We are analyzing https://link.springer.com/article/10.1186/1471-2164-9-159.

Title:
Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes | BMC Genomics
Description:
Background Several recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so far to elucidate the functional relevance of alternative splicing in higher plants. Representing a frequent and universal subtle alternative splicing event among eukaryotes, alternative splicing at NAGNAG acceptors contributes to transcriptome diversity and therefore, proteome plasticity. Alternatively spliced NAGNAG acceptors are overrepresented in genes coding for proteins with RNA-recognition motifs (RRMs). As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes. Results In a comprehensive analysis of the Arabidopsis thaliana genome, we identified 6,772 introns that exhibit a NAGNAG acceptor motif. Alternative splicing at these acceptors was assessed using available EST data, complemented by a sequence-based prediction method. Of the 36 identified introns within 30 SR and SR-related protein-coding genes that have a NAGNAG acceptor, we selected 15 candidates for an experimental analysis of alternative splicing under several conditions. We provide experimental evidence for 8 of these candidates being alternatively spliced. Quantifying the ratio of NAGNAG-derived splice variants under several conditions, we found organ-specific splicing ratios in adult plants and changes in seedlings of different ages. Splicing ratio changes were observed in response to heat shock and most strikingly, cold shock. Interestingly, the patterns of differential splicing ratios are similar for all analyzed genes. Conclusion NAGNAG acceptors frequently occur in the Arabidopsis genome and are particularly prevalent in SR and SR-related protein-coding genes. A lack of extensive EST coverage can be compensated by using the proposed sequence-based method to predict alternative splicing at these acceptors. Our findings indicate that the differential effects on NAGNAG alternative splicing in SR and SR-related genes are organ- and condition-specific rather than gene-specific.
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Keywords {🔍}

splicing, nagnag, alternative, pubmed, genes, article, arabidopsis, google, scholar, cas, acceptors, proteins, plant, cases, acceptor, est, splice, protein, table, srrelated, central, plants, spliced, alternatively, data, atg, prediction, minor, forward, reverse, genome, ratios, gene, seedlings, etranscript, rna, sites, analysis, proteincoding, motif, frequency, transcript, introns, sequencebased, found, cold, coverage, ests, predicted, results,

Topics {✒️}

c-terminal arginine/serine-rich serine/arginine-rich protein interact arginine/serine-rich splicing factor serine/arginine-rich protein family palusa & anireddy sn reddy sr-related protein-coding genes plant serine/arginine-rich proteins arginine/serine-rich splicing factors arabidopsis serine/arginine-rich proteins org/tigr-scripts/tgi/t_index sr/sr-related protein genes article download pdf sr/sr-related gene family sr-related protein genes molecular plant biology respective exon-exon junction arabidopsis u1–70k protein est-based e-transcript frequency wu-blastn search sr-related protein transcripts resulting exon-exon junctions albert-ludwigs-university freiburg e-transcript proportions based tight spatio-temporal control prosystemin pre-mrna produces temperature-controlled splicing ratios short-distance tandem sites minor u12-type spliceosome nagnag-derived splice variants est-confirmed splice sites proposed sequence-based method sequence-specific splicing regulators existing rna-recognition motifs predicted e-transcript proportions detected organ-specific variations sequence-based prediction argues methyl jasmonate pre-treatment 15 sr/sr-related cases full size table nuclear pre-mrna splicing splice-variant analysis e-transcript proportions obtained nuclear pre-mrna processing underlie tissue-specific regulation sequence-based prediction method organ-specific alternative splicing column 'e-transcript predicted' stress-induced differences exist full access splice variant distribution

Questions {❓}

Kalyna M, Barta A: A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions?

