Fig. 6

Characterisation of anciently conserved elements in the Pax6 promoter and proximal region. (A) VISTA plot of multispecies sequence conservation in the PAX6 genomic region containing the promoters and immediate upstream CNEs. PAX6 exons are shown as blue peaks and non-coding peaks of conservation are in pink. The positions of the validated Pax6 promoters P0, P1 and Pα are indicated, as are the known enhancers P/EE and Panc2 corresponding to agCNEs 12-14. agCNEs 9-11 are well conserved in all vertebrate Pax6 loci analysed with the exception of agCNE11 which is absent in the zebrafish pax6b locus. Tracks underneath the plot show the presence of several CpG islands in the region, including one at the agCNE9-10 location, and a simplified overview of transcripts produced from the region. In addition to the various Pax6 transcripts two transcripts are found on the opposite strand, the multi-exon Pax6OS and the 2.8 kb single exon ncRNA AK032637. (B) rtPCR analysis of AK032637 in comparison with Pax6 and Gapdh in a selection of cell lines and embryo tissues. N2A, neuroblastoma, bTC3, pancreatic β-cell line, MV+, lens epithelium, RAG, renal adenocarcinoma, vTh, ventral thalamus, eye, E17.5dpc whole eye, mb, midbrain, ctx, cortex. (C) Reporter transgenic zebrafish with construct agCNE10-mCherry show ubiquitous low level signal but lack specific expression. (D) Transgenic fish for agCNE9-GFP show expression in the pineal gland with additional signal in the fore- and hindbrain in some lines. Fluorescent signal in transgenic fish with the agCNE11-GFP construct is restricted to the pineal gland only.