Genome-wide occupancy of H3K27me3 in human gingival mesenchymal and periodontal ligament stem cells in response to Electronic-cigarette
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ABSTRACT: The epigenetic regulation on gene transcription affected by Electronic-cigarette (E-cig) to human gingival mesenchymal (GMSC) is not fully understood. Here, we collected GMSCs from systemically healthy patients due to the premolars and extracted for orthodontic reasons, and treated with E-cig smoke with original flavor (G2), E-cig smoke with menthol flavor (G3), E-cig liquid with original flavor (G4), and E-cig liquid with menthol flavor (G5) by the optimal conditions of LC50, and conducted H3K27me3 ChIP-seq to compare with untreated control (G0).
Project description:The change of transcriptome and related biological functions affected by tobacco smoke and Electronic-cigarette (E-cig) to human gingival mesenchymal (GMSC) and periodontal ligament stem cells (PDLSCs) are not fully understood. Here, we collected GMSCs and PDLSCs from systemically healthy patients due to the premolars and extracted for orthodontic reasons, and treated with tobacco smoke (G1, P1), E-cig smoke with original flavor (G2, P2), E-cig smoke with menthol flavor (G3, P3), E-cig liquid with original flavor (G4, P4), and E-cig liquid with menthol flavor (G5, P5) by the optimal conditions of LC50, and conducted RNA-seq to compare with untreated control (G0, P0).
Project description:Analysis of primary human bronchial epithelial cells grown in air liquid interface, exposed in vitro to whole tobacco cigarette smoke (48 puffs, 48 minutes) and electronic cigarette aerosol (400 puffs, 200 minutes). Electronic cigarette exposures included two flavors (menthol, tobacco) both with, and without nicotine.
Project description:Menthol, a naturally occurring cooling compound of peppermint oil, induces an anti-proliferative activity in androgen-independent prostate cancer (AIPC). Previously, we found that menthol affects PC-3 cells viability through activating JNK but the mechanism is not fully clear. We thus studied that dysregulated cell cycle progression of PC-3 cells to menthol. We performed microarray experiments to obtain a global view of how menthol affects prostate cancer biology in gene expression profile. Our study demonstrated that menthol induced G2/M arrest by dysregulating PLK1 in the AICP cell model.
Project description:10^7 HL-60 cells were treated with 10 uM ATRA for two and five days. 10% whole cell lysates were saved as input after genomic DNA was broken into 200-500 bp by sonication. 1 μg IP grade antibodies of CTCF, H3K4me3 or H3K27me3 (CST, Boston, USA) were incubated with the rest of the lysate overnight, followed by 2 h protein-A beads incubation at 4 °C for target protein pull down. The CTCF enriched or H3K4/27me3 modified DNA or input DNA were repaired to 3’-dA overhang and added the ligated adapter. The DNA library was eliminated the unligated adapters and selected the appropriate size for sequence using an Illumina X Ten platform. The raw sequence reads of input and IP were trimmed adaptors and filter out low quality reads using Cutadapt (v1.9.1) and Trimmomatic (v0.35), and checked the quality of clean reads using Fastqc. Next, clean reads were mapped to the human genome (assembly hg38) using the Bowtie 2 (v2.2.6) algorithm. The process of peak calling (p<0.01) were performed by MACS 2 (v2.1.1) and analyzed the different binding domains based on FDR value less than 0.05 and annotated by DiffBind. De novo motif were analyzed using the R language and MEME. The peaks on certain genomic loci were visualized by Integrative Genomics Viewer (IGV). Gene ontology (GO) Analysis was used to interpret the biological function of the genes associated with differential peaks.
Project description:Gene expression patterns were assessed in normal human bronchial epithelial (NHBE) cells exposed to cigarette smoke (CS) from a typical "full flavor" American brand of cigarettes in order to develop a better understanding of the genomic impact of tobacco exposure, which can ultimately define biomarkers that discriminate tobacco-related effects and outcomes in a clinical setting. NHBE cells were treated with CS for 15 minutes and alterations to the transcriptome assessed at 1,2,4 and 24 hours post-CS-exposure using high-density oligonucleotide microarrays. Experiment Overall Design: Cells were exposed to smoke or air (âmock-exposedâ) for 15 min, after which they were refed with fresh media and allowed to incubate for 1h, 2h, 4h or 24h. Smoke and mock samples were compared at each time point.
Project description:The H3K27me3 is a repressive histone mark associated with repressive chromatin and is important for X chromosome inactivation. ChIP-chip of H3K27me3 along the mouse X chromosome in male and female livers and p12.5 embryos demonstrated that H3K27me3 is absent at the genes that escape X inactivation. Comparison of H3K27me3 enrichment along the X chromosome in male and female adult livers and P12.5 embryos
Project description:Gene expression patterns were assessed in normal human bronchial epithelial (NHBE) cells exposed to cigarette smoke (CS) from a typical "full flavor" American brand of cigarettes in order to develop a better understanding of the genomic impact of tobacco exposure, which can ultimately define biomarkers that discriminate tobacco-related effects and outcomes in a clinical setting. NHBE cells were treated with CS for 15 minutes and alterations to the transcriptome assessed at 1,2,4 and 24 hours post-CS-exposure using high-density oligonucleotide microarrays. Keywords: Time course
Project description:Menthol, a naturally occurring cooling compound of peppermint oil, induces an anti-proliferative activity in androgen-independent prostate cancer (AIPC). Previously, we found that menthol affects PC-3 cells viability through activating JNK but the mechanism is not fully clear. We thus studied that dysregulated cell cycle progression of PC-3 cells to menthol. We performed microarray experiments to obtain a global view of how menthol affects prostate cancer biology in gene expression profile. Our study demonstrated that menthol induced G2/M arrest by dysregulating PLK1 in the AICP cell model. Menthol was dissolved in ethanol as a vehicle at 0.1% working concentration and treated in PC-3 cells in triplicate Vehicle-treated PC-3 cells in triplicate were used as control.
Project description:Chromatin immunoprecipitation followed by Solexa sequencing for H3K27me3 and H3K79me2 in Fibroblasts, Embryonic stem cells, and fibroblast undergoing reprogramming Inhibition of the histone 3 lysine 79 (H3K79) methyltransferase increases repgoramming efficiency and genome-wide analysis of H3K79me2 distribution revealed that fibroblast-specific genes associated with the epithelial to mesenchymal transition lose H3K79me2 in the initial phases of reprogramming. Dot1L inhibition facilitates the loss of this mark from genes that are fated to be repressed in the pluripotent state.