ArticleCell2012
Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification.
Article in Cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
56 citing papers in PubMed, 88 citations in OpenAlex.
- Flexible use of conserved motifs constrains genome access in cell type evolution.Nature ecology & evolution · 2026Article
- Divergence in a eukaryotic transcription factor's co-TF dependence involves multiple intrinsically disordered regions.Nature communications · 2025Article
- Divergence in a Eukaryotic Transcription Factor's co-TF Dependence Involves Multiple Intrinsically Disordered Regions.bioRxiv : the preprint server for biology · 2025Article
- Protein moonlighting by a target gene dominates phenotypic divergence of the Sef1 transcriptional regulatory network in yeasts.Nucleic acids research · 2024Article
- Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum.Genetics · 2024Article
- Inferring gene regulatory networks using transcriptional profiles as dynamical attractors.PLoS computational biology · 2023Article
- Ancient transcriptional regulators can easily evolve new pair-wise cooperativity.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Evolution of a new form of haploid-specific gene regulation appearing in a limited clade of ascomycete yeast species.Genetics · 2023Article
- Mechanisms of regulatory evolution in yeast.Current opinion in genetics & development · 2022Review
- Insights on life cycle and cell identity regulatory circuits for unlocking genetic improvement in Zygosaccharomyces and Kluyveromyces yeasts.FEMS yeast research · 2021Article
- Article
- Sporulation inJournal of fungi (Basel, Switzerland) · 2020Review
- Design of orthogonal regulatory systems for modulating gene expression in plants.Nature chemical biology · 2020Article
- Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit.Science (New York, N.Y.) · 2020Article
- Article
- Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies.Science (New York, N.Y.) · 2019Article
- Structural modules of the stress-induced protein HflX: an outlook on its evolution and biological role.Current genetics · 2019Review
- Interplay of Chimeric Mating-Type Loci Impairs Fertility Rescue and Accounts for Intra-Strain Variability inFrontiers in genetics · 2019Article
- Ancient mechanisms for the evolution of the bicoid homeodomain's function in fly development.eLife · 2018Article
- Intrinsic cooperativity potentiates paralleleLife · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
We examine how different transcriptional network structures can evolve from an ancestral network. By characterizing how the ancestral mode of gene regulation for genes specific to a-type cells in yeast species evolved from an activating paradigm to a repressing one, we show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel regulatory mode. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species.
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Registered trials
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.