Molecular and evolutionary processes generating variation in gene expression

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

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

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

Understanding how cis -regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences

(2015) Michael A. White   GENOMICS

Decoding enhancers using massively parallel reporter assays

(2015) Fumitaka Inoue et al.   GENOMICS

Molecular Mechanisms and Evolutionary Processes Contributing to Accelerated Divergence of Gene Expression on theDrosophilaX Chromosome

(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

Temperature Stress Mediates Decanalization and Dominance of Gene Expression in Drosophila melanogaster

(2015) Jun Chen et al.   PLoS Genetics

Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors

(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

The Nature and Extent of Mutational Pleiotropy in Gene Expression of Male Drosophila serrata

(2014) K. McGuigan et al.   GENETICS

TargetOrtho: A Phylogenetic Footprinting Tool to Identify Transcription Factor Targets

(2014) Lori Glenwinkel et al.   GENETICS

Evolution of splicing regulatory networks in Drosophila

(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

An integrated encyclopedia of DNA elements in the human genome

(2012)   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