Publications (7)101.24 Total impact
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Article: RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription.
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ABSTRACT: The RNA-binding proteins FCA and FPA were identified based on their repression of the flowering time regulator FLC but have since been shown to have widespread roles in the Arabidopsis thaliana genome. Here, we use whole-genome tiling arrays to show that a wide spectrum of genes and transposable elements are misexpressed in the fca-9 fpa-7 (fcafpa) double mutant at two stages of seedling development. There was a significant bias for misregulated genomic segments mapping to the 3' region of genes. In addition, the double mutant misexpressed a large number of previously unannotated genomic segments corresponding to intergenic regions. We characterized a subset of these misexpressed unannotated segments and established that they resulted from extensive transcriptional read-through, use of downstream polyadenylation sites, and alternative splicing. In some cases, the transcriptional read-through significantly reduced expression of the associated genes. FCA/FPA-dependent changes in DNA methylation were found at several loci, supporting previous associations of FCA/FPA function with chromatin modifications. Our data suggest that FCA and FPA play important roles in the A. thaliana genome in RNA 3' processing and transcription termination, thus limiting intergenic transcription.Proceedings of the National Academy of Sciences 05/2011; 108(20):8508-13. · 9.68 Impact Factor -
Article: Altered interactions within FY/AtCPSF complexes required for Arabidopsis FCA-mediated chromatin silencing.
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ABSTRACT: The role of RNA metabolism in chromatin silencing is now widely recognized. We have studied the Arabidopsis RNA-binding protein FCA that down-regulates an endogenous floral repressor gene through a chromatin mechanism involving histone demethylase activity. This mechanism needs FCA to interact with an RNA 3' processing/polyadenylation factor (FY/Pfs2p), but the subsequent events leading to chromatin changes are unknown. Here, we show that this FCA-FY interaction is required for general chromatin silencing roles where hairpin transgenes induce DNA methylation of an endogenous gene. We also show 2 conserved RNA processing factors, AtCPSF100 and AtCPSF160, but not FCA, are stably associated with FY in vivo and form a range of different-sized complexes. A hypomorphic fy allele producing a shorter protein, able to provide some FY functions but unable to interact with FCA, reduces abundance of some of the larger MW complexes. Suppressor mutants, which specifically disrupt the FY motif through which FCA interacts, also lacked these larger complexes. Our data support a model whereby FCA, perhaps after recognition of a specific RNA feature, transiently interacts with FY, an integral component of the canonical RNA 3' processing machinery, changing the interactions of the different RNA processing components. These altered interactions would appear to be a necessary step in this RNA-mediated chromatin silencing.Proceedings of the National Academy of Sciences 06/2009; 106(21):8772-7. · 9.68 Impact Factor -
Article: Differential interactions of the autonomous pathway RRM proteins and chromatin regulators in the silencing of Arabidopsis targets.
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ABSTRACT: We have recently shown that two proteins containing RRM-type RNA-binding domains, FCA and FPA, originally identified through their role in flowering time control in Arabidopsis, silence transposons and other repeated sequences in the Arabidopsis genome. In flowering control, FCA and FPA function in the autonomous pathway with conserved chromatin regulators, the histone demethylase FLD and the MSI1-homologue FVE, a conserved WD-repeat protein found in many chromatin complexes. Here, we investigate how the RRM proteins interact genetically with these chromatin regulators at a range of loci in the Arabidopsis genome. We also investigate their interaction with the DNA methylation pathway. In several cases the RRM protein activity at least partially required a chromatin regulator to effect silencing. However, the interactions of the autonomous pathway components differed at each target analysed, most likely determined by certain properties of the target loci and/or other silencing pathways. We speculate that the RNA-binding proteins FCA and FPA function as part of a transcriptome surveillance mechanism linking RNA recognition with chromatin silencing mechanisms.PLoS ONE 01/2008; 3(7):e2733. · 4.09 Impact Factor -
Article: The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC.
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ABSTRACT: A repressor of the transition to flowering in Arabidopsis is the MADS box protein FLOWERING LOCUS C (FLC). FCA, an RNA-binding protein, and FY, a homolog of the yeast RNA 3' processing factor Pfs2p, downregulate FLC expression and therefore promote flowering. FCA/FY physically interact and alter polyadenylation/3' processing to negatively autoregulate FCA. Here, we show that FCA requires FLOWERING LOCUS D (FLD), a homolog of the human lysine-specific demethylase 1 (LSD1) for FLC downregulation. FCA also partially depends on DICER-LIKE 3, involved in chromatin silencing. fca mutations increased levels of unspliced sense FLC transcript, altered processing of antisense FLC transcripts, and increased H3K4 dimethylation in the central region of FLC. These data support a close association of FCA and FLD in mediating H3K4 demethylation and thus transcriptional silencing of FLC and reveal roles for antisense RNA processing and DCL3 function in this regulation.Molecular Cell 12/2007; 28(3):398-407. · 14.18 Impact Factor -
Article: Widespread role for the flowering-time regulators FCA and FPA in RNA-mediated chromatin silencing.
