Project description:Methylation of Histone 3 Lysine 4 (H3K4) is largely associated with promoters and enhancers of actively transcribed genes and it is finely regulated during development by the action of histone methyltransferases and demethylases. H3K4me3 demethylases of the KDM5 family have been previously implicated in development, but how the regulation of H3K4me3 level controls developmental processes is not fully established. Here, we show that the H3K4 demethylase RBR-2, the unique member of the KDM5 family in C. elegans, acts cell-autonomously and in a catalytic- dependent manner to control vulva precursor cells fate acquisition, by promoting the LIN-12/Notch pathway. Using genome-wide approaches, we show that RBR-2 reduces the H3K4me3 level at transcription start sites (TSSs) and in regions upstream the TSSs, and acts both as a transcription repressor and activator. The analysis of the lin-11 genetic locus, a direct RBR-2 target gene required for vulva precursor cell fate acquisition, shows that RBR-2 controls the epigenetic signature of the lin-11 vulva- specific enhancer and lin-11 expression, providing in vivo evidences that RBR-2 can positively regulate transcription and cell fate acquisition by controlling enhancer activity.
Project description:The nucleosome remodeling and deacetylase (NuRD) complex is essential for gene expression and cell fate determination, and missense mutations of NuRD caused neurodevelopmental diseases. However, the molecular pathogenesisof clinic NuRD variants is unknown. Here, we introduced a clinic CHD3(L915F) variant into C. elegans homolog LET-418, impairing germline and vulva development and ultimately causing animal sterility. Our ATAC-seq and RNA-seq analyses revealed that this variant generated an abnormal open chromatin structure and disrupted the expression of developmental genes. Through genetic suppressor screens, we uncovered that intragenic mutations, likely renovating NuRD activity, restored animal viability. We also found that intergenic mutations in nucleosome remodeling factor NURF that counteracts NuRD rescued abnormal chromatin structure, gene expression, and animal sterility. We propose that two antagonistic chromatin-remodeling factors coordinate to establish the proper chromatin status and transcriptome and that inhibiting NURF may provide insights for treatment of NuRD mutation-related diseases.
Project description:The nucleosome remodeling and deacetylase (NuRD) complex is essential for gene expression and cell fate determination, and missense mutations of NuRD caused neurodevelopmental diseases. However, the molecular pathogenesisof clinic NuRD variants is unknown. Here, we introduced a clinic CHD3(L915F) variant into C. elegans homolog LET-418, impairing germline and vulva development and ultimately causing animal sterility. Our ATAC-seq and RNA-seq analyses revealed that this variant generated an abnormal open chromatin structure and disrupted the expression of developmental genes. Through genetic suppressor screens, we uncovered that intragenic mutations, likely renovating NuRD activity, restored animal viability. We also found that intergenic mutations in nucleosome remodeling factor NURF that counteracts NuRD rescued abnormal chromatin structure, gene expression, and animal sterility. We propose that two antagonistic chromatin-remodeling factors coordinate to establish the proper chromatin status and transcriptome and that inhibiting NURF may provide insights for treatment of NuRD mutation-related diseases.
Project description:Genome and transcriptome sequence data from an adenomacarcinoma of vulva patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
Project description:Genome and transcriptome sequence data from a squamous cell carcinoma of vulva patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study
Project description:Conserved Ras and Notch cell-signaling pathways promote Caenorhabditis elegans vulval cell fates. Ras pathway activity promotes the 1º vulval fate and inhibits the 2º vulval fate, and Notch pathway activity promotes the 2º vulval fate and inhibits the 1º vulval fate. Vulval cell fates are inhibited by the parallel-acting synthetic multivulva (synMuv) genes, which are grouped into either class A or B genes. We identified a new synMuv class B gene ccar-1, that works redundantly with class A genes to regulate vulva development. ccar-1 is activated by the Notch pathway to inhibit the Ras pathway in presumptive 2º vulval cells to ensure low levels of Ras pathway activity and proper 2º vulval fate specification. Our findings indicate that ccar-1 might inhibit the Ras pathway by repressing the transcription of the Ras pathway ligand lin-3 EGF. By analogy, we suggest that CCAR-1 might act as a tumor suppressor by inhibiting the expression of growth factor signals. Our study also highlights the identification of a first gain-of-function mutation that suppresses the synMuv phenotype.