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Coupled evolution of transcription and mRNA degradation.

Dori-Bachash M, Shema E, Tirosh I - PLoS Biol. (2011)

Bottom Line: Surprisingly, we find that around half of the evolutionary changes in mRNA degradation were coupled to transcriptional changes that exert opposite effects on mRNA levels.Coupled changes are associated with divergence of two complexes that were previously implicated both in transcription and in mRNA degradation (Rpb4/7 and Ccr4-Not), as well as with sequence divergence of transcription factor binding motifs.These results suggest that an opposite coupling between the regulation of transcription and that of mRNA degradation has shaped the evolution of gene regulation in yeast.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

ABSTRACT
mRNA levels are determined by the balance between transcription and mRNA degradation, and while transcription has been extensively studied, very little is known regarding the regulation of mRNA degradation and its coordination with transcription. Here we examine the evolution of mRNA degradation rates between two closely related yeast species. Surprisingly, we find that around half of the evolutionary changes in mRNA degradation were coupled to transcriptional changes that exert opposite effects on mRNA levels. Analysis of mRNA degradation rates in an interspecific hybrid further suggests that opposite evolutionary changes in transcription and in mRNA degradation are mechanistically coupled and were generated by the same individual mutations. Coupled changes are associated with divergence of two complexes that were previously implicated both in transcription and in mRNA degradation (Rpb4/7 and Ccr4-Not), as well as with sequence divergence of transcription factor binding motifs. These results suggest that an opposite coupling between the regulation of transcription and that of mRNA degradation has shaped the evolution of gene regulation in yeast.

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Enrichment of opposite effects only for cis-cis and trans-trans combinations supports a mechanistic coupling.Inter-species differences in mRNA levels (or estimated transcription rates) and mRNA degradation were divided into the contribution of cis- and trans-mutations based on the hybrid data. The enrichment of opposite transcription and degradation effects was examined for each of the four combinations of cis and trans, by a sliding window analysis of the percentage of opposite effects as a function of the fold-changes in mRNA degradation.
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pbio-1001106-g004: Enrichment of opposite effects only for cis-cis and trans-trans combinations supports a mechanistic coupling.Inter-species differences in mRNA levels (or estimated transcription rates) and mRNA degradation were divided into the contribution of cis- and trans-mutations based on the hybrid data. The enrichment of opposite transcription and degradation effects was examined for each of the four combinations of cis and trans, by a sliding window analysis of the percentage of opposite effects as a function of the fold-changes in mRNA degradation.

Mentions: If coupled changes in transcription and degradation are due to independent mutations, then each change can be either in cis or in trans, and thus the coupling should be observed for all combination of cis- and trans-effects; for example, cis-effects in mRNA degradation should be coupled both to cis-effects in transcription (cis-cis combination) and to trans-effects in transcription (cis-trans combination). However, if transcription and degradation changes are mechanistically coupled and the observed opposite effects are generated by the same individual mutations, then these coupled changes would be generated by a single effect, either in cis (cis-cis combination) or in trans (trans-trans combination), but not by cis-trans or trans-cis combinations. Consistent with this, a strong coupling is observed only for cis-cis and trans-trans combinations but not for cis-trans or trans-cis combinations (Figure 4).


Coupled evolution of transcription and mRNA degradation.

Dori-Bachash M, Shema E, Tirosh I - PLoS Biol. (2011)

Enrichment of opposite effects only for cis-cis and trans-trans combinations supports a mechanistic coupling.Inter-species differences in mRNA levels (or estimated transcription rates) and mRNA degradation were divided into the contribution of cis- and trans-mutations based on the hybrid data. The enrichment of opposite transcription and degradation effects was examined for each of the four combinations of cis and trans, by a sliding window analysis of the percentage of opposite effects as a function of the fold-changes in mRNA degradation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3139634&req=5

pbio-1001106-g004: Enrichment of opposite effects only for cis-cis and trans-trans combinations supports a mechanistic coupling.Inter-species differences in mRNA levels (or estimated transcription rates) and mRNA degradation were divided into the contribution of cis- and trans-mutations based on the hybrid data. The enrichment of opposite transcription and degradation effects was examined for each of the four combinations of cis and trans, by a sliding window analysis of the percentage of opposite effects as a function of the fold-changes in mRNA degradation.
Mentions: If coupled changes in transcription and degradation are due to independent mutations, then each change can be either in cis or in trans, and thus the coupling should be observed for all combination of cis- and trans-effects; for example, cis-effects in mRNA degradation should be coupled both to cis-effects in transcription (cis-cis combination) and to trans-effects in transcription (cis-trans combination). However, if transcription and degradation changes are mechanistically coupled and the observed opposite effects are generated by the same individual mutations, then these coupled changes would be generated by a single effect, either in cis (cis-cis combination) or in trans (trans-trans combination), but not by cis-trans or trans-cis combinations. Consistent with this, a strong coupling is observed only for cis-cis and trans-trans combinations but not for cis-trans or trans-cis combinations (Figure 4).

Bottom Line: Surprisingly, we find that around half of the evolutionary changes in mRNA degradation were coupled to transcriptional changes that exert opposite effects on mRNA levels.Coupled changes are associated with divergence of two complexes that were previously implicated both in transcription and in mRNA degradation (Rpb4/7 and Ccr4-Not), as well as with sequence divergence of transcription factor binding motifs.These results suggest that an opposite coupling between the regulation of transcription and that of mRNA degradation has shaped the evolution of gene regulation in yeast.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

ABSTRACT
mRNA levels are determined by the balance between transcription and mRNA degradation, and while transcription has been extensively studied, very little is known regarding the regulation of mRNA degradation and its coordination with transcription. Here we examine the evolution of mRNA degradation rates between two closely related yeast species. Surprisingly, we find that around half of the evolutionary changes in mRNA degradation were coupled to transcriptional changes that exert opposite effects on mRNA levels. Analysis of mRNA degradation rates in an interspecific hybrid further suggests that opposite evolutionary changes in transcription and in mRNA degradation are mechanistically coupled and were generated by the same individual mutations. Coupled changes are associated with divergence of two complexes that were previously implicated both in transcription and in mRNA degradation (Rpb4/7 and Ccr4-Not), as well as with sequence divergence of transcription factor binding motifs. These results suggest that an opposite coupling between the regulation of transcription and that of mRNA degradation has shaped the evolution of gene regulation in yeast.

Show MeSH
Related in: MedlinePlus