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Nature Communications Jun 2024Intron 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...
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.
Topics: Arabidopsis Proteins; Arabidopsis; Introns; Gene Expression Regulation, Plant; Spliceosomes; Light; Ubiquitin-Protein Ligases; Cell Nucleus; Seedlings; Alternative Splicing; Ubiquitination
PubMed: 38879536
DOI: 10.1038/s41467-024-49571-9 -
Cellular & Molecular Biology Letters Jun 2024CircR-loop, a recently unearthed regulatory mechanism situated at the crossroads of circular RNA and DNA interactions, constitute a subset of R-loop. This circR-loop... (Review)
Review
CircR-loop, a recently unearthed regulatory mechanism situated at the crossroads of circular RNA and DNA interactions, constitute a subset of R-loop. This circR-loop have emerged as a crucial player in pivotal regulatory functions within both animal and plant systems. The journey into the realm of circR-loop commenced with their discovery within the human mitochondrial genome, where they serve as critical directors of mitochondrial DNA replication. In the plant kingdom, circR-loop wield influence over processes such as alternative splicing and centromere organization, impacting the intricacies of floral development and genome stability, respectively. Their significance extends to the animal domain, where circR-loop has captured attention for their roles in cancer-related phenomena, exerting control over transcription, chromatin architecture, and orchestrating responses to DNA damage. Moreover, their involvement in nuclear export anomalies further underscores their prominence in cellular regulation. This article summarizes the important regulatory mechanisms and physiological roles of circR-loop in plants and animals, and offers a comprehensive exploration of the methodologies employed for the identification, characterization, and functional analysis of circR-loop, underscoring the pressing need for innovative approaches that can effectively distinguish them from their linear RNA counterparts while elucidating their precise functions. Lastly, the article sheds light on the challenges and opportunities that lie ahead in the field of circR-loop research, emphasizing the vital importance of continued investigations to uncover their regulatory roles and potential applications in the realm of biology. In summary, circR-loop represents a captivating and novel regulatory mechanism with broad-reaching implications spanning the realms of genetics, epigenetics, and disease biology. Their exploration opens new avenues for comprehending gene regulation and holds significant promise for future therapeutic interventions.
Topics: Genomic Instability; Humans; Animals; RNA, Circular; DNA; R-Loop Structures; RNA; DNA Replication
PubMed: 38877420
DOI: 10.1186/s11658-024-00606-5 -
Life Science Alliance Sep 2024Transcriptomic analysis of dengue-infected patients reveals altered immune response pathways, transcript diversity, and splicing efficiency, underscoring potential...
Transcriptomic analysis of dengue-infected patients reveals altered immune response pathways, transcript diversity, and splicing efficiency, underscoring potential therapeutic targets for treatment.
PubMed: 38876798
DOI: 10.26508/lsa.202402882 -
BMC Genomics Jun 2024Nuclear introns in Euglenida have been understudied. This study aimed to investigate nuclear introns in Euglenida by identifying a large number of introns in Euglena...
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.
Topics: Euglena gracilis; Introns; RNA Splice Sites; Alternative Splicing; RNA Splicing
PubMed: 38872102
DOI: 10.1186/s12864-024-10495-9 -
Cell Genomics Jun 2024Alternative splicing contributes to shaping lineage-specific gene expression and phenotypes. In this issue of Cell Genomics, Recinos, Bao, Wang, et al. report that the...
Alternative splicing contributes to shaping lineage-specific gene expression and phenotypes. In this issue of Cell Genomics, Recinos, Bao, Wang, et al. report that the balance between splicing isoforms of the microtubule-associated protein Tau in the brain is differentially regulated among primates by the RNA-binding protein MBNL2, with consequences for protein aggregation and neurodegeneration in humans.
Topics: Humans; Alternative Splicing; Brain; Animals; RNA-Binding Proteins; tau Proteins; Protein Isoforms
PubMed: 38870907
DOI: 10.1016/j.xgen.2024.100584 -
Frontiers in Immunology 2024[This corrects the article DOI: 10.3389/fimmu.2024.1354500.].
[This corrects the article DOI: 10.3389/fimmu.2024.1354500.].
PubMed: 38868772
DOI: 10.3389/fimmu.2024.1430718 -
NAR Genomics and Bioinformatics Jun 2024We present GTDrift, a comprehensive data resource that enables explorations of genomic and transcriptomic characteristics alongside proxies of the intensity of genetic...
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 (d/d) 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 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.
