Comment[ArrayExpressAccession] E-GEOD-21852 Public Release Date 2011-05-02 Investigation Title Environment-responsive transcription factors bind proto-silencer elements and regulate subtelomeric silencing Comment[Submitted Name] Environment-responsive transcription factors bind proto-silencer elements and regulate subtelomeric silencing Experiment Description Subtelomeric chromatin is subject to evolutionarily conserved complex epigenetic regulation and is implicated in numerous aspects of cellular function including formation of heterochromatin, regulation of different stress response pathways, and control of lifespan. Subtelomeric DNA is characterized by the presence of specific repeated segments that serve to propagate silencing activities or to protect chromosomal regions from spreading epigenetic control. Using condition-specific genome wide chromatin immunoprecipitation and expression data, we show that several yeast transcription factors regulate subtelomeric silencing in response to various environmental stimuli through conditional association with proto-silencing regions called X elements. In this context, some factors control the propagation of silencing toward centromeres in response to stimuli affecting stress responses and metabolism, whereas others appear to influence boundaries of silencing, regulating telomere-proximal genes in Y’ elements. The factors implicated here have previously been shown to control adjacent genes at intrachromosomal positions, suggesting dual functionality of the factors and a possible mechanism of coordinating intrachromosomal gene expression with subtelomeric silencing. These data suggest a fundamental mechanism to coordinate telomere biology related to aging and adaptation with cellular environment and the activities of other cellular processes. These are Chip-CHIP data for myc tagged Oaf1p transcription factor from S. cerevisiae grown in the presence or absence of the fatty acid oleate. ChIP-CHIP analysis was performed to determine the genomic distribution of Oaf1p transcription factor in the BY4742 yeast strain after growth in 0.1% glucose, or in the presence of the fatty acid oleate. Three biological replicates for each growth condition (in the presence of low glucose or 5 h after a shift to medium containing oleate as a carbon source). ChIP samples were amplified by PCR, labelled and hybridized to 50-mer tiling arrays covering both strands of the entire yeast genome at a 64 bp resolution. Date of Experiment Term Source Name EFO Term Source Version Term Source File http://www.ebi.ac.uk/efo/efo.owl Person Last Name Smith Smith Miller Vazquez Wan Aitchison Person First Name Jennifer Jennifer Leslie Laura Yakun John Person Mid Initials Joy J D Person Email jsmith@systemsbiology.org Person Affiliation Institute for Systems Biology Person Phone 205-732-1304 Person Fax 206-732-1299 Person Address Institute for Systems Biology, 1441 North 34th Street, Seattle, WA, USA Person Roles submitter Person Roles Term Source REF Person Roles Term Accession Number Normalization Type Normalization Term Accession Number Normalization Term Source REF Replicate Type Replicate Term Accession Number Replicate Term Source REF Experimental Design Experimental Design Term Accession Number Experimental Design Term Source REF Quality Control Type Quality Control Term Accession Number Quality Control Term Source REF Protocol Name P-GSE21852-1 P-GSE21852-6 P-GSE21852-5 P-GSE21852-3 P-GSE21852-8 P-GSE21852-2 P-GSE21852-4 P-GSE21852-7 Protocol Description ID_REF =
VALUE = scaled, log2 (ChIP/WCE) ratio Performed by Roche NimbleGen by method described in the Chip User Guide at http://www.nimblegen.com/products/lit/ (version chip_userguide_2008_10_27.pdf). IP and WCE samples were pooled and co-hybridized to tiled arrays (platform GPL5683) at 42 degC by Roche NimbleGen by the method described in the Chip User Guide at http://www.nimblegen.com/products/lit/ (version chip_userguide_2008_10_27.pdf). This was done by previously a published method (Ren et al., Genome-wide location and function of DNA binding proteins. Science. 2000 Dec 22; 290(5500):2306-9). Proteins were crosslinked to their cognate DNA binding sites by incubating cultures with 3.7% formaldehyde for 20 min at RT and then for 16 h at 4 deg C. Cells were disrupted and chromatin sheared into fragments by glass bead lysis followed by sonication. myc-tagged factors were collected by ChIP with magnetic beads. Crosslinking was reversed in fractions of the ChIP and WCE, proteins and RNA were degraded by protease digestion and treatment with RNase A. DNA ends were blunted and linkers were ligated to the DNA ends. DNA was amplified by LM-PCR. Cells were grown in YPD overnight and subcultured in SCIM medium (1.7 g YNB without amino acids and ammonium sulfate/L, 0.5% yeast extract, 0.5% peptone, 0.79 g CSM/L, 5 g ammonium sulfate/L) containing 0.1% glucose for 16 h to a density of 8x10E6 cells/mL, and then transferred to fresh SCIM containing 0.1% glucose and grown for an additional 1.75 h. Cells were grown in YPD overnight and subcultured in SCIM medium (1.7 g YNB without amino acids and ammonium sulfate/L, 0.5% yeast extract, 0.5% peptone, 0.79 g CSM/L, 5 g ammonium sulfate/L) containing 0.1% glucose for 16 h to a density of 8x10E6 cells/mL, and then transferred to SCIM containing 0.15% oleate and 0.5% Tween 40, and grown for an additional 5 h. IP and WCE samples were labeled in separate reactions with Cy5 and Cy3, respectively by Roche NimbleGen by the method described in the chip user guide at http://www.nimblegen.com/products/lit (version chip_userguide_2008_10_27.pdf). Preliminary data processing was performed by Roche NimbleGen by method described in the Chip User Guide at http://www.nimblegen.com/products/lit/ (version chip_userguide_2008_10_27.pdf). NimbleScan software (version 2.4) was used to extract the data, calculate scaled log2-ratios of IP versus WCE, call peaks from ratio data, and map peaks to the transcription start site of genes (using the S. cerevisiae annotation file from NimbleGen (created on 2007-02-02)). Protocol Software Protocol Hardware Protocol Contact Protocol Type bioassay_data_transformation image_aquisition hybridization nucleic_acid_extraction grow grow labeling feature_extraction Protocol Term Source REF Protocol Term Accession Number Experimental Factor Name CHIP ANTIBODY Experimental Factor Type chip antibody Experimental Factor Term Source REF Experimental Factor Term Accession Number Publication Title Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Publication Author List Smith JJ, Miller LR, Kreisberg R, Vazquez L, Wan Y, Aitchison JD PubMed ID 21206489 Publication DOI 10.1038/msb.2010.110 Publication Status Publication Status Term Source REF Publication Status Term Accession Number Comment[SecondaryAccession] GSE21852 Comment[GEOLastUpdateDate] 2012-03-22 Comment[AEExperimentType] ChIP-chip by tiling array Comment[GEOReleaseDate] 2011-05-01 Comment[ArrayExpressSubmissionDate] 2010-05-13 SDRF File E-GEOD-21852.sdrf.txt