Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression

Evolution of Gene Regulation in Humans

(2016) Steven K. Reilly et al.   Annual Review of Genomics and Human Genetics

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes

(2016) Sakthi D. Moorthy et al.   GENOME RESEARCH

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

Hierarchy within the mammary STAT5-driven Wap super-enhancer

(2016) Ha Youn Shin et al.   NATURE GENETICS

Histone H3 globular domain acetylation identifies a new class of enhancers

(2016) Madapura M Pradeepa et al.   NATURE GENETICS

Origin and evolution of developmental enhancers in the mammalian neocortex

(2016) Deena Emera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of Epigenetic Regulation in Vertebrate Genomes

(2016) Rebecca F. Lowdon et al.   TRENDS IN GENETICS

Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris

(2016) Jennifer W. Israel et al.   PLOS BIOLOGY

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest

(2015) Sara L. Prescott et al.   CELL

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

The frequent evolutionary birth and death of functional promoters in mouse and human

(2015) Robert S. Young et al.   GENOME RESEARCH

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

Enhancer Turnover Is Associated with a Divergent Transcriptional Response to Glucocorticoid in Mouse and Human Macrophages

(2015) Alasdair W. Jubb et al.   JOURNAL OF IMMUNOLOGY

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Evolutionary changes in promoter and enhancer activity during human corticogenesis

(2015) S. K. Reilly et al.   SCIENCE

Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals

(2014) Emily S. Wong et al.   GENOME RESEARCH

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

(2014) Cosmas D Arnold et al.   NATURE GENETICS

Evolutionary dynamics of coding and non-coding transcriptomes

(2014) Anamaria Necsulea et al.   NATURE REVIEWS GENETICS

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

Defining functional DNA elements in the human genome

(2014) M. Kellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

Phylogenetic Analysis of Gene Expression

(2013) C. W. Dunn et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Modeling Gene Expression Evolution with an Extended Ornstein–Uhlenbeck Process Accounting for Within-Species Variation

(2013) Rori V. Rohlfs et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data

(2013) Weronika Sikora-Wohlfeld et al.   PLoS Computational Biology

Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

(2013) Mathilde Paris et al.   PLoS Genetics

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression

(2012) Claudia Kutter et al.   PLoS Genetics

Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes

(2011) Sumantra Chatterjee et al.   BMC DEVELOPMENTAL BIOLOGY

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification

(2011) C. E. Cain et al.   GENETICS

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

(2011) G. H. Perry et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Large-scale discovery of enhancers from human heart tissue

(2011) Dalit May et al.   NATURE GENETICS

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

Transphyletic conservation of developmental regulatory state in animal evolution

(2011) J. L. Royo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   CELL

Developmental gene regulation in the era of genomics

(2010) Julia Zeitlinger et al.   DEVELOPMENTAL BIOLOGY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Functional autonomy of distant-acting human enhancers

(2009) Axel Visel et al.   GENOMICS

The enhanceosome

(2008) Daniel Panne   CURRENT OPINION IN STRUCTURAL BIOLOGY

Dispensability of mammalian DNA

(2008) C. McLean et al.   GENOME RESEARCH

Qualifying the relationship between sequence conservation and molecular function

(2008) G. M. Cooper et al.   GENOME RESEARCH