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Tracing the Evolutionary History of Drosophila Regulatory Regions with Models that Identify Transcription Factor Binding Sites
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Information Content of Individual Genetic Sequences
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Epistasis and Pleiotropy as Natural Properties of Transcriptional Regulation
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Evolution of cis-Acting Elements in 5′ Flanking Regions of Vertebrate Actin Genes
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Selection of DNA binding sites by regulatory proteins
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Molecular evolutionary genetics
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From gradients to stripes in Drosophila embryogenesis: filling in the gaps
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Regulatory and coding regions of the segmentation gene hunchback are functionally conserved between Drosophila virilis and Drosophila melanogaster
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Biological sequence analysis
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Conserved noncoding sequences are reliable guides to regulatory elements
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Promoter shuffling has occurred during the evolution of the vertebrate growth hormone gene
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Evolution of transcriptional regulation
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Biological Sequence Analysis
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Differing strategies for organizing anterior and posterior body pattern in Drosophila embryos
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Determination of spatial domains of zygotic gene expression in the Drosophila embryo by the affinity of binding sites for the bicoid morphogen
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Evidence for stabilizing selection in a eukaryotic enhancer element
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The segment polarity network is a robust developmental module
inferredcites →https://doi.org/10.1038/79965openalex-snapshot
Human-mouse genome comparisons to locate regulatory sites
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Rapid restructuring of bicoid‐dependent hunchback promoters within and between Dipteran species: implications for molecular coevolution
inferredcites →https://doi.org/10.1046/j.1525-142x.2002.02016.xopenalex-snapshot
Coevolution in bicoid‐dependent promoters and the inception of regulatory incompatibilities among species of higher Diptera
inferredcites →https://doi.org/10.1073/pnas.231608898openalex-snapshot
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
inferredcites →https://doi.org/10.1073/pnas.97.12.6614openalex-snapshot
Identification of phylogenetic footprints in primate tumor necrosis factor-α promoters
inferredcites →https://doi.org/10.1093/bioinformatics/13.5.555openalex-snapshot
PAML: a program package for phylogenetic analysis by maximum likelihood
inferredcites →https://doi.org/10.1093/bioinformatics/14.4.317openalex-snapshot
Automatic extraction of motifs represented in the hidden Markov model from a number of DNA sequences.
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Profile hidden Markov models.
inferredcites →https://doi.org/10.1093/bioinformatics/16.1.16openalex-snapshot
DNA binding sites: representation and discovery
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Comparison of genomic DNA sequences: solved and unsolved problems
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Species‐specific organization of CpG island promoters at mammalian homologous genes
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Cooperative DNA‐binding by Bicoid provides a mechanism for threshold‐dependent gene activation in the Drosophila embryo
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Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
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A new method of inference of ancestral nucleotide and amino acid sequences.
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Evidence for Redundancy But Not trans Factor-cis Element Coevolution in the Regulation of Drosophila Yp Genes
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Substitution Rates in Drosophila Nuclear Genes: Implications for Translational Selection
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TRANSFAC: an integrated system for gene expression regulation
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Differential Selection After Duplication in Mammalian Developmental Genes
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Rapid Evolution of cis-Regulatory Sequences via Local Point Mutations
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Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover
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Intraspecific nuclear DNA variation in Drosophila
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Microevolutionary Divergence Pattern of the Segmentation Gene hunchback in Drosophila
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026107openalex-snapshot
High sequence turnover in the regulatory regions of the developmental gene hunchback in insects
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The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup.
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Evolutionary dynamics of the enhancer region of even-skipped in Drosophila.
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A test for adaptive change in DNA sequences controlling transcription
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Transcriptional regulation of a pair-rule stripe in Drosophila.
