ArticleProceedings of the National Academy of Sciences of the United States of America2005
Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers.
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151 citing papers in PubMed, 272 citations in OpenAlex.
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- Species-aware DNA language models capture regulatory elements and their evolution.Genome biology · 2024Article
- Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum.Genetics · 2024Article
- Rapid evolutionary repair by secondary perturbation of a primary disrupted transcriptional network.EMBO reports · 2023Article
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- Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data.Genome biology and evolution · 2019Article
- Functional duplication of Rap1 in methylotrophic yeasts.Scientific reports · 2019Article
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- Patterns of Conservation and Diversification in the Fungal Polarization Network.Genome biology and evolution · 2018Article
91 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcriptional modules of coregulated genes play a key role in regulatory networks. Comparative studies show that modules of coexpressed genes are conserved across taxa. However, little is known about the mechanisms underlying the evolution of module regulation. Here, we explore the evolution of cis-regulatory programs associated with conserved modules by integrating expression profiles for two yeast species and sequence data for a total of 17 fungal genomes. We show that although the cis-elements accompanying certain conserved modules are strictly conserved, those of other conserved modules are remarkably diverged. In particular, we infer the evolutionary history of the regulatory program governing ribosomal modules. We show how a cis-element emerged concurrently in dozens of promoters of ribosomal protein genes, followed by the loss of a more ancient cis-element. We suggest that this formation of an intermediate redundant regulatory program allows conserved transcriptional modules to gradually switch from one regulatory mechanism to another while maintaining their functionality. Our work provides a general framework for the study of the dynamics of promoter evolution at the level of transcriptional modules and may help in understanding the evolvability and increased redundancy of transcriptional regulation in higher organisms.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.