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a Tg(−505/−310 (unc45b)gata2:gfp) embryos were injected with hsp90a morpholinos (hsp90a-mo) or with hsp90a-mo together with a mix of CRISPR RNA directed against hsf1 and cas9 mRNA (hsp90a-mo + guide hsf1). We note a decrease of GFP in the hsf1/hsp90a double knock-down compared with the hsp90a single morphant. b–b’ Injection of the plasmid encoding a Hsf1–mOrange fusion protein does not activate the unc45b promoter. Expression of TFP reporter in hsf1-morange injected embryos (+hsf1:morange) (a, b) is as high as in uninjected tg(−1.8unc45b:tfp) embryos (cont) (a). c–h’ Heat shock triggers unc45b up-regulation. −505/−310(unc45b)gata2:gfp injected embryos (c, d, c’, d’), Tg(−505/−310 (unc45b)gata2:gfp) (e, f, e’, f’) and tg(−1.8unc45b:tfp) (g, h, g’, h’) transgenic embryos were raised at 28 °C until 48 hpf and heat shock at 37 °C for 12 hours (d, d’, f, f’, h, h’). Embryos shown in (c, c’, e, e, g, g’) were kept at 28 °C. The heat shock embryos show up-regulation of GFP in skeletal and cardiac muscles, demonstrating that the regulatory sequences of unc45b react to heat shock. (PDF 1668 kb)

Summary of the transgenes used to map the regulatory elements mediating the misfolded myosin response A-B: tg(-1.8unc45b:tfp) (“1”) and its deletion derivatives were expressed transiently (trs) or as transgenesstably integrated into the genome (stb). By serial deletion analysis 645 bp upstream of the ATG of unc45bwas identified to still drive basal muscle expression and respond to unc45b deficiency (B). Furthertruncation of the unc45b sequences to the region from -369 bp to +390 bp abolished the response.C-E: Refined analysis of the unc45b regulatory sequences contained in tg(-645/+533unc45b:tfp). Theunc45b deletion fragments were cloned in front of the gata2 promoter (blue bars). Transgenes containingthe 195 bp fragment (“16”, D) harboring sequences from -505 to -310 drove GFP expression in skeletalmuscle (D, cont) and reacted to the accumulation of unfolded myosin (D, +unc45b-mo). Deletion constructs12-20 retained basal muscle expression and responded to misfolded myosin. In contrast, constructs 21-24give no GFP expression (see E).Further mutations of the 195 bp unc45b fragment separates the regulatory sequences responsible for basalmuscle expression and the response to misfolded myosin. Construct 28 drove basal GFP expression inskeletal muscles but did not respond when co-injected with the unc45b-mo (G). Construct 30 (55 bp)reacted similarly (H). These constructs retained a binding site of the Mef2 transcription factor. Constructs 31-37 lack the muscle basal expression but still respond to misfolded myosin (I). Thus, the region from -445 to -425 is important to mediate the response. This region contains a homology to the heat shock responseelement (HSE, J). The HSE was mutated by introduction of 4 point mutations (asterisks J, F, I) in constructs“26”, “38”, “41” and “42”. Mutation of the HSE leads to loss of the misfolded myosin response. Abbreviations:ME: muscle expression. The numbers above constructs indicate position relative to the ATG of unc45b. (PDF 2497 kb)

a, b Heatmap of Euclidian distance of RNASeq experiments. Pairwise comparison of conditions is displayed as a matrix of Euclidean distances with red colors indicating similarities (short distance) and yellow dissimilarities (high distance) between conditions. a RNA was prepared from either wild-type siblings (C1 and C2) or unc45b mutants (U) at 24, 48 and 72 hpf. Biological repeats are indicated by the numbers (1–3). C control, U unc45 −/− . b Clustering of Euclidean distances of the unc45b, hsp90a and ache mutants and their respective wild-type siblings at 72 hpf. c–e Fold-change expression of selected genes between wild-type and unc45b mutant embryos at 24, 48 and 72 hpf as detected in the RNASeq data. The expression of unc45b (c), hsp90a (d) and smyd1b (e) mRNA steadily increases from 24–72 hpf. f, g Log2 fold change of genes found upregulated at 72 hpf in unc45b and hsp90a mutants but not in ache mutants (f), or upregulated in the three mutants (g). Note that the level of upregulation in ache mutant is really low compared with the unc45b and hsp90a mutants. h–j MA plots displaying log10 (mean expression) between control and unc45b −/− mutants against log2 (fold change) at three developmental stages obtained with DESeq: 24 hpf (h), 48 hpf (i), 72 hpf (j). Genes up- or down-regulated with FDR 1.5 are shown in red. Numbers indicate the total number of detected genes with FDR 1.5. The error bars indicate "standard deviation". (PDF 3965 kb)