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ABSTRACT: The RRM-domain proteins FCA and FPA have previously been characterized as flowering-time regulators in Arabidopsis. We show that they are required for RNA-mediated chromatin silencing of a range of loci in the genome. At some target loci, FCA and FPA promote asymmetric DNA methylation, whereas at others they function in parallel to DNA methylation. Female gametophytic development and early embryonic development are particularly susceptible to malfunctions in FCA and FPA. We propose that FCA and FPA regulate chromatin silencing of single and low-copy genes and interact in a locus-dependent manner with the canonical small interfering RNA-directed DNA methylation pathway to regulate common targets.Science 11/2007; 318(5847):109-12. · 31.20 Impact Factor -
Article: The timing of developmental transitions in plants.
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ABSTRACT: Plants rely heavily on environmental cues to control the timing of developmental transitions. We are beginning to better understand what determines the timing of two of these transitions, the switch from juvenile to adult vegetative development and the transition to flowering. In this review, we discuss how RNA silencing mechanisms may influence the juvenile-to-adult vegetative switch. We also describe the discovery and regulation of a component of "florigen," the mobile flowering promotion signal that is involved in the transition to flowering. Parallel themes are beginning to emerge from a molecular comparison of these two developmental transitions.Cell 06/2006; 125(4):655-64. · 32.40 Impact Factor -
Article: RNA 3′ processing functions of Arabidopsis FCA and FPA limit intergenic transcription
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ABSTRACT: The RNA-binding proteins FCA and FPA were identified based on their repression of the flowering time regulator FLC but have since been shown to have widespread roles in the Arabidopsis thaliana genome. Here, we use whole-genome tiling arrays to show that a wide spectrum of genes and transposable elements are misex-pressed in the fca-9 fpa-7 (fcafpa) double mutant at two stages of seedling development. There was a significant bias for misregulated genomic segments mapping to the 3′ region of genes. In addition, the double mutant misexpressed a large number of previously un-annotated genomic segments corresponding to intergenic regions. We characterized a subset of these misexpressed unannotated seg-ments and established that they resulted from extensive transcrip-tional read-through, use of downstream polyadenylation sites, and alternative splicing. In some cases, the transcriptional read-through significantly reduced expression of the associated genes. FCA/FPA-dependent changes in DNA methylation were found at several loci, supporting previous associations of FCA/FPA function with chroma-tin modifications. Our data suggest that FCA and FPA play important roles in the A. thaliana genome in RNA 3′ processing and transcrip-tion termination, thus limiting intergenic transcription. T he Arabidopsis thaliana proteins FCA and FPA were identified through their effects as regulators of the floral transition (1). They were classified as functioning in the autonomous floral pathway, which comprises a set of activities that promotes flowering by down-regulating expression of the MADS box floral repressor FLOWERING LOCUS C (FLC) (2). FCA and FPA are RNA recognition motif (RRM)-containing proteins (3, 4), which nega-tively regulate their own expression through promotion of an in-ternal polyadenylation site (5, 6). FCA, but not FPA, physically interacts with FY, a protein homologous to the RNA 3′ processing component named Pfs2p in Saccharomyces cerevisiae and WDR33a in humans (7, 8). An extensive suppressor mutagenesis analysis combined with detailed molecular analysis revealed how FCA and FPA down-regulate expression of FLC (9). Both were found to promote proximal polyadenylation of an FLC antisense RNA (6, 9), and this leads to down-regulation of FLC sense transcription in a mechanism involving the activity of the histone 3-lysine 4-demethylase (FLD) (9). The mechanism linking alternative poly-adenylation of the antisense transcript, histone demethylation of the locus, and down-regulation of FLC sense transcription remains to be resolved. A more general genomic role for FCA and FPA was suggested when they were identified in a genetic screen targeting factors required for transgene-induced silencing. fca and fpa mutants suppressed systemic silencing and DNA methylation of the homologous endogenous A. thaliana gene in response to a mobile RNA silencing signal generated from a hairpin construct (10). FCA and FPA were also shown to be required for DNA methylation changes at low copy transposon and retrotransposon sequences in the A. thaliana genome (10), although a general role for the au-tonomous pathway in the repression of gene expression through DNA methylation does not seem to be the case (11). RNA 3′ processing and chromatin modification have been linked previously in a study of the yeast Paf chromatin complex (12). Mutations in core 3′ processing components (CstF64, symplekin, and CPSF100) are also thought to trigger chromatin silencing through generation of aberrant RNA substrates (13). However, to further investigate this link, we undertook a genome-wide analysis to identify the ex-tent of FCA and FPA regulation in A. thaliana. Here, we describe our analysis using whole-genome tiling arrays of A. thaliana, where we characterize the misexpression profile in an fca-9 fpa-7 (fcafpa) double mutant. A number of genes and transposable elements were misexpressed, with a significant bias for genomic segments mapping to the 3′ region of genes. In addition, a large number of previously unannotated (UA) genomic segments corresponding to intergenic regions were misexpressed in the double mutant. Characterization of these UA segments suggests that FCA and FPA play important genome-wide roles in 3′ processing and transcription termination, and in several cases, their function overlaps with other pathways mediating chromatin regulation.
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Institutions
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2006–2011
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John Innes Centre
- Department of Cell and Developmental Biology
Norwich, ENG, United Kingdom
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