Molecular and evolutionary processes generating variation in gene expression
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Title
Molecular and evolutionary processes generating variation in gene expression
Authors
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Journal
NATURE REVIEWS GENETICS
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2020-12-02
DOI
10.1038/s41576-020-00304-w
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Note: Only part of the references are listed.- Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit
- (2020) Candace S. Britton et al. SCIENCE
- Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments
- (2020) Christopher A Jackson et al. eLife
- Dense and pleiotropic regulatory information in a developmental enhancer
- (2020) Timothy Fuqua et al. NATURE
- Systematic interrogation of human promoters
- (2019) Shira Weingarten-Gabbay et al. GENOME RESEARCH
- Chromatin accessibility and the regulatory epigenome
- (2019) Sandy L. Klemm et al. NATURE REVIEWS GENETICS
- Massively Parallel Assays and Quantitative Sequence–Function Relationships
- (2019) Justin B. Kinney et al. Annual Review of Genomics and Human Genetics
- Trans Effects on Gene Expression Can Drive Omnigenic Inheritance
- (2019) Xuanyao Liu et al. CELL
- The role of chromatin accessibility in cis-regulatory evolution
- (2019) Pei-Chen Peng et al. Genome Biology and Evolution
- Actors with Multiple Roles: Pleiotropic Enhancers and the Paradigm of Enhancer Modularity
- (2019) Gonzalo Sabarís et al. TRENDS IN GENETICS
- Gephebase, a database of genotype–phenotype relationships for natural and domesticated variation in Eukaryotes
- (2019) Virginie Courtier-Orgogozo et al. NUCLEIC ACIDS RESEARCH
- Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae
- (2019) Andrea Hodgins-Davis et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Determinants of enhancer and promoter activities of regulatory elements
- (2019) Robin Andersson et al. NATURE REVIEWS GENETICS
- Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution
- (2019) Martin Kircher et al. Nature Communications
- Resolving noise–control conflict by gene duplication
- (2019) Michal Chapal et al. PLOS BIOLOGY
- DNA variants affecting the expression of numerous genes in trans have diverse mechanisms of action and evolutionary histories
- (2019) Sheila Lutz et al. PLoS Genetics
- The great hairball gambit
- (2019) Jonathan Flint et al. PLoS Genetics
- Deciphering eukaryotic gene-regulatory logic with 100 million random promoters
- (2019) Carl G. de Boer et al. NATURE BIOTECHNOLOGY
- Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
- (2018) Aline S. M. Cesar et al. BMC GENOMICS
- The Evolution of Gene Expression in cis and trans
- (2018) Sarah A. Signor et al. TRENDS IN GENETICS
- The evolution of posttranscriptional regulation
- (2018) Bernhard Schaefke et al. Wiley Interdisciplinary Reviews-RNA
- Genetics of trans-regulatory variation in gene expression
- (2018) Frank Wolfgang Albert et al. eLife
- Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing
- (2018) Eilon Sharon et al. CELL
- Improving Estimates of Compensatory cis–trans Regulatory Divergence
- (2018) Hunter B. Fraser TRENDS IN GENETICS
- The Human Transcription Factors
- (2018) Samuel A. Lambert et al. CELL
- Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches
- (2018) Vaishali Katju et al. Genome Biology and Evolution
- Functional micro RNA binding site variants
- (2018) Ye Yuan et al. Molecular Oncology
- Resistance against Ralstonia solanacearum in tomato depends on the methionine cycle and the γ-aminobutyric acid metabolic pathway
- (2018) Guoping Wang et al. PLANT JOURNAL
- Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species
- (2017) Brian P.H. Metzger et al. Genome Biology and Evolution
- Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations
- (2017) Mi Wang et al. Genome Biology and Evolution
- Quantifying the regulatory effect size ofcis-acting genetic variation using allelic fold change
- (2017) Pejman Mohammadi et al. GENOME RESEARCH
- Fitness Effects of Cis-Regulatory Variants in the Saccharomyces cerevisiae TDH3 Promoter
- (2017) Fabien Duveau et al. MOLECULAR BIOLOGY AND EVOLUTION
- Structure of the Transcriptional Regulatory Network Correlates with Regulatory Divergence in Drosophila
- (2017) Bing Yang et al. MOLECULAR BIOLOGY AND EVOLUTION
- Genetic effects on gene expression across human tissues
- (2017) François Aguet et al. NATURE
- High-resolution mapping ofcis-regulatory variation in budding yeast
