ArticleMolecular systems biology2012
A functional selection model explains evolutionary robustness despite plasticity in regulatory networks.
Article in Molecular systems biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed, 51 citations in OpenAlex.
- Extensive binding of poorly characterized human transcription factors to genomic dark matter.Nature communications · 2026Article
- CroCoNet: a framework for the quantitative comparison of gene regulatory networks across species.Genome biology · 2026Article
- Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts.Molecular biology and evolution · 2026Article
- Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells.Genome biology · 2024Article
- Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells.bioRxiv : the preprint server for biology · 2023Article
- FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi.PLoS computational biology · 2023Article
- Article
- Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Transcriptional enhancers and their communication with gene promoters.Cellular and molecular life sciences : CMLS · 2021Review
- Evolutionary dynamics of microRNA target sites across vertebrate evolution.PLoS genetics · 2020Article
- Functional duplication of Rap1 in methylotrophic yeasts.Scientific reports · 2019Article
- Patterns of Conservation and Diversification in the Fungal Polarization Network.Genome biology and evolution · 2018Article
- Systematic and synthetic approaches to rewire regulatory networks.Current opinion in systems biology · 2018Article
- Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human PathogenFrontiers in microbiology · 2018Article
- The rewiring of transcription circuits in evolution.Current opinion in genetics & development · 2017Review
- How transcription circuits explore alternative architectures while maintaining overall circuit output.Genes & development · 2017Review
- Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies.Cell systems · 2017Article
- Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway.eLife · 2017Article
- Evolution of transcriptional networks in yeast: alternative teams of transcriptional factors for different species.BMC genomics · 2016Article
- Assessment of transfer methods for comparative genomics of regulatory networks in bacteria.BMC bioinformatics · 2016Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Evolutionary rewiring of regulatory networks is an important source of diversity among species. Previous evidence suggested substantial divergence of regulatory networks across species. However, systematically assessing the extent of this plasticity and its functional implications has been challenging due to limited experimental data and the noisy nature of computational predictions. Here, we introduce a novel approach to study cis-regulatory evolution, and use it to trace the regulatory history of 88 DNA motifs of transcription factors across 23 Ascomycota fungi. While motifs are conserved, we find a pervasive gain and loss in the regulation of their target genes. Despite this turnover, the biological processes associated with a motif are generally conserved. We explain these trends using a model with a strong selection to conserve the overall function of a transcription factor, and a much weaker selection over the specific genes it targets. The model also accounts for the turnover of bound targets measured experimentally across species in yeasts and mammals. Thus, selective pressures on regulatory networks mostly tolerate local rewiring, and may allow for subtle fine-tuning of gene regulation during evolution.
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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.