Journal: Molecular Systems Biology

Article Title: Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing

doi: 10.1038/msb.2010.110

Figure Lengend Snippet: Network cluster negatively regulated by Oaf1p is enriched 5–7 kb from telomeres. ( A ) Histogram of distance to closest telomere for targets of Oaf1p (in a network cluster enriched for those downregulated by Oaf1p) . More than 12% of these targets were found within 10 kb of telomeres, whereas only about 2% of all intergenic regions on the microarray were in this position. In contrast, network clusters upregulated by Oaf1p were not found within 10 kb of telomeres (data not shown). ( B ) High-resolution histogram of DNA segments within 10 kb of telomeres shows that the same targets are enriched 5–7 kb from telomeres (blue bars). The expected binding frequency if targets had no positional preference is shown (green vector). The region within 1 kb of telomeres had no detectable interaction with the factors, but <10% of this region was present on the microarrays (data not shown).

Article Snippet: For each replicate, linkers were annealed to DNA ends in whole-cell extract and IP fractions, and fragments were amplified by ligation-mediated PCR with high-fidelity Taq polymerase, and shipped to NimbleGen Systems of Iceland for labeling, hybridization, scanning and preliminary analysis as described below: Equal amounts of DNA in whole-cell extracts and IP fraction were labeled with Cy3 and Cy5, respectively, combined and co-hybridized at 42°C to microarrays of 50-mer DNA probes that span both strands of the entire genome positioned every 64 bp (resulting in 14 bases of DNA between probes).

Techniques: Microarray, Binding Assay, Plasmid Preparation

Journal: Molecular Systems Biology

Article Title: Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing

doi: 10.1038/msb.2010.110

Figure Lengend Snippet: Binding profiles of transcription factors (TFs) correlate with X-element positions. Subtelomeric-binding profiles are shown for factors found to enriched at X elements in . The densities of TF binding and X elements present on the microarrays are represented as heat maps. Binding conditions other than rich medium are marked with colored dots as in . With the exception of Phd1p, all factors had maximal binding 5–7 kb from telomeres, matching the position of X element enrichment. Pearson's correlation coefficients ( ρ ) comparing each binding profile to the positions of X elements are shown at the right.

Article Snippet: For each replicate, linkers were annealed to DNA ends in whole-cell extract and IP fractions, and fragments were amplified by ligation-mediated PCR with high-fidelity Taq polymerase, and shipped to NimbleGen Systems of Iceland for labeling, hybridization, scanning and preliminary analysis as described below: Equal amounts of DNA in whole-cell extracts and IP fraction were labeled with Cy3 and Cy5, respectively, combined and co-hybridized at 42°C to microarrays of 50-mer DNA probes that span both strands of the entire genome positioned every 64 bp (resulting in 14 bases of DNA between probes).

Techniques: Binding Assay