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An additional 907 clones Evodiamine were obtained, resulting in a total of 2149?TR cDNAs. This collection represents 83% of the 2593?TR transcripts detected by RNAseq over all stages and 86% of the 2488?TR transcripts expressed in the 24?hpf embryo. 72% of cloned genes are TFs followed by chromatin remodelling TRs (12%) and 5% are general transcription factors reflecting the abundance of these different classes in the genome. The remaining 11% clones represented putative TRs with less well-characterised functions in mammalian systems. This library of 2149?TR cDNAs constitutes a unique resource to study the transcriptional regulation of zebrafish development and body homeostasis. We next determined the spatial expression of the TR genes by generating 1871 probes for whole mount in situ hybridisation in 24?hpf embryos, thus focusing on the phylotypic stage. We successfully obtained in situ expression patterns of 1711 TR genes. Among these, 746 (44%) are new patterns that complement existing databases of expression pattern in zebrafish ( Bradford et al., 2011) ( Fig. 4A). Fewer than half of the TRs assessed (768 genes, 45%) BMS-777607 solubility dmso are expressed in a tissue-restricted manner. The remaining clones (55%, n=1711) showed a more or less uniform signal throughout the embryo. This together with the signal detected by RNAseq demonstrates clearly that these TRs are expressed ubiquitously. Thus, the majority of TRs have either a ��housekeeping�� function in many cell types, or their activity is regulated at the post-transcriptional level in a region- or stage-specific manner. The central nervous system (CNS) and especially the selleck screening library spinal cord and forebrain express the highest diversity of TR genes (Fig. 4A). For instance, in the telencephalon, we detected mRNAs of 183 TR genes representing 91 InterPro families. If one includes the pan-neural (37 genes expressed in the whole neural tube) and the ubiquitously expressed genes (918 genes expressed in the whole embryo), the telencephalon of the 24?hpf zebrafish embryo expresses a total of 1138 TRs representing 67% (1138 out of 1711) of the entire transcriptional regulome analysed by in situ hybridisation. Another tissue with a high diversity of spatially restricted TRs is the somite with 139 genes from 116 InterPro families. In both somites and telencephalon, homeobox-containing TFs are the most abundant followed by TFs containing C2H2 zinc fingers (Supplementary Fig. S6). In some instances, we found also preferences for one or the other class of TRs in individual tissues. The number of tissue-restricted HMG-domain containing TFs expressed in the telencephalon was higher compared to the somites (single-sided Fisher's exact test p