We are analyzing https://link.springer.com/article/10.1186/1745-6150-7-20.

Title:
Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes | Biology Direct
Description:
Background Recent mapping of eukaryotic transcriptomes and spliceomes using massively parallel RNA sequencing (RNA-seq) has revealed that the extent of alternative splicing has been considerably underestimated. Evidence also suggests that many pre-mRNAs undergo unproductive alternative splicing resulting in incorporation of in-frame premature termination codons (PTCs). The destinies and potential functions of the PTC-harboring mRNAs remain poorly understood. Unproductive alternative splicing in circadian clock genes presents a special case study because the daily oscillations of protein expression levels require rapid and steep adjustments in mRNA levels. Results We conducted a systematic survey of alternative splicing of plant circadian clock genes using RNA-seq and found that many Arabidopsis thaliana circadian clock-associated genes are alternatively spliced. Results were confirmed using reverse transcription polymerase chain reaction (RT-PCR), quantitative RT-PCR (qRT-PCR), and/or Sanger sequencing. Intron retention events were frequently observed in mRNAs of the CCA1/LHY-like subfamily of MYB transcription factors. In contrast, the REVEILLE2 (RVE2) transcript was alternatively spliced via inclusion of a "poison cassette exon" (PCE). The PCE type events introducing in-frame PTCs are conserved in some mammalian and plant serine/arginine-rich splicing factors. For some circadian genes such as CCA1 the ratio of the productive isoform (i.e., a representative splice variant encoding the full-length protein) to its PTC counterpart shifted sharply under specific environmental stress conditions. Conclusions Our results demonstrate that unproductive alternative splicing is a widespread phenomenon among plant circadian clock genes that frequently generates mRNA isoforms harboring in-frame PTCs. Because LHY and CCA1 are core components of the plant central circadian oscillator, the conservation of alternatively spliced variants between CCA1 and LHY and for CCA1 across phyla [2] indicates a potential role of nonsense transcripts in regulation of circadian rhythms. Most of the alternatively spliced isoforms harbor in-frame PTCs that arise from full or partial intron retention events. However, a PTC in the RVE2 transcript is introduced through a PCE event. The conservation of AS events and modulation of the relative abundance of nonsense isoforms by environmental and diurnal conditions suggests possible regulatory roles for these alternatively spliced transcripts in circadian clock function. The temperature-dependent expression of the PTC transcripts among members of CCA1/LHY subfamily indicates that alternative splicing may be involved in regulation of the clock temperature compensation mechanism. Reviewers This article was reviewed by Dr. Eugene Koonin, Dr. Chungoo Park (nominated by Dr. Kateryna Makova), and Dr. Marcelo Yanovsky (nominated by Dr. Valerian Dolja).
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Keywords {🔍}

circadian, genes, splicing, alternative, events, clock, spliced, transcripts, cca, plant, expression, intron, arabidopsis, article, pubmed, mrna, lhy, rnaseq, figure, alternatively, rve, isoforms, regulation, google, scholar, authors, rtpcr, gene, ptcs, unproductive, transcript, splice, stress, nmd, conditions, event, data, cas, pce, analysis, levels, retention, central, additional, rna, qrtpcr, conserved, isoform, plants, response,

Topics {✒️}

arabidopsis serine/arginine-rich proteins /cgi-bin/gbrowse/arabidopsis-gbrowse/ glycine-rich rna-binding proteins full-length protein-encoding counterparts full-length protein-coding counterpart rna-seq dataset derived semi-quantitative rt-pcr analysis full-length protein-coding transcripts full-length protein-encoding transcript arabidopsis[2] serine/arginine-rich constructed rna-seq libraries nonsense-mediated mrna decay article download pdf rnase-free turbo dnase rna-seq reads plotted arabidopsis rna-seq gbrowse morning-expressed transcription factors central circadian oscillator dark/light transition period rna-seq read coverage full-length spliced variant rna-seq reads density rapid post-transcriptional adjustments rna-seq data predicted recent rna-seq survey nonsense-mediated decay rna-seq read data extensive alternative splicing central clock genes light/dark-dependent shift premature termination codons evening-expressed toc1 activates quantitative rt-pcr analysis steady-state translation pool poison cassette exon frame nonsense codon saf developed rt-pcr gene-counter computational pipeline alternative donor/acceptor sites myb transcription factors selected rt-pcr products dna binding domains approaches including rt-pcr exon/exon junctions clock-output genes genome-wide mapping initiation codon fail nmd-impaired upf1-1 mutant nmd-impaired mutant upf1-1 upf1-1 nmd-impaired mutant

