Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of human fibroblast cell cultures treated with resveratrol against DMSO treated controls, with and without siRNA treatment targeting SIRT1

ABSTRACT: Resveratrol (RSV) is a small compound with many reported beneficial effects, including increased expression of genes involved in inborn errors of metabolism. We wanted to investigate the effects of RSV on gene regulation on a global scale in order to detect new target genes for RSV mediated up-regulation with respect to disease treatment. Because fibroblasts are widely used diagnostically and reflect many metabolically important tissues well, we chose to investigate normal fibroblasts treated with RSV. We performed this with and without knock down of sirtuin 1 (SIRT1) since SIRT1 has been reported as a key mediator of RSV effects. We performed Next Generation Sequencing of RNA on 2 normal fibroblast cell line with and without the respective treatments.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Homo sapiens

SUBMITTER: Henriette Andersen

PROVIDER: E-MTAB-7360 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Beneficial effects of SIRT1 on healthspan are likely to be pleiotropic and may include effects on DNA methylation. We demonstrated recently that manipulating SIRT1 in human cells affected DNA methylation of a panel of test genes, and that genes with expression modified by dietary restriction corresponded with genes that underwent changes in DNA methylation during ageing. Here we tested the hypothesis that genes particularly susceptible to SIRT1-induced effects on DNA methylation across the genome map to genes for which DNA methylation changes during ageing. We increased or reduced SIRT1 expression in human intestinal (Caco-2) and vascular endothelial (HuVEC) cells by transient transfection with an expression construct or with siRNA, respectively. Effects on DNA methylation were measured by enriching for the methylated fraction then either sequencing (HuVEC) or hybridising to a human promoter microarray (Caco-2). Effects using these two different cell lines and techniques for analysis were remarkably consistent. Genes with a DNA methylation status affected by SIRT1 manipulation were enriched for those that undergo age-dependent changes in DNA methylation, thus supporting our hypothesis. Polycomb group protein target genes (PCGTs), which are suppressed by epigenetic mechanisms in stem cells and have been shown previously to correspond with loci particularly susceptible to age-related changes in DNA methylation, were over-represented within the set of genes showing altered DNA methylation in response to SIRT1 manipulation in both cell lines. We thus propose that effects of SIRT1 to extend healthspan include influences on the DNA methylation status of genes affected during ageing, in particular PCGTs. Analysis of methylation profiles of Caco-2 cells meeting the following conditions: SIRT1 overexpressed by transfection with pCMV6-ENTRY-SIRT1 (2 replicates), corresponding vector control (2 replicates), each of the siRNAs that target SIRT1 (1 & 2 replicates, respectively) and control siRNA (2 replicates).

Dataset Information

RNA-seq of human fibroblast cell cultures treated with resveratrol against DMSO treated controls, with and without siRNA treatment targeting SIRT1

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