic. We here present a case where a collective body of evidence resulted in the identification and conclusive classification of a pathogenic deep intronic variant in ATRX. This report demonstrates the utility of a multi-platform approach in aiding the identification of pathogenic variants outside coding regions. Furthermore, it marks the first reported instance of a deep intronic pathogenic variant in ATRX.


Assuntos
Íntrons , Proteína Nuclear Ligada ao X , Humanos , Proteína Nuclear Ligada ao X/genética , Masculino , Mutação , Deficiência Intelectual Ligada ao Cromossomo X/genética , Deficiência Intelectual Ligada ao Cromossomo X/patologia , Deficiência Intelectual Ligada ao Cromossomo X/diagnóstico
20.
Gene ; 925: 148602, 2024 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-38782218

RESUMO

OBJECTIVE: ACAN gene variants, prevalent monogenic defects linked to short stature, are characterized by impaired cartilage generation in growth plates. We aimed to unravel the genetic basis of short stature in a specific pedigree by investigating the role of a novel non-canonical splicing-site variant, c.630-13G > A, within the ACAN gene. METHOD: Sanger sequencing was used for pedigree verification, and the effects of this variant on mRNA splicing were analyzed through minigene assay. RESULTS: The study revealed that this variant led to the creation of a previously unreported splice site in the fourth intron, resulting in the incorporation of an 11 bp sequence from the intron into the final transcript. This alteration led to a frameshift and formation of a premature termination codon, impacting the structure of the aggrecan protein. CONCLUSIONS: We document the pathogenicity of an ACAN non-canonical splicing-site variant, emphasizing the significance of considering intronic variants during genetic testing.


Assuntos
Agrecanas , Íntrons , Linhagem , Splicing de RNA , Humanos , Agrecanas/genética , Agrecanas/metabolismo , Feminino , Masculino , Nanismo/genética , Sítios de Splice de RNA/genética
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