Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Short-term time course of the effects of 1Î±,25-dihydroxyvitamin D3 treatment on open chromatin regions in THP-1 monocytic leukemia cells

ABSTRACT: Open chromatin regions have been shown to associate with the location of transcriptiotal enhancers, i.e., the binding locations of DNA-binding transcription factors. To investigate the effects of short-term treatment by the nuclear hormone 1Î±,25-dihydroxyvitamin D3 (VD), a specific ligand of the transcription factor vitamin D receptor, on chromatin accessibility, FAIRE-seq was utilized on the chromatin samples from THP-1 monocytic leukemia cells that were treated with 100 nM 1Î±,25-dihydroxyvitamin D3 for 20, 40, 60, 80, 100 and 120 min, or with vehicle (0.1% (v/v) ethanol) for 20 and 100 min. THP-1 monocytic leukemia cells were treated with 100 nM 1Î±,25-dihydroxyvitamin D3 for 20, 40, 60, 80, 100 and 120 min or with vehicle (0.1% (v/v) ethanol) for 20 and 100 min. Chromatin sample from one biological replicate for each time point was subjected to the FAIRE-seq protocol and subsequent data analysis using an Input chromatin sample as control.

ORGANISM(S): Homo sapiens

SUBMITTER: Sami Heikkinen

PROVIDER: E-GEOD-40075 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1α,25-dihydroxyvitamin D3 and histone deacetylase inhibitors on gene expression.

Seuter Sabine S Heikkinen Sami S Carlberg Carsten C

Nucleic acids research 20121023 1

The nuclear hormone 1α,25-dihydroxyvitamin D(3) (1α,25(OH)(2)D(3) or 1,25D) regulates its target genes via activation of the transcription factor vitamin D receptor (VDR) far more specifically than the chromatin modifier trichostatin A (TsA) via its inhibitory action on histone deacetylases. We selected the thrombomodulin gene locus with its complex pattern of five VDR binding sites and multiple histone acetylation and open chromatin regions as an example to investigate together with a number of ...[more]

PMID: 23093607

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Project description:To investigate chromatin organization dynamics during the transition from vegetative growth to meiosis, we used Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in vegetative cells (YPD) and in cells undergoing synchronous meiosis/sporulation in the budding yeast Saccharomyces cerevisiae. There is growing recognition that the binding of a transcription factor near a gene does not always indicate regulatory function, and further that a single factor may function to either activate or repress its targets depending on the cellular context. We examined these issues through a series of experiments involving the S. cerevisiae transcription factor Rap1, and its function throughout critical metabolic and developmental transitions between vegetative growth, respiratory growth, meiosis and sporulation. We simultaneously monitored the expression of all genes and the genomic binding locations of Rap1 throughout the timecourse. Genes downstream of Rap1 binding were activated and repressed dynamically, but a change - or lack of change - in Rap1 binding status was not predictive of activation, repression, or no change in regulation. Despite this, we show that Rap1 is required, at a given point in time, for both activation and repression of different gene targets, within the same cell. Specification of the transcriptional consequences of Rap1 binding is thus highly promoter-specific. The presence of other transcription factor binding motifs, the subtype of Rap1 motif, and the underlying chromatin structure of the promoter cannot fully account for the observed transcriptional outcomes. There is a better accounting for the dynamic binding behavior of Rap1 including specification of an expanded meiotic target set through a Tup1- dependent nucleosome-loss mechanism. The variable and dynamic association between binding and transcription in this simple unicellular system portends a similarly volatile relationship in more complex eukaryotes. Biological interpretations of transcription factor occupancy should be made cautiously and in conjunction with supporting data obtained under the precise condition of interest. SK1 yeast strain SHy002 (MATa/MATÎ± ho::LYS2/ho::LYS2 leu2::hisG/leu2::hisG lys2/lys2 ura3/ura3). Meiosis timecourse with samples collected during vegetative growth (YPD), and 0 hr, 1.5hr, and 3hr after transfer to sporulation media (SM). 3 separate biological replicates were used for each condition/time-point. Labeled FAIRE enriched DNA from each sample and a labeled genomic DNA common reference were competitively hybridized to Agilent yeast whole genome 4 x 44k tiling microarrays (resolution ~270bp). The Rap1 ChIP, RNA abundance/expression analysis, and FAIRE analysis were all carried out on the same biological samples. The three FAIRE timecourse replicates correspond to timecourse replicates 1, 4, and 6.

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Dataset Information

Short-term time course of the effects of 1Î±,25-dihydroxyvitamin D3 treatment on open chromatin regions in THP-1 monocytic leukemia cells

Publications

Chromatin acetylation at transcription start sites and vitamin D receptor binding regions relates to effects of 1α,25-dihydroxyvitamin D3 and histone deacetylase inhibitors on gene expression.

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