Project description:We explored the relationship between the distribution of DNase I hypersensitive site(DHSs) and levels of gene expression. Expression values from 5 to 11 are raw log2 ratio-transformed data from gene expression arrays. We found that the distribution of DHSs in promoter region and CpG islands is positively correlated with gene expression levels and 3’UTR DHSs are negatively correlated with active expression of genes. Total RNA obtained from HeLa S3 cells.
Project description:We explored the relationship between the distribution of DNase I hypersensitive site(DHSs) and levels of gene expression. Expression values from 5 to 11 are raw log2 ratio-transformed data from gene expression arrays. We found that the distribution of DHSs in promoter region and CpG islands is positively correlated with gene expression levels and 3’UTR DHSs are negatively correlated with active expression of genes.
Project description:Treatment with the histone deacetylase inhibitor trichostatin a (TSA) changes the radial positioning of the CFTR gene in HeLa S3 cells. The gene relocates from the nuclear periphery to the nuclear interior. In Calu-3 cells the gene is located in the nuclear interior. To identifiy potential regulatory elements for the positioning of CFTR, the histone h3 and h4 acetylation patterns of untreated and TSA-treated HeLa S3 and untreated Calu-3 cells were determined by ChIP-chip. A CTCF site close to the CFTR promoter displayed consistent histone H3 hyperacetylation in TSA treated HeLa S3 cells and Calu-3 cells.
Project description:The goal of this study was to define how loss of full-length DEK reshapes global transcriptional programs in HeLa S3 cells by comparing gene-expression profiles of wild-type (WT) HeLa S3 and the 1E7 DEK-knockout cells generated by TALEN-mediated genomic disruption. The 1E7 clone lacks detectable full-length DEK, while retaining a low-abundance truncated DEK species, consistent with an alternative transcriptional start site/allelic expression.
Project description:The distribution of histone variants H2Abbd and macroH2A in 13 regions of the HG18 assembly have been studied using a variant of the ChIP-on-Chip technique. HeLa S3 cell lines expressing tagged histones H2A, H2Abbd or macroHA were obtained using retroviral transfer. DNA fractions associated with tagged histones were isolated using a two-step purification procedure that involved affinity chromatography on a column with anti-FLAG antibodies, followed by affinity chromatography on a Ni-agarose column. The obtained genomic DNA samples were analyzed by hybridization with custom NimbleGene genomic microarrays. Two samples. Test sample 1 is HeLa S3 cells expressing epitope-tagged histone H2Abbd and test sample 2 is HeLa S3 cells expressing epitope-tagged histone macroH2A . The control for both test sample 1 and test sample 2 is HeLa S3 expressing epitope-tagged histone H2A. Two copies of each probe per array were made.
Project description:Mediator complex has been known as pivotal regulator of RNA polymerase II. Mediator complex has two CDK subunits in vertebrates, named CDK8 and CDK19. To elucidate functional difference between CDK8 and CDK19 in human cell, we employ siRNA mediate knockdown assay using HeLa S3 cell line. According to this assay these CDKs possess highly redundancy in HeLa S3 cell transcription regulation mechanism but in several genes, each CDK shows gene specific regulatory function.
Project description:Mediator complex has been known as pivotal regulator of RNA polymerase II. Mediator complex has two CDK subunits in vertebrates, named CDK8 and CDK19. To elucidate functional difference between CDK8 and CDK19 in human cell, we employ siRNA mediate knockdown assay using HeLa S3 cell line. According to this assay these CDKs possess highly redundancy in HeLa S3 cell transcription regulation mechanism but in several genes, each CDK shows gene specific regulatory function.