Project description:Cells were treated with 5mM sodium butyrate treatment (HDAC) for one hour and resulting methylation states of Lysine 4 of histone H3 were observed.
Project description:In nucleosomes, histone N-terminal tails exist in dynamic equilibrium between free/accessible and collapsed/DNA-bound states. The latter state is expected to impact histone N-termini availability to the epigenetic machinery. Notably, H3 tail acetylation (e.g. K9ac, K14ac, K18ac) is linked to increased H3K4me3 engagement by the BPTF PHD finger, but it is unknown if this mechanism has a broader extension. Here, we show that H3 tail acetylation promotes nucleosomal accessibility to other H3K4 methyl readers, and importantly, extends to H3K4 writers, notably methyltransferase MLL1. This regulation is not observed on peptide substrates yet occurs on the cis H3 tail, as determined with fully-defined heterotypic nucleosomes. In vivo, H3 tail acetylation is directly and dynamically coupled with cis H3K4 methylation levels. Together, these observations reveal an acetylation 'chromatin switch' on the H3 tail that modulates read-write accessibility in nucleosomes and resolves the long-standing question of why H3K4me3 levels are coupled with H3 acetylation.
Project description:HEK-293 cells transfected with non-targeting control siRNA or UPF1LL-specific siRNA were treated with vehicle control, puromycin, or thapsigargin as indicated and used for total RNA-seq.
Project description:The aim of this study is to discover genes regulated by miR-204. Differential gene expression in HEK-293 cells transfected with miR-204-mimic compared to HEK-293 cells transfected with control oligo (HEK-293 control) was analyzed using the Agilent Human Whole Genome 4x44K gene expression array (Agilent Technologies, Santa Clara, CA).
Project description:The aim of this study is to discover genes regulated by miR-204. Differential gene expression in HEK-293 cells transfected with miR-204-mimic compared to HEK-293 cells transfected with control oligo (HEK-293 control) was analyzed using the Agilent Human Whole Genome 4x44K gene expression array (Agilent Technologies, Santa Clara, CA). HEK-293 cells were transfected with either miR-204 or a control, and gene expression was analyzed using the Agilent Human Whole Genome 4x44K array. A dye-swap was performed.
Project description:We used high-throughput sequencing to investigate the genome-wide transcriptional response in human cells to treatment with Borrelia burgdorferi. We chose a time point of 72 h as ticks feed on their host for several days and at the same time the early response in Lyme disease is expected to occur at this time period at a cellular level. We found that the two cell models studied (HUVEC and HEK-293 cells) had significantly different responses. More significantly differentially expressed genes (69 in total) were found in HUVEC cells than in HEK-293 cells (8 in total). Functional analysis indicated induction of the immune response in HUVEC and suggest changes in the extracellular matrix in HEK-293.
Project description:Human embryonal kidney cells (HEK-293) are the most common host cells used for transient recombinant adeno-associated virus (rAAV) production in pharmaceutical industry. To better cover the expected gene therapy product demands in the future, different traditional strategies such as cell line sub-cloning and/or addition of chemical substances to the fermentation media have been used to maximize titers and improve product quality. A more effective and advanced approach to boost yield can be envisaged by characterizing the transcriptome of different HEK-293 cell line pedigrees with distinct rAAV productivity patterns to subsequently identify potential gene targets for cell engineering. In this work, the mRNA expression profile of three HEK-293 cell lines, resulting in various yields during a fermentation batch process for rAAV production, was investigated to gain basic insight into cell variability and eventually to identify genes that correlate with productivity. Mock runs using only transfection reagents were performed in parallel as a control. We found significant differences in gene regulatory behaviors between the three cell lines at different growth and production stages. The evaluation of these transcriptomics profiles combined with collected in-process control parameters and titers shed some light on potential cell engineering targets to maximize transient production of rAAV in HEK-293 cells Comparison of three HEK-293 suspension cell lines transcriptomics during an AAV production process
Project description:To determine the target genes of RBM10,we have employed microarray based gene expression profiling by knocking down RBM10 in HEK 293 cells. Microarray analysis after RBM10 knockdown on HEK 293 cells showed that over 1000 genes were down regulated while another 800 genes up regulated as a result of the knockdown. Among the down regulated genes, we found the significant presence of cardiovascular disease related genes, especially cardiac hypertrophy and heart failure.
Project description:This SuperSeries is composed of the SubSeries listed below. GSE206058: Paired-end total RNA-seq of triplicate biological replicate treatments of HEK-293 cells with negative control siRNAs or siRNAs targeting ZFR, ILF2, or ILF3. GSE206059: eCLIP analysis of FLAG-ZFR binding in HEK-293 Flp-In TREx cell lines, with size-matched input control. GSE206060: RNA Bind-n-Seq of recombinantly expressed and purified ZFR-ILF2 complexes, with PTBP1 as a positive control for successful library generation.
Project description:HEK 293 cells with or without overexpression of ICER IIg were treated with forskolin for 0, 1 h, 2 h, 4 h or 8 h. The cell line used in the experiments is HEK 293 cells stable transfected with tetracycline-inducible ICER (Inducible cAMP early repressor) expression.