Fig. 3: prdm1a regulates the expression of target genes in the ear.

a Schematic of the s100a1 locus showing lateral line (gray) or ear (black) ATAC-seq reads with location of Prdm1 binding motifs in red. Exons and introns in purple. Cloned enhancer-promoter fusion of Tg(s100a1:H2B-EGFP) in green. s100a1 HCR (yellow) and H2B-GFP expression (cyan) in 5 dpf wild type embryos driven by Tg(s100a1:H2B-EGFP) in the posterior macula (b) and lateral crista (c). 5 dpf sibling neuromast (d) and prdm1a^-/- dorsal neuromast (e). Scale bars= 10 µm. Representative images of two independent experiments. f Illustration of the zebrafish ear from a ventral view and orientation of the larva during imaging. AC anterior crista, LC lateral crista, PC posterior crista, AM anterior macula, PM posterior macula, NM neuromast. Ventral view of the zebrafish ear. Created in BioRender. Piotrowski, T. (2025) https://BioRender.com/vl2w553 (g), HCR with a prdm1a probe (magenta) in a Tg(myo6b:prdm1a) larva (h). Generated using Biorender. Representative images of six independent experiments. Scale bars= 20 µm (i–k) HCR signals for prdm1a (yellow), pvalb9, s100a1, and ckbb (cyan) in the lateral crista of sibling and the Tg(myo6:prdm1a; cryaa:mTurqoise2) embryos, respectively. Scale bars= 10 µm. Images are representative of embryos from two independent experiments. l Quantification of fluorescent signal from HCRs of pvalb9 (p = 0.0081), s100a1 (p = 0.0018), ckbb (p = 0.0003), tbx2b (p = 0.3699), and tmc2b (p = 0.2497). n = 8 embryos (two ears each) imaged per probe and genotype. Multiple unpaired two-sided t-test, ns>0.05, **p < 0.01, ***p < 0.001. Data are presented as mean ± SD. m HCRs of ckbb in sibling and prdm1a mutant neuromasts. Images representative of two independent experiments. n Expression of ckbb in prdm1a^-/- hair cells using the Tg(myo6:prdm1a; cryaa:mTurqoise2) line downregulates the expression of ckbb. Scale bars= 10 µm. Images representative of two independent experiments. o Quantification of ckbb expression in the various conditions. n = 12 for sibling, n = 11 for prdm1a^-/-, n = 15 for ectopic prdm1a-expressing sibling and n = 8 for ectopic prdm1a-expressing prdm1a^-/-. Two-way Anova with Tukey’s multiple comparisons test, *p < 0.05, **p < 0.01(**p = 0.0069), ***p < 0.001, ****p < 0.0001. Data are presented as mean ± SD. p Quantification of tmc2a HCR fluorescence intensity in the various conditions. n = 21 for sibling, n = 12 for prdm1a^-/-, n = 23 for ectopic prdm1a-expressing sibling and n = 23 for ectopic prdm1a-expressing prdm1a^-/-. Two-way Anova with Tukey’s multiple comparisons test, *p < 0.05(*p = 0.0262), **p < 0.01, ***p < 0.001, ****p < 0.0001. Data are presented as mean ± SD.