Unknown,Transcriptomics,Genomics,Proteomics

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


ABSTRACT: 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

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Andre Gerber 

PROVIDER: E-GEOD-16103 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Distinct roles of non-canonical poly(A) polymerases in RNA metabolism.

San Paolo Salvatore S   Vanacova Stepanka S   Schenk Luca L   Scherrer Tanja T   Blank Diana D   Keller Walter W   Gerber AndrĂ© P AP  

PLoS genetics 20090710 7


Trf4p and Trf5p are non-canonical poly(A) polymerases and are part of the heteromeric protein complexes TRAMP4 and TRAMP5 that promote the degradation of aberrant and short-lived RNA substrates by interacting with the nuclear exosome. To assess the level of functional redundancy between the paralogous Trf4 and Trf5 proteins and to investigate the role of the Trf4-dependent polyadenylation in vivo, we used DNA microarrays to compare gene expression of the wild-type yeast strain of S. cerevisiae w  ...[more]

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