Genome-wide occupancy of LSD1 in differentiating and differentiated C2C12 myoblasts.
ABSTRACT: ChIP-seq analysis of LSD1 in C2C12 cells. We found that LSD1 directly regulates the expression of fiber and metabolism genes during myogenesis. Results provide insight into the metabolic prgramming mechanisms of myogenesis. Overall design: Examination of LSD1/DNA interaction in C2C12 myoblasts 48 h (day 2) and 120 h (day 5) post-differentiation.
The metabolic properties of cells are formed under the influence of environmental factors such as nutrients and hormones. Although such a metabolic program is likely initiated through epigenetic mechanisms, the direct links between metabolic cues and activities of chromatin modifiers remain largely unknown. In this study, we show that lysine-specific demethylase-1 (LSD1) controls the metabolic program in myogenic differentiation, under the action of catabolic hormone, glucocorticoids. By using t ...[more]
Project description:ChIP-seq analysis of LSD1 in C2C12 cells. We found that LSD1 directly regulates the expression of fiber and metabolism genes during myogenesis. Results provide insight into the molecular mechanisms of myogenesis. Overall design: Examination of LSD1/DNA interaction in C2C12 myoblasts 48 h post-differentiation.
Project description:ChIP-seq analysis of methylated H3K4 in LSD1-inhibited C2C12 cells. We found that LSD1 widely regulates the methylation levels of H3K4. Results provide insight into the molecular mechanisms of regulation of histone modification in myogenesis. Overall design: Examination of H3, H3K4me1, H3K4me2 and H3K4me3/DNA interaction in LSD1-inhibited C2C12 myoblasts 48 h (day 2) post-differentiation.
Project description:Analysis of differentiating LSD1-KD C2C12 myoblasts. We found LSD1 is an important regulator of oxidative phenotypes in skeletal muscle cells. Results provide insight into the molecular mechanisms underlying roles of LSD1 in myocytes. Overall design: C2C12 cells were transfected with SureSilencing Plasmids harboring shRNA against LSD1 (shLSD1, #336312 KM27305H, Qiagen) and non-targeting control (shControl, Qiagen #336312). Stable transfectants were selected in the presence of hygromycin. The selected C2C12 cells were induced to differentiate. 48 hours later total RNAs were isolated and subjected with microarray analysis.
Project description:Analysis of differentiating C2C12 myoblasts treated with two LSD1 specific inhibitors. We found LSD1 is an important regulator of oxidative phenotypes in skeletal muscle cells. Results provide insight into the molecular mechanisms underlying roles of LSD1 in myocytes. Overall design: C2C12 cells were induced to differentiate with LSD1 inhibitors, tranylcypromine (TC) or S2101, or vehicle control. 48 hours later total RNAs were isolated and subjected with microarray analysis.
Project description:We performed total transcriptome analysis by RNA-seq to find novel long non-coding RNAs which are differentiatlly expressed in myogenesis or osteogenesis. Overall design: Total RNA extracted from C2C12 myoblasts, 3-days differentiated myotubes, and 3-days trans-differentiated osteoblasts using BMP2 was used for transcriptome analysis.
Project description:First, we aimed to identify genes whose transcript levels change at the onset of myogenic versus adipogenic differentiation of muscle precursors. We therefore compared RNA-seq results obtained from C2C12 cells differentiated for 1 day in myogenic and adipogenic medium. Out of these genes, we wanted to determine those whose expression was affected by altered Lsd1 levels. To this end, we performed RNA-seq in C2C12 cells upon LSD1 overexpression and Lsd1 knock-down in adipogenic medium and compared them to corresponding control cells. Overall design: Stable inducible LSD1 overexpressing C2C12 cell line was generated by infecting the cells with the lentivirus containing pSlik-Neo tetracycline-controlled transactivator (tTA) plasmid with Flag-tagged LSD1 construct downstream of the tetracycline-dependent promoter or empty vector and selecting with G418. To induce LSD1 overexpression, cells were treated with doxycycline (2 mg/ml) 48 h prior to differentiation and throughout the differentiation process. Lsd1 knock-down in C2C12 cells was induced by transfecting the cells with 20 nM siRNA against Lsd1 or unrelated control (Invitrogen) using DharmaFECT 3 reagent. Cells were differentiated for 1 day in adipogenic or myogenic medium and RNA was extracted with trizol. RNA integrity was confirmed by Bioanalyzer and cDNA library preparation and sequencing was performed (HiSeq 2000, paired-end, 100 bp). RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files). Reads were mapped to the mouse mm10 genome (NCBI Build 37) using TopHat version 2. The aligned reads were counted with the Homer software and differentially regulated genes were identified using EdgeR.
Project description:Maps of genomic regions in proximity to the nuclear lamina were determined in undifferentiated C2C12 myoblasts (MBs) and 6 day differentiated C2C12 myotubes (MTs) using DamID with a Dam-Lamin B1-encoding lentivirus. Overall design: Examination of Lamin B1-chromatin contacts in one cell line in undifferentiated myoblast and differentiated myotube conditions.