- (2017) Ryosuke Kita et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Effects of mutation and selection on plasticity of a promoter activity inSaccharomyces cerevisiae
- (2017) Fabien Duveau et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Using Drosophila pigmentation traits to study the mechanisms of cis -regulatory evolution
- (2017) Mark Rebeiz et al. Current Opinion in Insect Science
- Developmental constraints shape the evolution of the nematode mid-developmental transition
- (2017) Harel Zalts et al. Nature Ecology & Evolution
- Massively Parallel Interrogation of the Effects of Gene Expression Levels on Fitness
- (2016) Leeat Keren et al. CELL
- Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution
- (2016) Hannah K. Long et al. CELL
- Genome-wide patterns of regulatory divergence revealed by introgression lines
- (2016) Rafael F. Guerrero et al. EVOLUTION
- Gene regulation and speciation in house mice
- (2016) Katya L. Mack et al. GENOME RESEARCH
- Contrasting Frequencies and Effects ofcis- andtrans-Regulatory Mutations Affecting Gene Expression
- (2016) Brian P. H. Metzger et al. MOLECULAR BIOLOGY AND EVOLUTION
- Global analysis of regulatory divergence in the evolution of mouse alternative polyadenylation
- (2016) Mei‐Sheng Xiao et al. Molecular Systems Biology
- Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets
- (2016) Mina Fazlollahi et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Gene Regulatory Evolution During Speciation in a Songbird
- (2016) John H. Davidson et al. G3-Genes Genomes Genetics
- Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia
- (2016) Xu Wang et al. PLOS BIOLOGY
- Spontaneous mutations and the origin and maintenance of quantitative genetic variation
- (2016) Wen Huang et al. eLife
- Enhancer Evolution across 20 Mammalian Species
- (2015) Diego Villar et al. CELL
- Identification of the Bile Acid Transporter Slco1a6 as a Candidate Gene That Broadly Affects Gene Expression in Mouse Pancreatic Islets
- (2015) J. Tian et al. GENETICS
- The frequent evolutionary birth and death of functional promoters in mouse and human
- (2015) Robert S. Young et al. GENOME RESEARCH
- Core promoter sequence in yeast is a major determinant of expression level
- (2015) Shai Lubliner et al. GENOME RESEARCH
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- (2015) Michael A. White GENOMICS
- Decoding enhancers using massively parallel reporter assays
- (2015) Fumitaka Inoue et al. GENOMICS
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- (2015) Joseph D. Coolon et al. MOLECULAR BIOLOGY AND EVOLUTION
- Predominant contribution of cis-regulatory divergence in the evolution of mouse alternative splicing
- (2015) Q. Gao et al. Molecular Systems Biology
- Selection on noise constrains variation in a eukaryotic promoter
- (2015) Brian P. H. Metzger et al. NATURE
- The role of regulatory variation in complex traits and disease
- (2015) Frank W. Albert et al. NATURE REVIEWS GENETICS
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- (2015) Jun Chen et al. PLoS Genetics
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- (2014) Patrick Kemmeren et al. CELL
- Leveraging Cross-Species Transcription Factor Binding Site Patterns: From Diabetes Risk Loci to Disease Mechanisms
- (2014) Melina Claussnitzer et al. CELL
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- (2014) K. McGuigan et al. GENETICS
- TargetOrtho: A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets
- (2014) Lori Glenwinkel et al. GENETICS
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- (2014) C. J. McManus et al. GENOME RESEARCH
- Tempo and mode of regulatory evolution in Drosophila
- (2014) J. D. Coolon et al. GENOME RESEARCH
- A comparative encyclopedia of DNA elements in the mouse genome
- (2014) Feng Yue et al. NATURE
- Heritability and genomics of gene expression in peripheral blood
- (2014) Fred A Wright et al. NATURE GENETICS
- The Most Deeply Conserved Noncoding Sequences in Plants Serve Similar Functions to Those in Vertebrates Despite Large Differences in Evolutionary Rates
- (2014) Diane Burgess et al. PLANT CELL
- A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding Specificity
- (2014) C. Sayou et al. SCIENCE
- Mapping Small Effect Mutations in Saccharomyces cerevisiae : Impacts of Experimental Design and Mutational Properties
- (2014) Fabien Duveau et al. G3-Genes Genomes Genetics
- Enhancer variants: evaluating functions in common disease
- (2014) Olivia Corradin et al. Genome Medicine