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Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome
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Target Selectivity of Bicoid Is Dependent on Nonconsensus Site Recognition and Protein-Protein Interaction
inferredcites →https://doi.org/10.1242/dev.117.2.585openalex-snapshot
Conservation of regulatory elements controlling hairy pair-rule stripe formation
inferredcites →https://doi.org/10.1242/dev.124.7.1393openalex-snapshot
Drosophila embryonic pattern repair: how embryos respond to bicoid dosage alteration
inferredcites →https://doi.org/10.1242/dev.125.5.949openalex-snapshot
Functional analysis of eve stripe 2 enhancer evolution in Drosophila: rules governing conservation and change
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Biometry. The Principles and Practice of Statistics in Biological Research
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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The Biological Significance of Conserved Nongenic DNA
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Detecting Regulatory Sites Using PhyloGibbs
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Evolution of cis-Regulatory Sequences in Drosophila
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PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information
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From Biophysics to Evolutionary Genetics: Statistical Aspects of Gene Regulation
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Evolution of Prokaryotic Genes by Shift of Stop Codons
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Parsing regulatory DNA: General tasks, techniques, and the PhyloGibbs approach
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Evolution of Gene Regulatory Networks Controlling Body Plan Development
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Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same
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An ancient transcriptional regulatory linkage
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Flexibility of transcription factor target site position in conserved cis-regulatory modules
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Conservation patterns in different functional sequence categories of divergent Drosophila species
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Evolutionary trends of GC/AT distribution patterns in promoters
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The evolution of gene regulation by transcription factors and microRNAs
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Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting
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Correlating Gene Expression Variation with cis-Regulatory Polymorphism in Saccharomyces cerevisiae
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Is Transcription Factor Binding Site Turnover a Sufficient Explanation for Cis-Regulatory Sequence Divergence?
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What Does It Take to Evolve an Enhancer? A Simulation-Based Study of Factors Influencing the Emergence of Combinatorial Regulation
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Inference of Positive and Negative Selection on the 5′ Regulatory Regions of Drosophila Genes
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Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests
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Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila
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The Origins of Eukaryotic Gene Structure
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Inferring Natural Selection on Fine-Scale Chromatin Organization in Yeast
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Ancestral Resurrection of the Drosophila S2E Enhancer Reveals Accessible Evolutionary Paths through Compensatory Change
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Identification of Lineage-SpecificCis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein–Uhlenbeck Models
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Divergent MLS1 Promoters Lie on a Fitness Plateau for Gene Expression
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Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication
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Functional characterization of motif sequences under purifying selection
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The evolution and mutational robustness of chromatin accessibility in Drosophila
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Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
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An effective model for natural selection in promoters
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Genome-wide identification of conserved regulatory function in diverged sequences
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Identification of functional transcription factor binding sites using closely related Saccharomyces species
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Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
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Allele-Specific Assay Reveals Functional Variation in theChalcone SynthasePromoter ofArabidopsis thalianaThat Is Compatible with Neutral Evolution
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Evolutionary and functional analysis of the tailless enhancer in Musca domestica and Drosophila melanogaster
inferred← citeshttps://doi.org/10.1126/science.1087047openalex-snapshot
Evolutionary Discrimination of Mammalian Conserved Non-Genic Sequences (CNGs)
inferred← citeshttps://doi.org/10.1126/science.1145893openalex-snapshot
Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression
inferred← citeshttps://doi.org/10.1186/1471-2105-4-57openalex-snapshot
Conservation of regulatory elements between two species of Drosophila
inferred← citeshttps://doi.org/10.1186/1471-2105-7-143openalex-snapshot
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
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Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
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From biophysics to evolutionary genetics: statistical aspects of gene regulation
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Evidence of association between Nucleosome Occupancy and the Evolution of Transcription Factor Binding Sites in Yeast
