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ABSTRACT: Epigenome analysis of Rh(III) in HeLa cell line

PROVIDER: PRJNA913445 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22799073_1.fastq.gz	Fastqsanger.gz
	SRR22799073_2.fastq.gz	Fastqsanger.gz
	SRR22799074_1.fastq.gz	Fastqsanger.gz
	SRR22799074_2.fastq.gz	Fastqsanger.gz
	SRR22799075_1.fastq.gz	Fastqsanger.gz

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Effect of Rh(III) on gene expression in HeLa cell line

Project description:We designed a highly emissive rhodium(III) complex ( Rh(III) complex) as the mtDNA intercalator. Rh(III) complex can specifically bind to mtDNA to cause the cytoplasmic release of mtDNA fragments to activate the cGAS-STING pathway. Moreover, Rh(III) complex activates the mitochondrial retrograde signaling by disturbing the key metabolites. Herein,we performed RNA-seq to illustrate the function of Rh(III) complex on HeLa cells. RNA-seq was performed on HeLa cells, which were treated by 1% DMSO or Rh(III) complex (1 uM, 6h), respectively.

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Effect of Rh(III) on gene expression in HeLa cell line

Project description:Effect of Rh(III) on gene expression in HeLa cell line

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Proteomic and metabolic changes in cancer cells after alternation of SHMT2 expressions

Project description:In order to understand the underline mechanism of SHMT2 (serine hydroxymethyltransferase 2) effect on tumor growth, proteome and metabolome analysis were carried on an engineered HeLa cell line (HeLa-SHMT2-shSHMT2, short as HeLa-Ss), which has inducible SHMT2 over-expression or suppression by treating cell with tetracycline or IPTG, respectively. SHMT2 over-expression in HeLa-ss cell increased cell proliferation in vitro and in vivo, deceased expression of several mitochondrial complex I and III proteins, and increased glycine and glutathione levels in cells. BioID method identified more than 20 SHMT2 associated proteins that are involved in oxidation-reduction process. These results indicate SHMT2 involves in the regulation of cellular redox balance. SHMT2 suppression only reduced growth of cells under glycine depletion condition in cell culture. It increased expression of several proteins involved in glutaminolysis and amino acid transporters, and elevated metabolites related to glutamine metabolism. These results indicate tumor cells have a compensatory reaction after SHMT2 suppression. Further reducing glycine levels in cells by sodium benzoate caused cell death in cultured cell and slightly reduced tumor growth in vivo. Benzoate treatment induces more changes in protein expressions and metabolite levels, and it may provide a new addition for tumor treatment.

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Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors.

Project description:RNA polymerase (Pol) III transcribes many noncoding RNAs (for example, transfer RNAs) important for translational capacity and other functions. We localized Pol III, alternative TFIIIB complexes (BRF1 or BRF2) and TFIIIC in HeLa cells to determine the Pol III transcriptome, define gene classes and reveal 'TFIIIC-only' sites. Pol III localization in other transformed and primary cell lines reveals previously uncharacterized and cell type–specific Pol III loci as well as one microRNA. Notably, only a fraction of the in silico–predicted Pol III loci are occupied. Many occupied Pol III genes reside within an annotated Pol II promoter. Outside of Pol II promoters, occupied Pol III genes overlap with enhancer-like chromatin and enhancer-binding proteins such as ETS1 and STAT1. Moreover, Pol III occupancy scales with the levels of nearby Pol II, active chromatin and CpG content. These results suggest that active chromatin gates Pol III accessibility to the genome. Use of ChIP-seq to identify genomic regions bound by RNA Polymerase III machinery in multiple cell types as well as RNA-seq in HeLa for gene expression analysis. See GSE20609 for whole human genome raw Pol III ChIP-array data. See link below for supplementary methods and analysis.

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