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WebPage:
      mainEntity:
         headline:Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes
         description:Several recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so far to elucidate the functional relevance of alternative splicing in higher plants. Representing a frequent and universal subtle alternative splicing event among eukaryotes, alternative splicing at NAGNAG acceptors contributes to transcriptome diversity and therefore, proteome plasticity. Alternatively spliced NAGNAG acceptors are overrepresented in genes coding for proteins with RNA-recognition motifs (RRMs). As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes. In a comprehensive analysis of the Arabidopsis thaliana genome, we identified 6,772 introns that exhibit a NAGNAG acceptor motif. Alternative splicing at these acceptors was assessed using available EST data, complemented by a sequence-based prediction method. Of the 36 identified introns within 30 SR and SR-related protein-coding genes that have a NAGNAG acceptor, we selected 15 candidates for an experimental analysis of alternative splicing under several conditions. We provide experimental evidence for 8 of these candidates being alternatively spliced. Quantifying the ratio of NAGNAG-derived splice variants under several conditions, we found organ-specific splicing ratios in adult plants and changes in seedlings of different ages. Splicing ratio changes were observed in response to heat shock and most strikingly, cold shock. Interestingly, the patterns of differential splicing ratios are similar for all analyzed genes. NAGNAG acceptors frequently occur in the Arabidopsis genome and are particularly prevalent in SR and SR-related protein-coding genes. A lack of extensive EST coverage can be compensated by using the proposed sequence-based method to predict alternative splicing at these acceptors. Our findings indicate that the differential effects on NAGNAG alternative splicing in SR and SR-related genes are organ- and condition-specific rather than gene-specific.
         datePublished:2008-04-10T00:00:00Z
         dateModified:2008-04-10T00:00:00Z
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            Splice Variant
            Splice Factor
            Alternative Splice Event
            NAGNAG Acceptor
            Life Sciences
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            Microarrays
            Proteomics
            Animal Genetics and Genomics
            Microbial Genetics and Genomics
            Plant Genetics and Genomics
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ScholarlyArticle:
      headline:Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes
      description:Several recent studies indicate that alternative splicing in Arabidopsis and other plants is a common mechanism for post-transcriptional modulation of gene expression. However, few analyses have been done so far to elucidate the functional relevance of alternative splicing in higher plants. Representing a frequent and universal subtle alternative splicing event among eukaryotes, alternative splicing at NAGNAG acceptors contributes to transcriptome diversity and therefore, proteome plasticity. Alternatively spliced NAGNAG acceptors are overrepresented in genes coding for proteins with RNA-recognition motifs (RRMs). As SR proteins, a family of RRM-containing important splicing factors, are known to be extensively alternatively spliced in Arabidopsis, we analyzed alternative splicing at NAGNAG acceptors in SR and SR-related genes. In a comprehensive analysis of the Arabidopsis thaliana genome, we identified 6,772 introns that exhibit a NAGNAG acceptor motif. Alternative splicing at these acceptors was assessed using available EST data, complemented by a sequence-based prediction method. Of the 36 identified introns within 30 SR and SR-related protein-coding genes that have a NAGNAG acceptor, we selected 15 candidates for an experimental analysis of alternative splicing under several conditions. We provide experimental evidence for 8 of these candidates being alternatively spliced. Quantifying the ratio of NAGNAG-derived splice variants under several conditions, we found organ-specific splicing ratios in adult plants and changes in seedlings of different ages. Splicing ratio changes were observed in response to heat shock and most strikingly, cold shock. Interestingly, the patterns of differential splicing ratios are similar for all analyzed genes. NAGNAG acceptors frequently occur in the Arabidopsis genome and are particularly prevalent in SR and SR-related protein-coding genes. A lack of extensive EST coverage can be compensated by using the proposed sequence-based method to predict alternative splicing at these acceptors. Our findings indicate that the differential effects on NAGNAG alternative splicing in SR and SR-related genes are organ- and condition-specific rather than gene-specific.
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         Splice Variant
         Splice Factor
         Alternative Splice Event
         NAGNAG Acceptor
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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         name:Institute of Computer Science, Bioinformatics Group, Albert-Ludwigs-University Freiburg, Freiburg, Germany
         type:PostalAddress
      name:Leibniz Institute for Age Research – Fritz Lipmann Institute
      address:
         name:Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
         type:PostalAddress
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               type:PostalAddress
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      affiliation:
            name:Albert-Ludwigs-University Freiburg
            address:
               name:Institute of Computer Science, Bioinformatics Group, Albert-Ludwigs-University Freiburg, Freiburg, Germany
               type:PostalAddress
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      name:Gul Shad Ali
      affiliation:
            name:Colorado State University
            address:
               name:Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, USA
               type:PostalAddress
            type:Organization
      name:Saiprasad G Palusa
      affiliation:
            name:Colorado State University
            address:
               name:Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, USA
               type:PostalAddress
            type:Organization
      name:Rolf Backofen
      affiliation:
            name:Albert-Ludwigs-University Freiburg
            address:
               name:Institute of Computer Science, Bioinformatics Group, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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      name:Matthias Platzer
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            name:Leibniz Institute for Age Research – Fritz Lipmann Institute
            address:
               name:Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
               type:PostalAddress
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      name:Anireddy SN Reddy
      affiliation:
            name:Colorado State University
            address:
               name:Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, USA
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      name:Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, USA
      name:Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, USA
      name:Institute of Computer Science, Bioinformatics Group, Albert-Ludwigs-University Freiburg, Freiburg, Germany
      name:Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Jena, Germany
      name:Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, USA

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