Extensive intergenic transcription from loss of Arabidopsis 3’ regulators FCA and FPA

The Arabidopsis RNA-binding proteins FCA and FPA were initially identified based on their suppression of the flowering time regulator FLC. Recently, however, they have been found to influence expression of a wide range of targets in the Arabidopsis genome. Here, we use whole-genome tiling arrays to determine the extent of their targets at two stages of seedling development. A wide range of genes and transposable elements were mis-expressed in the fcafpa double mutant with a significant bias for mis-regulated genomic segments mapping to the 3’ region of genes. A large number of previously unannotated (UA) genomic segments, which mapped to intergenic regions, were also mis-expressed in the fcafpa double mutant. We characterized a subset of these UA segments in detail and established them as strand-specific and direct targets of FCA and FPA, with a complex interplay between their functions. Only a few of the UA segments also showed regulation by a histone demethylase previously linked to FCA FPA function; however, others were associated with siRNA production and DNA methylation. Our data suggest that FCA/FPA play important roles in terminating transcription at many loci, often via promotion of proximal polyadenylation, and that in their absence, ectopic transcription and/or extensive read-through transcription occurs. These transcriptional products have the potential to interfere with overlapping transcripts and flanking genes and appear to form the basis for how modulation of FCA FPA function triggers RNA-mediated chromatin silencing mechanisms at a variety of loci in the Arabidopsis genome. We compared genome-wide transcript levels in three biological replicates of Arabidopsis thaliana Columbia (Col-0) and fca-9fpa-7 (fcafpa) double mutant seedlings. Two developmental stages, 7 and 17 days after germination, were analysed.