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:The regulation of gene expression in the developing brain is coordinated by changes in chromatin regulation. Chromatin regulation involves the deposition and removal of molecular modifications on the histone proteins that give structure to and control the function of genomic DNA. The trimethylation of histone H3 at lysine 27 (H3K27me3) is a chromatin mark that recruits transcriptional repressors, silencing gene transcription. The JmjC family lysine demethylase KDM6B has been identified as an enzyme that removes H3K27me3, allowing for expression of genes critical for brain development. Genetic variants in human KDM6B have been found to be associated with intellectual disability and autism spectrum disorder (ASD); however, the molecular mechanisms by which these genetic variants affect KDM6B function remain unknown. We mapped these variants into the structure of KDM6B, and computationally assessed their likely effects on KDM6B protein function. To experimentally determine how ASD-associated sequence variants in KDM6B affect the function of this protein in cells, we generated ASD-associated mutations into a KDM6B expression construct and assessed their effects on the enzymatic function of this protein as well as its stability and nuclear localization. We found that several ASD-associated mutations occur in the H3K27me3 binding pocket of KDM6B and impair the ability of this enzyme to demethylate histones. In parallel, through RNA sequencing experiments in cerebellar granule neurons from mouse, we found that expression of the enzymatically active form but not the enzymatically dead form of KDM6B was sufficient to rescue synaptic gene expression following knockdown of endogenous KDM6B. Together, these findings elucidate a novel role of KDM6B in controlling gene expression in maturing neurons, and they expand our knowledge on how chromatin dysregulation can lead to neurodevelopmental disorders like ASD.
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:This study aims to characterize the transcriptome in wild type and Kdm6b B KO pre-Plasma germinal center B cells, and find the potential mechanism of the Kdm6b B KO pre-Plasma germinal center B cells。
Project description:This study aims to characterize the H3K27me3 modification in wild type and Kdm6b B KO pre-Plasma germinal center B cells, and find the potential mechanism of the Kdm6b B KO pre-Plasma germinal center B cells。
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:This study aims to characterize the H3K27me3 modification in wild type and Gls CD19cre B KO or Efnb1 ai3 B KO or Kdm6b OE CD83+ly75+GCB cells, and find the potential mechanism of the Gls CD19cre B KO or Efnb1 ai3 B KO or Kdm6b OE CD83+ly75+GCB cells。