Chart representing the mean TFP or GFP intensity of transgenic embryos. a Mean pixel intensity of tg(−1.8unc45b:tfp) embryos compared with tg(−1.8unc45b:tfp) injected with either unc45b-mo or hsp90a-mo, showing twice as much TFP fluorescence in the morphant compared with wild-type embryos. b Mean pixel intensity of tg(−1.8unc45b:tfp) embryos compared with tg(−1.8unc45b:tfp) unc45b mutant showing twice as much TFP fluorescence in the mutant compared with the wild-type embryos. c Mean pixel intensity of tg(−505/−310(unc45b)gata2:gfp) embryos compared with tg(−505/−310(unc45b)gata2:gfp) injected with hsp90a-mo. The GFP intensity in the morphant is increased six times compared with wild type. d Mean pixel intensity of tg(−505/−310(unc45b)gata2:gfp) embryos compared to tg(−505/−310(unc45b)gata2:gfp) injected with unc45b-mo or unc45b-mo and hsf1-mo. The hsf1-mo abolished the increased GFP expression obtained with unc45b-mo alone. e Mean pixel intensity of tg(−505/−310(unc45b)gata2:gfp) embryos compared with tg(−505/−310(unc45b)gata2:gfp) injected with unc45b-mo or unc45b-mo and hsf2-mo. The hsf2-mo does not reduce the increased GFP expression obtained with unc45b-mo alone. f Mean pixel intensity of tg(−505/−310(unc45b)gata2:gfp) embryos compared with tg(−505/−310(unc45b)gata2:gfp) injected with unc45b-mo or unc45b-mo and hsf1cont-mo. The hsf1cont-mo does not reduce the increased GFP expression obtained with unc45b-mo alone. For each measurement at least three embryos were examined. For each chart the measured embryos are progeny of homozygous transgenics crossed with wild-type adult fish, and were exposed to the same light intensity. The error bars indicate "standard deviation". (PDF 498 kb)

a, b Sequence comparison of the unc45b region mediating the misfolded myosin response with homologous regions in the unc45b genes of other fish species. a Scheme of the 195-bp zebrafish unc45b fragment (−505 to −310 relative to the ATG) containing the HSE at position −446/−422 and the Mef2 binding site at position −335/−313. The recognition sequence is depicted below each site. b Comparison of the zebrafish unc45b sequence from −505 to −310 with regions in the unc45b genes of four other fish species revealed the presence of a conserved HSE element (black ovals). c–e Injection of −505/−405(unc45b)gata2:gfp plasmid into wild-type embryos (cont) (c) do not generate any GFP expression, whereas co-injection with unc45b-mo activates the regulatory sequence (c) (unc45b-mo). Examination of the GFP fibrils revealed classic striations (d, e, z) (Z-line). f injection of −505/−405(unc45b)gata2:gfp plasmid into hel mutant (hel−/−) or wild-type siblings (cont) do not lead to GFP0 expression. g, h Injection of −505/−310(unc45b)gata2:gfp plasmid into wild type (cont) (g, h), unc45b morphant (unc45b-mo) (g) or hel mutants (hel−/−) (h) show a GFP upregulation in unc45b morphant but not in hel mutants. (PDF 3322 kb)

The cornea is a central component of the camera eye of vertebrates and even slight corneal disturbances severely affect vision. The transcription factor PAX6 is required for normal eye development, namely the proper separation of the lens from the developing cornea and the formation of the iris and anterior chamber. Human PAX6 mutations are associated with severe ocular disorders such as aniridia, Peters anomaly and chronic limbal stem cell insufficiency. To develop the zebrafish as a model for corneal disease, we first performed transcriptome and in situ expression analysis to identify marker genes to characterise the cornea in normal and pathological conditions. We show that, at 7 days post fertilisation (dpf), the zebrafish cornea expresses the majority of marker genes (67/84 tested genes) found also expressed in the cornea of juvenile and adult stages. We also characterised homozygous pax6b mutants. Mutant embryos have a thick cornea, iris hypoplasia, a shallow anterior chamber and a small lens. Ultrastructure analysis revealed a disrupted corneal endothelium. pax6b mutants show loss of corneal epithelial gene expression including regulatory genes (sox3, tfap2a, foxc1a and pitx2). In contrast, several genes (pitx2, ctnnb2, dcn and fabp7a) were ectopically expressed in the malformed corneal endothelium. Lack of pax6b function leads to severe disturbance of the corneal gene regulatory programme.