inferred← citeshttps://doi.org/10.1186/1471-2148-4-42openalex-snapshot
Adaptive evolution of transcription factor binding sites
inferred← citeshttps://doi.org/10.1186/1471-2148-7-125openalex-snapshot
A model of evolution with constant selective pressure for regulatory DNA sites
inferred← citeshttps://doi.org/10.1186/1471-2148-7-213openalex-snapshot
The limits of subfunctionalization
inferred← citeshttps://doi.org/10.1186/1471-2148-7-s1-s13openalex-snapshot
RNase MRP and the RNA processing cascade in the eukaryotic ancestor
inferred← citeshttps://doi.org/10.1186/1471-2148-9-286openalex-snapshot
Statistical tests for natural selection on regulatory regions based on the strength of transcription factor binding sites
inferred← citeshttps://doi.org/10.1186/1479-7364-2-2-126openalex-snapshot
The genetics of regulatory variation in the human genome
inferred← citeshttps://doi.org/10.1186/gb-2005-6-8-r67openalex-snapshot
Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content
inferred← citeshttps://doi.org/10.1186/gb-2007-8-6-r101openalex-snapshot
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
inferred← citeshttps://doi.org/10.1186/s13059-023-03079-5openalex-snapshot
The evolution and mutational robustness of chromatin accessibility in Drosophila
inferred← citeshttps://doi.org/10.1371/journal.pbio.0020398openalex-snapshot
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
inferred← citeshttps://doi.org/10.1371/journal.pbio.1000343openalex-snapshot
Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species
inferred← citeshttps://doi.org/10.1371/journal.pcbi.0010067openalex-snapshot
PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
inferred← citeshttps://doi.org/10.1371/journal.pcbi.0020130openalex-snapshot
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
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Large-scale turnover of functional transcription factor binding sites in Drosophila
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Frequent Gain and Loss of Functional Transcription Factor Binding Sites
inferred← citeshttps://doi.org/10.1371/journal.pcbi.0030254openalex-snapshot
Analysis of Sequence Conservation at Nucleotide Resolution
inferred← citeshttps://doi.org/10.1371/journal.pcbi.0030254.eoropenalex-snapshot
Analysis of sequence conservation at nucleotide resolution
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Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000848openalex-snapshot
Redundancy and the Evolution of Cis-Regulatory Element Multiplicity
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000935openalex-snapshot
Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression
inferred← citeshttps://doi.org/10.1371/journal.pgen.1000106openalex-snapshot
Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation
inferred← citeshttps://doi.org/10.1371/journal.pgen.1000330openalex-snapshot
Evolution of Regulatory Sequences in 12 Drosophila Species
inferred← citeshttps://doi.org/10.1371/journal.pone.0008155openalex-snapshot
A Biophysical Model for Analysis of Transcription Factor Interaction and Binding Site Arrangement from Genome-Wide Binding Data
inferred← citeshttps://doi.org/10.1371/journal.pone.0010669openalex-snapshot
Phylogeny Disambiguates the Evolution of Heat-Shock cis-Regulatory Elements in Drosophila
inferred← citeshttps://doi.org/10.1387/ijdb.14756342openalex-snapshot
Evolution of cis-regulatory regions versus codifying regions
inferred← citeshttps://doi.org/10.1387/ijdb.14756343openalex-snapshot
Transcriptional regulation and the evolution of development
inferred← citeshttps://doi.org/10.1534/genetics.105.042283openalex-snapshot
Hypervariable Noncoding Sequences in Saccharomyces cerevisiaeSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY942206, AY942556.
inferred← citeshttps://doi.org/10.1534/genetics.110.121590openalex-snapshot
Changes in Selective Effects Over Time Facilitate Turnover of Enhancer Sequences
inferred← citeshttps://doi.org/10.1534/genetics.111.133637openalex-snapshot
Evidence That Purifying Selection Acts on Promoter Sequences
inferred← citeshttps://doi.org/10.15781/t26w96r14openalex-snapshot
The transcriptional control of a newly identified potassium channel gene, Kv3.2
inferred← citeshttps://doi.org/10.1590/s1415-47572008000300028openalex-snapshot
Rapid sequence divergence rates in the 5 prime regulatory regions of young Drosophila melanogaster duplicate gene pairs
inferred← citeshttps://doi.org/10.3410/f.1022240.253657openalex-snapshot
Faculty Opinions recommendation of Conservation of regulatory elements between two species of Drosophila.
inferred← citeshttps://doi.org/10.3410/f.1022622.259625openalex-snapshot
Faculty Opinions recommendation of Conservation and evolution of cis-regulatory systems in ascomycete fungi.
inferred← citeshttps://doi.org/10.4161/rna.6.3.8584openalex-snapshot
Conserved and variable domains of RNase MRP RNA
inferred← citeshttps://doi.org/10.48550/arxiv.0802.3876openalex-snapshot
The evolution of microRNA-regulation in duplicated genes facilitates expression divergence
inferred← citeshttps://doi.org/10.48550/arxiv.cond-mat/0301574openalex-snapshot
Adaptive evolution of transcription factor binding sites
inferred← citeshttps://doi.org/10.6084/m9.figshare.26627401openalex-snapshot
Additional file 1 of The evolution and mutational robustness of chromatin accessibility in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.26627404openalex-snapshot
Additional file 2 of The evolution and mutational robustness of chromatin accessibility in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.26627407openalex-snapshot
Additional file 3 of The evolution and mutational robustness of chromatin accessibility in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.26627410openalex-snapshot
Additional file 4 of The evolution and mutational robustness of chromatin accessibility in Drosophila
inferred← citeshttps://doi.org/10.6084/m9.figshare.26627413openalex-snapshot
Additional file 5 of The evolution and mutational robustness of chromatin accessibility in Drosophila
inferred← citeshttps://doi.org/10.7554/elife.04785openalex-snapshot
Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita
inferred← citeshttps://doi.org/10.7554/elife.04785.001openalex-snapshot
Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita
inferred← citeshttps://doi.org/10.82308/50038openalex-snapshot
Predicting transcription factor binding sites using phylogenetic footprinting and a probabilistic framework for evolutionary turnover
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