Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA

Celine Duc, Alexander Sherstnev, Christian Cole, Geoffrey Barton (Lead / Corresponding author), Gordon G. Simpson (Lead / Corresponding author)

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    32 Citations (Scopus)

    Abstract

    Alternative cleavage and polyadenylation influence the coding and regulatory potential of mRNAs and where transcription termination occurs. Although widespread, few regulators of this process are known. The Arabidopsis thaliana protein FPA is a rare example of a trans-acting regulator of poly(A) site choice. Analysing fpa mutants therefore provides an opportunity to reveal generic consequences of disrupting this process. We used direct RNA sequencing to quantify shifts in RNA 3' formation in fpa mutants. Here we show that specific chimeric RNAs formed between the exons of otherwise separate genes are a striking consequence of loss of FPA function. We define intergenic read-through transcripts resulting from defective RNA 3' end formation in fpa mutants, and detail cryptic splicing and antisense transcription associated with these read-through RNAs. We identify alternative polyadenylation within introns that is sensitive to FPA, and show FPA-dependent shifts in IBM1 poly(A) site selection that differ from those recently defined in mutants defective in intragenic heterochromatin and DNA methylation. Finally, we show that defective termination at specific loci in fpa mutants is shared with dicer-like 1 (dcl1) or dcl4 mutants, leading us to develop alternative explanations for some silencing roles of these proteins. We relate our findings to the impact that altered patterns of 3' end formation can have on gene and genome organisation.
    Original languageEnglish
    Article numbere1003867
    JournalPLoS Genetics
    Volume9
    Issue number10
    DOIs
    Publication statusPublished - 31 Oct 2013

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    Arabidopsis
    RNA
    Arabidopsis thaliana
    transcription (genetics)
    mutants
    Polyadenylation
    Poly A
    Arabidopsis Proteins
    RNA Sequence Analysis
    Heterochromatin
    DNA Methylation
    Introns
    Genes
    Exons
    protein
    gene
    methylation
    Genome
    heterochromatin
    DNA methylation

    Cite this

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    abstract = "Alternative cleavage and polyadenylation influence the coding and regulatory potential of mRNAs and where transcription termination occurs. Although widespread, few regulators of this process are known. The Arabidopsis thaliana protein FPA is a rare example of a trans-acting regulator of poly(A) site choice. Analysing fpa mutants therefore provides an opportunity to reveal generic consequences of disrupting this process. We used direct RNA sequencing to quantify shifts in RNA 3' formation in fpa mutants. Here we show that specific chimeric RNAs formed between the exons of otherwise separate genes are a striking consequence of loss of FPA function. We define intergenic read-through transcripts resulting from defective RNA 3' end formation in fpa mutants, and detail cryptic splicing and antisense transcription associated with these read-through RNAs. We identify alternative polyadenylation within introns that is sensitive to FPA, and show FPA-dependent shifts in IBM1 poly(A) site selection that differ from those recently defined in mutants defective in intragenic heterochromatin and DNA methylation. Finally, we show that defective termination at specific loci in fpa mutants is shared with dicer-like 1 (dcl1) or dcl4 mutants, leading us to develop alternative explanations for some silencing roles of these proteins. We relate our findings to the impact that altered patterns of 3' end formation can have on gene and genome organisation.",
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    T1 - Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA

    AU - Duc, Celine

    AU - Sherstnev, Alexander

    AU - Cole, Christian

    AU - Barton, Geoffrey

    AU - Simpson, Gordon G.

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