- Single Nucleotide Variants in Transcription Factors Associate More Tightly with Phenotype than with Gene Expression
- (2014) Priya Sudarsanam et al. PLoS Genetics
- Cis and Trans Effects of Human Genomic Variants on Gene Expression
- (2014) Julien Bryois et al. PLoS Genetics
- RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations
- (2013) Graeme D.M. Bell et al. Genome Biology and Evolution
- Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast
- (2013) C. J. McManus et al. GENOME RESEARCH
- Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
- (2013) A. Battle et al. GENOME RESEARCH
- A Novel Test for Selection on cis-Regulatory Elements Reveals Positive and Negative Selection Acting on Mammalian Transcriptional Enhancers
- (2013) Justin D. Smith et al. MOLECULAR BIOLOGY AND EVOLUTION
- Inheritance of Gene Expression Level and Selective Constraints on Trans- and Cis-Regulatory Changes in Yeast
- (2013) Bernhard Schaefke et al. MOLECULAR BIOLOGY AND EVOLUTION
- Transcriptome and genome sequencing uncovers functional variation in humans
- (2013) Tuuli Lappalainen et al. NATURE
- Expression quantitative trait loci: present and future
- (2013) A. C. Nica et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Intra-Specific Regulatory Variation in Drosophila pseudoobscura
- (2013) Anton Suvorov et al. PLoS One
- Emergence and Diversification of Fly Pigmentation Through Evolution of a Gene Regulatory Module
- (2013) L. Arnoult et al. SCIENCE
- The Molecular Mechanism of a Cis-Regulatory Adaptation in Yeast
- (2013) Jessica Chang et al. PLoS Genetics
- A Test for Selection Employing Quantitative Trait Locus and Mutation Accumulation Data
- (2012) D. P. Rice et al. GENETICS
- Extensive compensatory cis-trans regulation in the evolution of mouse gene expression
- (2012) A. Goncalves et al. GENOME RESEARCH
- Lessons from flower colour evolution on targets of selection
- (2012) Carolyn A. Wessinger et al. JOURNAL OF EXPERIMENTAL BOTANY
- Nonlinear Fitness Consequences of Variation in Expression Level of a Eukaryotic Gene
- (2012) J. S. Rest et al. MOLECULAR BIOLOGY AND EVOLUTION
- Nucleosome Organization Affects the Sensitivity of Gene Expression to Promoter Mutations
- (2012) Gil Hornung et al. MOLECULAR CELL
- Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function
- (2012) Colin R. Lickwar et al. NATURE
- Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
- (2012) Alexandre Melnikov et al. NATURE BIOTECHNOLOGY
- Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
- (2012) Eilon Sharon et al. NATURE BIOTECHNOLOGY
- Massively parallel functional dissection of mammalian enhancers in vivo
- (2012) Rupali P Patwardhan et al. NATURE BIOTECHNOLOGY
- Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast
- (2012) Tali Raveh-Sadka et al. NATURE GENETICS
- Genetics of gene expression in primary immune cells identifies cell type–specific master regulators and roles of HLA alleles
- (2012) Benjamin P Fairfax et al. NATURE GENETICS
- Mapping cis- and trans-regulatory effects across multiple tissues in twins
- (2012) Elin Grundberg et al. NATURE GENETICS
- Transcription factors: from enhancer binding to developmental control
- (2012) François Spitz et al. NATURE REVIEWS GENETICS
- Unraveling the thread of nature’s tapestry: the genetics of diversity and convergence in animal pigmentation
- (2012) Marcus R. Kronforst et al. Pigment Cell & Melanoma Research
- Complex effects of nucleotide variants in a mammalian cis-regulatory element
- (2012) J. C. Kwasnieski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Drift-barrier hypothesis and mutation-rate evolution
- (2012) W. Sung et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The many faces of pleiotropy
- (2012) Annalise B. Paaby et al. TRENDS IN GENETICS
- Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids
- (2012) Xiaoli Shi et al. Nature Communications
- The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels
- (2012) Athma A. Pai et al. PLoS Genetics
- Contrasting Properties of Gene-Specific Regulatory, Coding, and Copy Number Mutations in Saccharomyces cerevisiae: Frequency, Effects, and Dominance
- (2012) Jonathan D. Gruber et al. PLoS Genetics
- Regulatory Variation Within and Between Species
- (2011) Wei Zheng et al. Annual Review of Genomics and Human Genetics
- Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer
- (2011) Christina I. Swanson et al. CURRENT BIOLOGY
- Transcriptional Regulation inSaccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators
- (2011) Steven Hahn et al. GENETICS