Questions {❓}

In this study, which is different from previous study?
The only substantial question that I have is: would it be possible to compare the level of alternative splicing in clock genes to the overall background in Arabidopsis?

Schema {🗺️}

WebPage:
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         headline:Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes
         description:Recent mapping of eukaryotic transcriptomes and spliceomes using massively parallel RNA sequencing (RNA-seq) has revealed that the extent of alternative splicing has been considerably underestimated. Evidence also suggests that many pre-mRNAs undergo unproductive alternative splicing resulting in incorporation of in-frame premature termination codons (PTCs). The destinies and potential functions of the PTC-harboring mRNAs remain poorly understood. Unproductive alternative splicing in circadian clock genes presents a special case study because the daily oscillations of protein expression levels require rapid and steep adjustments in mRNA levels. We conducted a systematic survey of alternative splicing of plant circadian clock genes using RNA-seq and found that many Arabidopsis thaliana circadian clock-associated genes are alternatively spliced. Results were confirmed using reverse transcription polymerase chain reaction (RT-PCR), quantitative RT-PCR (qRT-PCR), and/or Sanger sequencing. Intron retention events were frequently observed in mRNAs of the CCA1/LHY-like subfamily of MYB transcription factors. In contrast, the REVEILLE2 (RVE2) transcript was alternatively spliced via inclusion of a "poison cassette exon" (PCE). The PCE type events introducing in-frame PTCs are conserved in some mammalian and plant serine/arginine-rich splicing factors. For some circadian genes such as CCA1 the ratio of the productive isoform (i.e., a representative splice variant encoding the full-length protein) to its PTC counterpart shifted sharply under specific environmental stress conditions. Our results demonstrate that unproductive alternative splicing is a widespread phenomenon among plant circadian clock genes that frequently generates mRNA isoforms harboring in-frame PTCs. Because LHY and CCA1 are core components of the plant central circadian oscillator, the conservation of alternatively spliced variants between CCA1 and LHY and for CCA1 across phyla [2] indicates a potential role of nonsense transcripts in regulation of circadian rhythms. Most of the alternatively spliced isoforms harbor in-frame PTCs that arise from full or partial intron retention events. However, a PTC in the RVE2 transcript is introduced through a PCE event. The conservation of AS events and modulation of the relative abundance of nonsense isoforms by environmental and diurnal conditions suggests possible regulatory roles for these alternatively spliced transcripts in circadian clock function. The temperature-dependent expression of the PTC transcripts among members of CCA1/LHY subfamily indicates that alternative splicing may be involved in regulation of the clock temperature compensation mechanism. This article was reviewed by Dr. Eugene Koonin, Dr. Chungoo Park (nominated by Dr. Kateryna Makova), and Dr. Marcelo Yanovsky (nominated by Dr. Valerian Dolja).
         datePublished:2012-07-02T00:00:00Z
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         Arabidopsis thaliana
         Alternative splicing
         Circadian clock
         RNA-seq
         Intron retention
         Cassette exon
         Nonsense mRNAs
         Premature termination codon
         CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)
         LATE ELONGATED HYPOCOTYL (LHY)
         REVEILLE 2 (RVE2).
         Life Sciences
         general
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         type:PostalAddress
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         name:Donald Danforth Plant Science Center, St. Louis, USA
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               type:PostalAddress
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            address:
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               type:PostalAddress
            type:Organization
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               name:Division of Biology and Biomedical Sciences, Washington University, St. Louis, USA
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      name:Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, USA
      name:Donald Danforth Plant Science Center, St. Louis, USA
      name:Division of Biology and Biomedical Sciences, Washington University, St. Louis, USA

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