title: RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription.
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.
authors.affiliation: Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom. cagla.altun@bbsrc.ac.uk
authors.forename: Cagla
authors.initials: C
authors.lastname: Sonmez
authors.forename: Isabel
authors.initials: I
authors.lastname: Bäurle
authors.forename: Andreas
authors.initials: A
authors.lastname: Magusin
authors.forename: Rene
authors.initials: R
authors.lastname: Dreos
authors.forename: Sascha
authors.initials: S
authors.lastname: Laubinger
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Caroline
authors.initials: C
authors.lastname: Dean
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000502:physiology*; D002843:Chromatin; D019175:DNA Methylation; D021901:DNA, Intergenic; D017343:Genes, Plant / Q000502:physiology*; D018745:Genome, Plant / Q000235:genetics* / Q000502:physiology; D026721:RNA 3' End Processing / Q000502:physiology*; D012323:RNA Processing, Post-Transcriptional; D016601:RNA-Binding Proteins / Q000502:physiology*; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; D002843:Chromatin; D021901:DNA, Intergenic; C432432:FPA protein, Arabidopsis; C106535:Flowering time control protein FCA, Arabidopsis; D016601:RNA-Binding Proteins