Neocortical projection neurons, which segregate into six cortical layers according to their birthdate, have diverse morphologies, axonal projections and molecular profiles, yet they share a common cortical regional identity and glutamatergic neurotransmission phenotype. Here we demonstrate that distinct genetic programs operate at different stages of corticogenesis to specify the properties shared by all neocortical neurons. Ngn1 and Ngn2 are required to specify the cortical (regional), glutamatergic (neurotransmitter) and laminar (temporal) characters of early-born (lower-layer) neurons, while simultaneously repressing an alternative subcortical, GABAergic neuronal phenotype. Subsequently, later-born (upper-layer) cortical neurons are specified in an Ngn-independent manner, requiring instead the synergistic activities of Pax6 and Tlx, which also control a binary choice between cortical/glutamatergic and subcortical/GABAergic fates. Our study thus reveals an unanticipated heterogeneity in the genetic mechanisms specifying the identity of neocortical projection neurons.

Formation of the contractile myofibril of the skeletal muscle is a complex process which when perturbed leads to muscular dystrophy. Herein, we provide a mRNAseq dataset on three different zebrafish mutants affecting muscle organization during embryogenesis. These comprise the myosin folding chaperone unc45b (unc45b−/−), heat shock protein 90aa1.1 (hsp90aa1.1−/−) and the acetylcholine esterase (ache−/−) gene. The transcriptome analysis was performed in duplicate experiments at 72 h post-fertilization (hpf) for all three mutants, with two additional times of development (24 hpf and 48 hpf) for unc45b−/−. A total of 20 samples were analyzed by hierarchical clustering for differential gene expression. The data from this study support the observation made in Etard et al. (2015) [1] (http://dx.doi.org/10.1186/s13059-015-0825-8) that a failure to fold myosin activates a unique transcriptional program in the skeletal muscles that is different from that induced in stressed muscle cells. Keywords: Genetics, mRNASeq, Zebrafish, Muscle mutant, Development

Targeting the activation function-1 (AF-1) domain located in the N-terminus of the androgen receptor (AR) is an attractive therapeutic alternative to the current approaches to inhibit AR action in prostate cancer (PCa). Here we show that the AR AF-1 is bound by the cochaperone Bag-1L. Mutations in the AR interaction domain or loss of Bag-1L abrogate AR signaling and reduce PCa growth. Clinically, Bag-1L protein levels increase with progression to castration-resistant PCa (CRPC) and high levels of Bag-1L in primary PCa associate with a reduced clinical benefit from abiraterone when these tumors progress. Intriguingly, residues in Bag-1L important for its interaction with the AR AF-1 are within a potentially druggable pocket, implicating Bag-1L as a potential therapeutic target in PCa.

Ruthenium complexes are considered as potential replacements for platinum compounds in oncotherapy. Their clinical development is handicapped by a lack of consensus on their mode of action. In this study, we identify three histones (H3.1, H2A, H2B) as possible targets for an anticancer redox organoruthenium compound (RDC11). Using purified histones, we confirmed an interaction between the ruthenium complex and histones that impacted on histone complex formation. A comparative study of the ruthenium complex versus cisplatin showed differential epigenetic modifications on histone H3 that correlated with differential expression of histone deacetylase (HDAC) genes. We then characterized the impact of these epigenetic modifications on signaling pathways employing a transcriptomic approach. Clustering analyses showed gene expression signatures specific for cisplatin (42%) and for the ruthenium complex (30%). Signaling pathway analyses pointed to specificities distinguishing the ruthenium complex from cisplatin. For instance, cisplatin triggered preferentially p53 and folate biosynthesis while the ruthenium complex induced endoplasmic reticulum stress and trans-sulfuration pathways. To further understand the role of HDACs in these regulations, we used suberanilohydroxamic acid (SAHA) and showed that it synergized with cisplatin cytotoxicity while antagonizing the ruthenium complex activity. This study provides critical information for the characterization of signaling pathways differentiating both compounds, in particular, by the identification of a non-DNA direct target for an organoruthenium complex.