- Erratum: Corrigendum: Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes
- (2011) Kerrin S Small et al. NATURE GENETICS
- Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence
- (2011) Patricia J. Wittkopp et al. NATURE REVIEWS GENETICS
- Extensive DNA-binding specificity divergence of a conserved transcription regulator
- (2011) C. R. Baker et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- POPULATION GENETICS, PLEIOTROPY, AND THE PREFERENTIAL FIXATION OF MUTATIONS DURING ADAPTIVE EVOLUTION
- (2010) Matthew A. Streisfeld et al. EVOLUTION
- Regulatory divergence in Drosophila revealed by mRNA-seq
- (2010) C. J. McManus et al. GENOME RESEARCH
- Natural selection on cis and trans regulation in yeasts
- (2010) J. J. Emerson et al. GENOME RESEARCH
- Transcriptional Network Structure Has Little Effect on the Rate of Regulatory Evolution in Yeast
- (2010) Artyom Kopp et al. MOLECULAR BIOLOGY AND EVOLUTION
- Identifying the genetic determinants of transcription factor activity
- (2010) Eunjee Lee et al. Molecular Systems Biology
- Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences
- (2010) Itay Tirosh et al. Molecular Systems Biology
- Dissection of genetically complex traits with extremely large pools of yeast segregants
- (2010) Ian M. Ehrenreich et al. NATURE
- Annotating non-coding regions of the genome
- (2010) Roger P. Alexander et al. NATURE REVIEWS GENETICS
- Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process
- (2010) Emily M. LeProust et al. NUCLEIC ACIDS RESEARCH
- Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
- (2010) et al. SCIENCE
- Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
- (2010) M. B. Gerstein et al. SCIENCE
- The Role of Nucleosome Positioning in the Evolution of Gene Regulation
- (2010) Alexander M. Tsankov et al. PLOS BIOLOGY
- Spontaneous Mutation Accumulation Studies in Evolutionary Genetics
- (2009) Daniel L. Halligan et al. Annual Review of Ecology Evolution and Systematics
- Regulation of gene expression via the core promoter and the basal transcriptional machinery
- (2009) Tamar Juven-Gershon et al. DEVELOPMENTAL BIOLOGY
- Global Analysis of Allele-Specific Expression in Arabidopsis thaliana
- (2009) Xu Zhang et al. GENETICS
- Roles of Trans and Cis Variation in Yeast Intraspecies Evolution of Gene Expression
- (2009) Huang-Mo Sung et al. MOLECULAR BIOLOGY AND EVOLUTION
- High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
- (2009) Rupali P Patwardhan et al. NATURE BIOTECHNOLOGY
- Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization
- (2009) Yair Field et al. NATURE GENETICS
- Optimization of gene expression by natural selection
- (2009) T. Bedford et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Genetic Interactions Between Transcription Factors Cause Natural Variation in Yeast
- (2009) J. Gerke et al. SCIENCE
- Is Genetic Evolution Predictable?
- (2009) D. L. Stern et al. SCIENCE
- Quantitative Genomics: Analyzing Intraspecific Variation Using Global Gene Expression Polymorphisms or eQTLs
- (2008) Dan Kliebenstein Annual Review of Plant Biology
- Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
- (2008) Sean B. Carroll CELL
- THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?
- (2008) David L. Stern et al. EVOLUTION
- RESURRECTING THE ROLE OF TRANSCRIPTION FACTOR CHANGE IN DEVELOPMENTAL EVOLUTION
- (2008) Vincent J. Lynch et al. EVOLUTION
- Two strategies for gene regulation by promoter nucleosomes
- (2008) I. Tirosh et al. GENOME RESEARCH
- Fast Evolution of Core Promoters in Primate Genomes
- (2008) H. Liang et al. MOLECULAR BIOLOGY AND EVOLUTION
- Cascading transcriptional effects of a naturally occurring frameshift mutation in Saccharomyces cerevisiae
- (2008) KYLE M. BROWN et al. MOLECULAR ECOLOGY
- Regulatory changes underlying expression differences within and between Drosophila species
- (2008) Patricia J Wittkopp et al. NATURE GENETICS
- Epigenetic regulation and the variability of gene expression
- (2008) Jung Kyoon Choi et al. NATURE GENETICS
- Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression
- (2008) B. Lemos et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The gene regulatory logic of transcription factor evolution
- (2008) Günter P. Wagner et al. TRENDS IN ECOLOGY & EVOLUTION
- Revealing the architecture of gene regulation: the promise of eQTL studies
- (2008) Yoav Gilad et al. TRENDS IN GENETICS
- A Catalog of Neutral and Deleterious Polymorphism in Yeast
- (2008) Scott W. Doniger et al. PLoS Genetics
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