Project description:We profiled basal and bicuculline+4-AP inducible mRNA expression in cultured mouse hippocampal neurons with or without viral shRNA mediated knockdown of Kdm6b We harvested mRNA from neurons under four conditions (pLKO vector/treatment control, pLKO vector/3hr bicuculline+4AP, Kdm6b knockdown/treatment control,Kdm6b knockdown/3hr bicuculline+4AP). Libraries were generated and used for RNA sequencing.
Project description:We profiled basal and bicuculline+4-AP inducible mRNA expression in cultured mouse hippocampal neurons with or without viral shRNA mediated knockdown of Kdm6b
Project description:Background& Aims: The incidence of nonhepatitis B and nonhepatitis C viral (NBNC)- HCC has been rising in recent years due to the increase in NAFLD and NASH worldwide with fibrosis. However, the molecular mechanisms underlying the progression of these HCC are not fully understood. Here we observed that KDM6B, an H3K27 demethylase, was commonly downregulated in human NBNC-HCC and mouse NASH-related HCC by microarray analysis. The study aims to elucidate the molecular mechanism of KDM6B downregulation in NBNC-HCC including NASH-related HCC. Approach & Results: By immunohistochemistry, KDM6B expression was decreased in 28.7% of human HCC tissues, most of which were NBNC-HCC type. The low KDM6B expression group was accompanied by NASH in the adjacent liver. The KDM6B knockout (KO) HCC cells altered pathways of lipid metabolism by microarray and GSEA analysis. The KDM6B-KO cells significantly decreased lipid accumulation and cell reduction rates. Expression of two lipid-metabolism-related genes, G0S2 and ACSL1, were suppressed in the KDM6B-KO cells and the histone H3K27 trimethylation levels at the promoter regions were decreased when compared to the wild-type cells. Knockdown of G0S2 but not ACSL1 expression showed resistance to lipotoxicity in HCC cells. Moreover, inhibition of ATGL, a downstream target of G0S2, caused a decrease in lipid accumulation and cell proliferation. Conclusions: KDM6B regulates G0S2 expression via histone demethylation of its promoter region. Decreased KDM6B-dependent G0S2 expression through the histone modification pathway causes resistance to lipotoxicity, which may be involved in the carcinogenic mechanism of NASH-related HCC among NBNC-HCC.
Project description:To investigate overaccumulated TTC3 inhibits translation initiation in Ltn1 KO neurons, we established harringtonine treated WT and Ltn1 KO mice primary cultured cortical neurons with Ttc3 RNAi or scrambled RNAi. We then performed read (footprint) count analysis at translation initiation site using data obtained from RNA-seq (Ribo-seq).
Project description:To investigate how histone demethylases KDM4B and KDM6B may be involved in osteogenic commitment of mesenchymal stem cells (MSCs), we performed gene expression profiling and comparison on control, KDM4B- and KDM6B-knockdown MSCs at different stages of osteogenic differentiation. Human MSCs infected with scramble shRNAs, shRNAs against KDM4B or KDM6B are treated with BMP4/7 for 0, 4 and 24hrs. Total RNA were extracted from these 9 samples.
Project description:In this study, we have investigated the effect of lysine-specific demethylase 6B (KDM6B) on gene expression in normal human germinal center (GC) B cells using a non-viral vector-based system. Gene expression was compared between KDM6B-transfected and control vector-transfected GC B cells from three patients. RNA from the MACS-sorted transfected GC B cells was amplified. 10ug of fragmented cRNA was hybridized to HG-U133 Plus 2.0 microarrays. Differentially expressed genes were identified using Affymetrix GCOS pairwise analysis.
