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preLekára.sk / Odborné časopisy / PLOS Genetics / 2015 - 3

Pervasive Variation of Transcription Factor Orthologs Contributes to Regulatory Network Evolution

English version České info

The phenotypic differences observed between closely related organisms are thought to be due largely to changes in regulatory networks. Changes in transcriptional networks can occur via mutations in cis binding sites, for which there are numerous known examples, as well as via binding specificity variation in transcription factors (TFs), a less studied phenomenon that has been observed primarily in multi-gene families. Though large-scale experimental studies ascertaining the extent to which TFs contribute to regulatory network variation across organisms are lacking and would be time-consuming, computational methods can begin to address this challenge. Here, we present a systematic, large-scale analysis of DNA-binding specificity evolution in TF orthologs by computationally leveraging specific features of Cys2-His2 zinc finger proteins, the largest class of TFs in animals and major components of their regulatory programs. We find not only that divergence of DNA-binding residues in 1-to-1 orthologous C2H2-ZFs is pervasive but also that these changes show evidence of functional constraint and occur in a gradual, evolutionarily viable manner. We conclude that the diversification of orthologous TFs has most likely played a major and largely unstudied role in gene regulatory network evolution in metazoans.

Vyšlo v časopise: Pervasive Variation of Transcription Factor Orthologs Contributes to Regulatory Network Evolution. PLoS Genet 11(3): e32767. doi:10.1371/journal.pgen.1005011
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005011

Souhrn

The phenotypic differences observed between closely related organisms are thought to be due largely to changes in regulatory networks. Changes in transcriptional networks can occur via mutations in cis binding sites, for which there are numerous known examples, as well as via binding specificity variation in transcription factors (TFs), a less studied phenomenon that has been observed primarily in multi-gene families. Though large-scale experimental studies ascertaining the extent to which TFs contribute to regulatory network variation across organisms are lacking and would be time-consuming, computational methods can begin to address this challenge. Here, we present a systematic, large-scale analysis of DNA-binding specificity evolution in TF orthologs by computationally leveraging specific features of Cys2-His2 zinc finger proteins, the largest class of TFs in animals and major components of their regulatory programs. We find not only that divergence of DNA-binding residues in 1-to-1 orthologous C2H2-ZFs is pervasive but also that these changes show evidence of functional constraint and occur in a gradual, evolutionarily viable manner. We conclude that the diversification of orthologous TFs has most likely played a major and largely unstudied role in gene regulatory network evolution in metazoans.

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Štítky
Genetika Reprodukčná medicína
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Článek Mutations of Human , Encoding the Mitochondrial Asparaginyl-tRNA Synthetase, Cause Nonsyndromic Deafness and Leigh Syndrome
Článek Exome Sequencing in an Admixed Isolated Population Indicates Variants Confer a Risk for Specific Language Impairment
Článek Genome-Wide Association Studies in Dogs and Humans Identify as a Risk Variant for Cleft Lip and Palate
Článek Rapid Evolution of Recombinant for Xylose Fermentation through Formation of Extra-chromosomal Circular DNA
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Článek Maternal Co-ordinate Gene Regulation and Axis Polarity in the Scuttle Fly
Článek Maternal Filaggrin Mutations Increase the Risk of Atopic Dermatitis in Children: An Effect Independent of Mutation Inheritance
Článek Inhibition of Telomere Recombination by Inactivation of KEOPS Subunit Cgi121 Promotes Cell Longevity
Článek Clonality and Evolutionary History of Rhabdomyosarcoma
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Článek The Role of China in the Global Spread of the Current Cholera Pandemic
Článek The Nuclear Receptor DAF-12 Regulates Nutrient Metabolism and Reproductive Growth in Nematodes
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Článek Mitochondrial Dysfunction Reveals the Role of mRNA Poly(A) Tail Regulation in Oculopharyngeal Muscular Dystrophy Pathogenesis
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Článek The Class Homeodomain Factors and Cooperate in . Embryonic Progenitor Cells to Regulate Robust Development
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Článek Synergistic Interactions between Orthologues of Genes Spanned by Human CNVs Support Multiple-Hit Models of Autism
Článek Gene Networks Underlying Convergent and Pleiotropic Phenotypes in a Large and Systematically-Phenotyped Cohort with Heterogeneous Developmental Disorders
Článek The ATM Signaling Cascade Promotes Recombination-Dependent Pachytene Arrest in Mouse Spermatocytes
Článek Combinatorial Control of Light Induced Chromatin Remodeling and Gene Activation in
Článek Linking Aβ42-Induced Hyperexcitability to Neurodegeneration, Learning and Motor Deficits, and a Shorter Lifespan in an Alzheimer’s Model
Článek The Complex Contributions of Genetics and Nutrition to Immunity in
Článek NatB Domain-Containing CRA-1 Antagonizes Hydrolase ACER-1 Linking Acetyl-CoA Metabolism to the Initiation of Recombination during . Meiosis
Článek Transcriptomic Profiling of Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs
Článek Osteopetrorickets due to Snx10 Deficiency in Mice Results from Both Failed Osteoclast Activity and Loss of Gastric Acid-Dependent Calcium Absorption
Článek A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations
Článek Sequence Features and Transcriptional Stalling within Centromere DNA Promote Establishment of CENP-A Chromatin
Článek Inhibits Neuromuscular Junction Growth by Downregulating the BMP Receptor Thickveins
Článek Replicative DNA Polymerase δ but Not ε Proofreads Errors in and in
Článek Unsaturation of Very-Long-Chain Ceramides Protects Plant from Hypoxia-Induced Damages by Modulating Ethylene Signaling in
Článek The Small Protein MntS and Exporter MntP Optimize the Intracellular Concentration of Manganese
Článek A Meta-analysis of Gene Expression Signatures of Blood Pressure and Hypertension
Článek Network Analyses Reveal Novel Aspects of ALS Pathogenesis
Článek A Role for the Budding Yeast Separase, Esp1, in Ty1 Element Retrotransposition
Článek Nab3 Facilitates the Function of the TRAMP Complex in RNA Processing via Recruitment of Rrp6 Independent of Nrd1
Článek A RecA Protein Surface Required for Activation of DNA Polymerase V
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PLOS Genetics

2015 Číslo 3
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Autori: doc. MUDr. David Zemánek, Ph.D., MUDr. Anna Chaloupka, Ph.D.
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