Wild-type versus trf4, trf5, and trf4-DADA mutant cells

Measurement of the relative changes of gene expression of S. cerevisiae cells lacking either trf4 (trf4delta) or trf5 (trf5delta), and trf4delta/TRF4-DADA mutants compared to wild-type (WT) cells using yeast oligo microarrays that contain features representing all annotated yeast ORFs, ncRNAs, introns, rRNA precursors, as well as some intergenic regions (IGRs) and tiled regions downstream of a few genes. Total RNA was isolated by hot phenol extraction from exponentially growing cells, and reverse transcribed with a mixture of random nonamers and oligo(dT) primers in the presence of amino-allyl dUTP/dNTP mixture. Cy5 fluorescently labeled cDNAs derived from total RNA isolated from either the trf4delta or the trf5delta mutants, and the trf4delta/TRF4-DADA mutants were then competitively hybridized with Cy3 labeled cDNAs from WT cells. cDNAs were hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. mutated gene: paralogous non-canonical poly(A) polymerases Trf4p and Trf5p forming TRAMP4 and TRAMP5 complexes Computed