Project description:We investigated the in vivo role of MLL3-dependent methylation of histone 3 lysine 4 at zeitgeber time 18, by performing H3K4me1 and H3K4me3 ChIP-seq in mouse liver, from MLL3 Delta mice and littermate wild-type controls.
Project description:The aim of this experiment was to decipher the role of retinoic acid receptor (RAR) on interleukin(IL)-17-producing gamma delta (gdT17) T cells. Therefore we generated mice where RAR activity is defective specifically in cells expressing the transcription factor RORgt, which is constitutively on in gdT17 cells. From these mice and their littermate controls we FACS-sorted the two major gdT17 populations from the lymph node (Vg4+ and Vg4-) and subjected them to RNA-seq.
Project description:Gene expression in the the pancreatic lymph node of 4, 12, and 30 week old Deaf1-knockout (KO) mice compared to BALB/c littermate controls.
Project description:The total liver proteomes of postnatal-day-7 mice with liver-specific UBA3 deficiency and their littermate controls were compared by two-dimensional (2-D) electrophoresis mapping. 25 protein spots were obviously changed in their expression upon UBA3 deficiency. These 25 protein spots were excised from 2-D gels. After in-gel digestion, the tryptic digests were subjected to mass spectrometric analysis by LC–MS/MS, followed by database searching. Here, we identified ETFA expression in spot 14, which was decreased in UBA3-deficient conditions.
Project description:Dual oxidases play a role in innate host defense at barrier epithelia. We examined the effect of loss of dual oxidase function (duoxa-/-) on gene expression in the mouse terminal ileum at homeostasis. To control for cage/litter effects, duoxa-/- were cohoused with wild type littermate controls.
Project description:FOXA1 is a pioneer factor that is important in hormone dependent cancer cells to stabilise nuclear receptors, such as estrogen receptor (ER) to chromatin. FOXA1 binds to enhancers regions that are enriched in H3K4mono- and dimethylation (H3K4me1, H3K4me2) histone marks and evidence suggests that these marks are requisite events for FOXA1 to associate with enhancers to initate subsequent gene expression events. However, exogenous expression of FOXA1 has been shown to induce H3K4me1 and H3K4me2 signal at enhancer elements and the order of events and the functional importance of these events is not clear. We performed a FOXA1 Rapid Immunoprecipitation Mass Spectrometry of Endogenous Proteins (RIME) screen in ERα-positive MCF-7 breast cancer cells in order to identify FOXA1 interacting partners and we found histone-lysine N-methyltransferase (MLL3) as the top FOXA1 interacting protein. MLL3 is typically thought to induce H3K4me3 at promoter regions, but recent findings suggest it may contribute to H3K4me1 deposition, in line with our observation that MLL3 associates with an enhancer specific protein. We performed MLL3 ChIP-seq in breast cancer cells and unexpectedly found that MLL3 binds mostly at non-promoter regions enhancers, in contrast to the prevailing hypothesis. MLL3 was shown to occupy regions marked by FOXA1 occupancy and as expected, H3K4me1 and H3K4me2. MLL3 binding was dependent on FOXA1, indicating that FOXA1 recruits MLL3 to chromatin. Motif analysis and subsequent genomic mapping revealed a role for Grainy head like protein-2 (GRHL2) which was shown to co-occupy regions of the chromatin with MLL3. Regions occupied by all three factors, namely FOXA1, MLL3 and GRHL2, were most enriched in H3K4me1. MLL3 silencing decreased H3K4me1 at enhancer elements, but had no appreciable impact on H3K4me3 at enhancer elements. We identify a complex relationship between FOXA1, MLL3 and H3K4me1 at enhancers in breast cancer and propose a mechanism whereby the pioneer factor FOXA1 can interact with a chromatin modifier MLL3, recruiting it to chromatin to facilitate the deposition of H3K4me1 histone marks, subsequently demarcating active enhancer elements.
Project description:Transcriptional profiles were compared in microdissected lateral walls of the inner ears from Errb mutant mice and wild type littermate controls. The goal is to identify transcriptional targets of Errb and candidate genes for inner ear diseases. Experiment Overall Design: Errb mutant mice were generated by conditional knock-out strategy. Inner ears from 10 mice were pooled for each sample and 3 replicates of wild type and mutant samples were analyzed.