PubMed: 38867915
DOI: 10.1093/nargab/lqae064 -
Haematologica Jun 2024Not available.
Not available.
PubMed: 38867588
DOI: 10.3324/haematol.2024.285368 -
Molecular Medicine (Cambridge, Mass.) Jun 2024Immunotherapies effectively treat human malignancies, but the low response and resistance are major obstacles. Neoantigen is an emerging target for tumor immunotherapy...
BACKGROUND
Immunotherapies effectively treat human malignancies, but the low response and resistance are major obstacles. Neoantigen is an emerging target for tumor immunotherapy that can enhance anti-tumor immunity and improve immunotherapy. Aberrant alternative splicing is an important source of neoantigens. HNRNPA1, an RNA splicing factor, was found to be upregulated in the majority of tumors and play an important role in the tumor immunosuppressive microenvironment.
METHODS
Whole transcriptome sequencing was performed on shHNRNPA1 SKOV3 cells and transcriptomic data of shHNRNPA1 HepG2, MCF-7M, K562, and B-LL cells were downloaded from the GEO database. Enrichment analysis was performed to elucidate the mechanisms underlying the activation of anti-tumor immunity induced by HNRNPA1 knockdown. mRNA alternative splicing was analyzed and neoantigens were predicted by JCAST v.0.3.5 and Immune epitope database. The immunogenicity of candidate neoantigens was calculated by Class I pMHC Immunogenicity and validated by the IFN-γ ELISpot assay. The effect of shHNRNPA1 on tumor growth and immune cells in vivo was evaluated by xenograft model combined with immunohistochemistry.
RESULTS
HNRNPA1 was upregulated in a majority of malignancies and correlated with immunosuppressive status of the tumor immune microenvironment. Downregulation of HNRNPA1 could induce the activation of immune-related pathways and biological processes. Disruption of HNRNPA1 resulted in aberrant alternative splicing events and generation of immunogenic neoantigens. Downregulation of HNRNPA1 inhibited tumor growth and increased CD8 T cell infiltration in vivo.
CONCLUSION
Our study demonstrated that targeting HNRNPA1 could produce immunogenic neoantigens that elicit anti-tumor immunity by inducing abnormal mRNA splicing. It suggests that HNRNPA1 may be a potential target for immunotherapy.
Topics: Heterogeneous Nuclear Ribonucleoprotein A1; Alternative Splicing; Humans; Animals; Antigens, Neoplasm; Cell Line, Tumor; Mice; Gene Expression Regulation, Neoplastic; Tumor Microenvironment; Female; Xenograft Model Antitumor Assays; Down-Regulation; Neoplasms
PubMed: 38867190
DOI: 10.1186/s10020-024-00849-0 -
BMC Genomics Jun 2024Reverse transcription quantitative PCR (RT-qPCR) with intercalating dyes is one of the main techniques to assess gene expression levels used in basic and applied...
BACKGROUND
Reverse transcription quantitative PCR (RT-qPCR) with intercalating dyes is one of the main techniques to assess gene expression levels used in basic and applied research as well as in diagnostics. However, primer design for RT-qPCR can be complex due to the high demands on primer quality. Primers are best placed on exon junctions, should avoid polymorphic regions, be specific to the target transcripts and also prevent genomic amplification accurately, among others. Current software tools manage to meet all the necessary criteria only insufficiently. Here, we present ExonSurfer, a novel, user-friendly web-tool for qPCR primer design.
RESULTS
ExonSurfer combines the different steps of the primer design process, encompassing target selection, specificity and self-complementarity assessment, and the avoidance of issues arising from polymorphisms. Amplification of potentially contaminating genomic DNA is avoided by designing primers on exon-exon junctions, moreover, a genomic alignment is performed to filter the primers accordingly and inform the user of any predicted interaction. In order to test the whole performance of the application, we designed primer pairs for 26 targets and checked both primer efficiency, amplicon melting temperature and length and confirmed the targeted amplicon by Sanger sequencing. Most of the tested primers accurately and selectively amplified the corresponding targets.
CONCLUSION
ExonSurfer offers a comprehensive end-to-end primer design, guaranteeing transcript-specific amplification. The user interface is intuitive, providing essential specificity and amplicon details. The tool can also be used by command line and the source code is available. Overall, we expect ExonSurfer to facilitate RT-qPCR set-up for researchers in many fields.
Topics: Exons; Software; DNA Primers; Internet; Humans; Reverse Transcriptase Polymerase Chain Reaction
PubMed: 38867172
DOI: 10.1186/s12864-024-10456-2