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YeastInteractionRewiring

Page history last edited by PBworks 16 years, 6 months ago

Yeast Transcriptional Rewiring

Pubmed reference

 

Sadly, my first example is one that I am familiar with but it is not open access. Once other examples are posted I can remove this one. I'll do my best to do a very rough summary from a previous presentation.

 

Yeast, a group of single celled eukaryotic organisms that exhibit strong gene conservation and different species exhibit major phenotypic differences.

 

Researchers made a gene-gene correlation matrix from 1000 published genome-wide expression profiles (note they didn't do the experiments themselves, they used the available data). They asked "if gene A is upregulated in the microarray data, is gene B regulation correlated? Is it upregulated at the same time, downregulated at the same time or is there no correlation?". They specificially looked at a few gene classes for an aerobe versus an anaerobe. Ribosomal proteins (RP) and rRNA are associated with fast growth. Stress genes (STR) are associated with a stress response. The final set they examined was mitochondrial ribosomal proteins (MRP). These are associated with metabolism with oxygen. The MRP group they found was upregulated along with fast growth genes in the aerobes (while stress genes were downregulated - these cells are in oxygen and are happy to grow quick and they aren't stressed). Meanwhile, the same MRP group was upregulated with the stress genes (while fast growing associated genes were downregulated) for the anaerobes. Anaerobes don't like oxygen, utilizing oxygen is now associated with a stress response and not fast growth.

 

 

(For figure, red is positive correlation, blue is negative correlation).

 

What the researchers identified was a class of genes that were upregulated with fast growth in the aerobe but downregulated with fast growth in the anaerobe. They then tried to identify exactly how the switch happened. Was there a change in the promoter element in front of these genes? Or did a transcription factor that bound to these promoters change so that it no longer recognized a promoter. What they then did is take their aerobe group and anaerobe group and look upstream of the MRP genes in the promoter region to see if there was a conserved region. They found in the aerobe there was a conserved AATTTT but this motif was absent in the anerobe. They looked at where this AATTTT motif was located in the promoter by comparing all the promoters and compared its presence or absence in different species. Using this information they asked if the AATTTT motif appeared recently or if it was present in ancestors and had been lost by a more recent subgroup.

 

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Figures belong to Science Magazine article

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