TR gene expression in developing zebrafish. (A) Temporal expression profile of 1219 TRs (rows) across six developmental stages (columns) by microarray analysis. Hierarchical clustering of normalised gene expression reveals two main clusters (black rectangles) discriminating genes either expressed prior (2 cells and 30% epiboly) or during organogenesis (1–6 somites to 120 hpf larvae). Blue: low expression; white: moderate expression; red: high expression. (B) Number of TR genes detected by microarray analysis. While the number of TF genes increases, the numbers of genes encoding chromatin remodelling and general transcription factors remain constant over the stages examined.

Assessment of TR gene expression by RNAseq. (A) Number of genes (white bars) and TRs (dashed bars) expressed at two different developmental stages and two adult body parts as determined by RNAseq. The total number of TR loci quantified by transcript counting over all stages is indicated as “Collapsed”. (B) Quantification of the total number of genes detected at 24 hpf by RNAseq in function of the sequencing depth. The number of detected genes is indicated as the mean from 3 biological replicates. (C) Level of expression of transcripts represented as FPKM from a selection of genes known to be expressed in the epiphysis (crx, otx5, nr2e3, aannt2), the retina (pax6b, hmx4) or tectum and retina (mycn and mych). The relative expression is indicated as the mean of FPKM from biological triplicates. (D) RNA in situ expression data of the selected transcripts at 24 hpf. *: epiphysis; arrow head: optic tectum.

Assessment of TR gene expression by RNAseq. (A) Number of genes (white bars) and TRs (dashed bars) expressed at two different developmental stages and two adult body parts as determined by RNAseq. The total number of TR loci quantified by transcript counting over all stages is indicated as “Collapsed”. (B) Quantification of the total number of genes detected at 24 hpf by RNAseq in function of the sequencing depth. The number of detected genes is indicated as the mean from 3 biological replicates. (C) Level of expression of transcripts represented as FPKM from a selection of genes known to be expressed in the epiphysis (crx, otx5, nr2e3, aannt2), the retina (pax6b, hmx4) or tectum and retina (mycn and mych). The relative expression is indicated as the mean of FPKM from biological triplicates. (D) RNA in situ expression data of the selected transcripts at 24 hpf. (*: epiphysis; arrow head: optic tectum.)

Correlation of co-expressed TRs. (A) Heat map of adjusted p-values from Pearson′s Chi-squared test showing significantly co-expressed TRs. Correlation of co-expression at 24 hpf is found mainly for neuronal regions (adjp: adjusted p-value). Example of in situ expression for TRs co-expressed in the retina and tectum (B–H), sensory placodes (I–M) or telencephalon, hypothalamus, thalamus and hindbrain (N–P). MHB: midbrain–hindbrain boundary.