<i>PIF5–PA03</i>, an example of chimeric RNA formation controlled by FPA.

(A) Normalised reads mapping to the locus encoding PIF5–PA03. Exons are denoted by coloured rectangles, UTRs by adjoining narrower rectangles and introns by lines. The image of normalised read alignments was made using the Integrated Genome Browser [55] and corresponds to combined reads from the three sequenced biological replicates for each genotype. (B) Location of RNA gel blot probes are indicated by numbers (P1–P6) and the tested fusion region by a dotted line. (C) RT-PCR analysis of a contiguous RNA between PIF5 and PA03 detected in fpa-8. UBIQUITIN LIGASE 21 (UBC) was used as a control. (D,E) RNA gel blot analysis of PIF5–PA03 chimeric RNAs in wild-type (WT) and fpa-8. P, PIF5; C, PA03 transcripts. β-TUBULIN (β-TUB.) was used as an internal control. Probes used are shown in (B). (F) 5′RACE analysis of the γ and γ′ RNAs with or without tobacco acid pyrophosphatase (TAP) treatment. PCR products were separated on an agarose gel and stained with ethidium bromide. (G) Schematic representation of the different RNAs expressed at the PIF5 locus in fpa mutants. The splicing event occurring in the β chimeric RNA is shown by a red line.