Enhancers Facilitate the Birth of De Novo Genes and Gene Integration into Regulatory Networks

Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity

(2019) Laura L. Colbran et al.   GENETICS

Rapid evolution of protein diversity by de novo origination in Oryza

(2019) Li Zhang et al.   Nature Ecology & Evolution

Genome plasticity in Papillomaviruses and de novo emergence of E5 oncogenes

(2019) Anouk Willemsen et al.   Genome Biology and Evolution

De novo gene birth

(2019) Stephen Branden Van Oss et al.   PLoS Genetics

Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

(2019) Evan Witt et al.   eLife

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

(2018) Arnau Sebé-Pedrós et al.   CELL

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

(2018) Rui R. Catarino et al.   GENES & DEVELOPMENT

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Widespread Enhancer Activity from Core Promoters

(2018) Alejandra Medina-Rivera et al.   TRENDS IN BIOCHEMICAL SCIENCES

Translation of neutrally evolving peptides provides a basis for de novo gene evolution

(2018) Jorge Ruiz-Orera et al.   Nature Ecology & Evolution

Early metazoan cell type diversity and the evolution of multicellular gene regulation

(2018) Arnau Sebé-Pedrós et al.   Nature Ecology & Evolution

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation

(2018) Michael S Werner et al.   GENOME RESEARCH

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Repurposing of promoters and enhancers during mammalian evolution

(2018) Francesco N. Carelli et al.   Nature Communications

Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover

(2018) Jonathan F. Schmitz et al.   Nature Ecology & Evolution

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Amphioxus functional genomics and the origins of vertebrate gene regulation

(2018) Ferdinand Marlétaz et al.   NATURE

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish radiations

(2018) Claudius F. Kratochwil et al.   SCIENCE

Translation of Small Open Reading Frames: Roles in Regulation and Evolutionary Innovation

(2018) Jorge Ruiz-Orera et al.   TRENDS IN GENETICS

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

(2018) Juliana G. Roscito et al.   Nature Communications

Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

(2017) Federico Gaiti et al.   eLife

Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

(2017) Raghavendran Partha et al.   eLife

FANTOM5 CAGE profiles of human and mouse samples

(2017) Shuhei Noguchi et al.   Scientific Data

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

(2017) Camille Berthelot et al.   Nature Ecology & Evolution

Are orphan genes protein-coding, prediction artifacts, or non-coding RNAs?

(2016) Neel Prabh et al.   BMC BIOINFORMATICS

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

(2016) Evgeny Z. Kvon et al.   CELL

Evolution of Hoxa11 regulation in vertebrates is linked to the pentadactyl state

(2016) Yacine Kherdjemil et al.   NATURE

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Open questions in the study of de novo genes: what, how and why

(2016) Aoife McLysaght et al.   NATURE REVIEWS 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

Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence

(2016) Rafik Neme et al.   eLife

Enhancer Evolution across 20 Mammalian Species

(2015) Diego Villar et al.   CELL

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse

(2015) Nadezda Kryuchkova-Mostacci et al.   PLoS One

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

Evolutionary conservation of the eumetazoan gene regulatory landscape

(2014) M. Schwaiger et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

(2014) Nicholas T. Ingolia et al.   Cell Reports

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution

(2013) Rafik Neme et al.   BMC GENOMICS

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

Integration of New Genes into Cellular Networks, and Their Structural Maturation

(2013) G. Abrusan   GENETICS

GWIPS-viz: development of a ribo-seq genome browser

(2013) Audrey M. Michel et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

(2011) Benjamin A. Wilson et al.   Genome Biology and Evolution

The Accumulation of Gene Regulation Through Time

(2011) Maria Warnefors et al.   Genome Biology and Evolution

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

Novel genes exhibit distinct patterns of function acquisition and network integration

(2011) John A Capra et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

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

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Properties of developmental gene regulatory networks

(2008) E. H. Davidson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA