Unknown,Multiomics

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8

Expression data from lack of DNA topoisomerase I, DNA topoisomerase II and complete lack of both topoisomerases


ABSTRACT: Here we dissect the transcriptional response in S. cerevisiae cells lacking DNA topoisomerases. We use microarray technology coupled with a functional genomics approach and demonstrate intimate connections between topoisomerase dependency, promoter chromatin architecture and gene transcription. Our findings suggest that DNA topoisomerases I and II play a role for transcription initiation. We observe a genome wide reduction in mRNA levels and identify a distinct functional subset of the genome with particular requirements for topoisomerases. These genes are characterized by high transcriptional plasticity, they are chromatin regulated and distinguished by having an enrichment of a nucleosome at a critical position in the promoter region, suggesting that topoisomerases influence transcription initiation by affecting promoter chromatin structure. In further support of a role of topoisomerases for initiation, we demonstrate that genome wide topoisomerase dependency reflects transcriptional activity but not transcriptional length. We exemplify the importance of topoisomerases for initiation of chromatin-regulated genes by showing that the enzymes are essential although redundant for PHO5 induction and are necessary for a step required for promoter nucleosome removal. W303 versus top1Δ, top2ts and top1Δtop2ts. 3 biological replicates for each mutant versus wildtype counterpart amounting to 12 microarrays.

OTHER RELATED OMICS DATASETS IN: PRJNA127897

PROVIDER: E-GEOD-22809 | ExpressionAtlas | 2015-09-15

REPOSITORIES: ExpressionAtlas

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Publications

DNA Topoisomerases maintain promoters in a state competent for transcriptional activation in Saccharomyces cerevisiae.

Pedersen Jakob Madsen JM   Fredsoe Jacob J   Roedgaard Morten M   Andreasen Lotte L   Mundbjerg Kamilla K   Kruhøffer Mogens M   Brinch Marie M   Schierup Mikkel Heide MH   Bjergbaek Lotte L   Andersen Anni Hangaard AH  

PLoS genetics 20121220 12


To investigate the role of DNA topoisomerases in transcription, we have studied global gene expression in Saccharomyces cerevisiae cells deficient for topoisomerases I and II and performed single-gene analyses to support our findings. The genome-wide studies show a general transcriptional down-regulation upon lack of the enzymes, which correlates with gene activity but not gene length. Furthermore, our data reveal a distinct subclass of genes with a strong requirement for topoisomerases. These g  ...[more]

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