We are analyzing https://link.springer.com/article/10.1186/s12864-020-06831-4.

Title:
Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure | BMC Genomics
Description:
Background Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses. Results By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing. Conclusions Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.
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Keywords {🔍}

genes, splicing, alternative, gene, response, expression, pubmed, exposure, google, scholar, daphnia, stress, analysis, differential, acute, table, copper, samples, clone, differentially, cas, genome, pulex, expressed, analyses, lineages, enriched, clones, study, spliced, splice, events, data, functional, molecular, responses, identified, metal, exon, central, variation, role, reported, studies, previous, biol, patterns, exons, pathways, global,

Topics {✒️}

org/packages/release/bioc/html/topgo replicate rna-seq data full size image heavy metal pollution pre-messenger rna splicing animal metabolic profiles fast-acting alternative approach reveal lineage-specific differences exon/intron inclusion level serine-type endopeptidase activity gene response profiles 21 rna-seq libraries article download pdf metal-induced acute stress exon/intron inclusion levels 100 bp paired-end reads exon skipping-rich transcriptomes rna-seq data micro-crustacean daphnia pulex clone-specific analyses overlapped post-translational modification full access recent genome-wide studies article suresh annotation-independent splicing visualization privacy choices/manage cookies copper-exposed samples compared ut3 paul sabatier sashimi plot revised previously published dataset rna-protein complex lower sample sizes post-translational control intron retention events premature stop codons alternative rna splicing related subjects fdr-corrected p-values sample names consist environmentally induced phenotypes cu stress-response pathways clone-specific analyses suggesting rna-sequencing author information authors creative commons licence soft-water culture multiple splicing events anthropogenic stressors [46 genomic view pulex genome published

Schema {🗺️}

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         description:Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses. By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing. Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.
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         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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      affiliation:
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            address:
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               type:PostalAddress
            type:Organization
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      affiliation:
            name:McGill University
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            type:Organization
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