Characterisation of intergenic read-through RNAs in <i>fpa</i> and <i>dc11</i> mutants.

(A–C) Characterisation of FCA intergenic read-through RNAs. (A) Normalised reads mapping to the locus encoding FCA. (B) Identification of R1 and R2 contiguous RNAs. Three biological replicates (1, 2 and 3) were used for each genotype: wild-type (WT), fpa-7 and dc11–11. (C) Description of the R1 and R2 read-through transcripts. (D–F) Characterisation of At1g51390 read-through RNAs. (D) Normalised reads mapping to At1g51390–At1g51402–At1g51400. (E) Identification of R1 and R2 contiguous RNAs. Three biological replicates (1, 2 and 3) were used for each genotype: WT, fpa-7 and dc11–11. (F) Description of the R1 and R2 read-through transcripts. The red dashed lines indicate the regions amplified by RT-PCR on reverse-transcribed poly(A)+ RNAs. Red narrower rectangles represent 3′UTR parts specific to the read-through transcript and red lines the 3′UTR introns. RT-PCR products were separated on agarose gels and stained with ethidium bromide. The purple line indicates the location and strand detected by the probe, which was used previously [24]. 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. Exons are denoted by coloured rectangles, UTRs by adjoining narrower rectangles and introns by lines.