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

De Novo Genes Arise at a Slow but Steady Rate along the Primate Lineage and Have Been Subject to Incomplete Lineage Sorting

(2016) Daniele Guerzoni et al.   Genome Biology and Evolution

Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution

(2016) Bryan A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Rafik Neme et al.   eLife

Pluripotency and the endogenous retrovirus HERVH: Conflict or serendipity?

(2015) Zsuzsanna Izsvák et al.   BIOESSAYS

Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates

(2015) Christopher D. Aakre et al.   CELL

Primate-Specific ORF0 Contributes to Retrotransposon-Mediated Diversity

(2015) Ahmet M. Denli et al.   CELL

Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells

(2015) Jonathan Göke et al.   Cell Stem Cell

Distinct evolutionary rate in the eye field transcription factors found by estimation of ancestral protein structure

(2015) Ai Kamijyo et al.   GENE

Baton pass hypothesis: successive incorporation of unconserved endogenous retroviral genes for placentation during mammalian evolution

(2015) Kazuhiko Imakawa et al.   GENES TO CELLS

Are Human Translated Pseudogenes Functional?

(2015) Jinrui Xu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic recapitulation of human pre-eclampsia risk during convergent evolution of reduced placental invasiveness in eutherian mammals

(2015) M. G. Elliot et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation

(2015) Aoife McLysaght et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Retroviral envelope gene captures andsyncytinexaptation for placentation in marsupials

(2015) Guillaume Cornelis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene essentiality and synthetic lethality in haploid human cells

(2015) V. A. Blomen et al.   SCIENCE

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Genes from scratch – the evolutionary fate of de novo genes

(2015) Christian Schlötterer   TRENDS IN GENETICS

Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates

(2015) Jia-Yu Chen et al.   PLoS Genetics

Origins of De Novo Genes in Human and Chimpanzee

(2015) Jorge Ruiz-Orera et al.   PLoS Genetics

Evolution: Dynamics of De Novo Gene Emergence

(2014) Rafik Neme et al.   CURRENT BIOLOGY

Purifying Selection on Splice-Related Motifs, Not Expression Level nor RNA Folding, Explains Nearly All Constraint on Human lincRNAs

(2014) Andreas Schüler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

(2014) B. A. Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells

(2014) Jichang Wang et al.   NATURE

Evolutionary dynamics of coding and non-coding transcriptomes

(2014) Anamaria Necsulea et al.   NATURE REVIEWS GENETICS

Emerging evidence for functional peptides encoded by short open reading frames

(2014) Shea J. Andrews et al.   NATURE REVIEWS GENETICS

Retroviral envelope syncytin capture in an ancestrally diverged mammalian clade for placentation in the primitive Afrotherian tenrecs

(2014) G. Cornelis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

Mapping ecologically relevant social behaviours by gene knockout in wild mice

(2014) Lea Chalfin et al.   Nature Communications

Pleiotropy of the de novo-originated gene MDF1

(2014) Dan Li et al.   Scientific Reports

NCYM, a Cis-Antisense Gene of MYCN, Encodes a De Novo Evolved Protein That Inhibits GSK3β Resulting in the Stabilization of MYCN in Human Neuroblastomas

(2014) Yusuke Suenaga et al.   PLoS Genetics

The life cycle of Drosophila orphan genes

(2014) Nicola Palmieri et al.   eLife

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Regulation of Mouse Retroelement MuERV-L/MERVL Expression by REX1 and Epigenetic Control of Stem Cell Potency

(2014) Jon Schoorlemmer et al.   Frontiers in Oncology

Open questions: A logic (or lack thereof) of genome organization

(2013) Laurence D Hurst   BMC BIOLOGY

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

Dynamics and adaptive benefits of modular protein evolution

(2013) Erich Bornberg-Bauer et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Endogenous miRNA Sponge lincRNA-RoR Regulates Oct4, Nanog, and Sox2 in Human Embryonic Stem Cell Self-Renewal

(2013) Yue Wang et al.   DEVELOPMENTAL CELL

On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

(2013) D. Graur et al.   Genome Biology and Evolution

Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation

(2013) C. Lavialle et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bidirectional Promoters as Important Drivers for the Emergence of Species-Specific Transcripts

(2013) Valer Gotea et al.   PLoS One

PBOV1 Is a Human De Novo Gene with Tumor-Specific Expression That Is Associated with a Positive Clinical Outcome of Cancer

(2013) Nikolay Samusik et al.   PLoS One

Captured retroviral envelope syncytin gene associated with the unique placental structure of higher ruminants

(2013) Guillaume Cornelis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is junk DNA bunk? A critique of ENCODE

(2013) W. F. Doolittle   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stepwise Evolution of Essential Centromere Function in a Drosophila Neogene

(2013) B. D. Ross et al.   SCIENCE

Differential Evolutionary Fate of an Ancestral Primate Endogenous Retrovirus Envelope Gene, the EnvV Syncytin, Captured for a Function in Placentation

(2013) Cécile Esnault et al.   PLoS Genetics

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

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

From ancestral infectious retroviruses to bona fide cellular genes: Role of the captured syncytins in placentation

(2012) A. Dupressoir et al.   PLACENTA

De Novo Origin of Protein-Coding Genes in Murine Rodents

(2012) Daniel N. Murphy et al.   PLoS One

Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

(2012) Chen Xie et al.   PLoS Genetics

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

(2011) Serban Nacu et al.   BMC Medical Genomics

Convergent Evolution of Endometrial Prolactin Expression in Primates, Mice, and Elephants Through the Independent Recruitment of Transposable Elements

(2011) Deena Emera et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Preventing Dangerous Nonsense: Selection for Robustness to Transcriptional Error in Human Genes

(2011) Brian P. Cusack et al.   PLoS Genetics

De Novo Origin of Human Protein-Coding Genes

(2011) Dong-Dong Wu et al.   PLoS Genetics

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

(2010) Dan Li et al.   CELL RESEARCH

The Proapoptotic Molecule BLID Interacts with Bcl-XL and Its Downregulation in Breast Cancer Correlates with Poor Disease-Free and Overall Survival

(2010) C. G. Broustas et al.   CLINICAL CANCER RESEARCH

Unique Cost Dynamics Elucidate the Role of Frameshifting Errors in Promoting Translational Robustness

(2010) Tobias Warnecke et al.   Genome Biology and Evolution

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

Emergence of a New Gene from an Intergenic Region

(2009) Tobias J.A.J. Heinen et al.   CURRENT BIOLOGY

Darwinian alchemy: Human genes from noncoding DNA

(2009) A. Siepel   GENOME RESEARCH

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Phylogenetic Evidence for Early Hemochorial Placentation in Eutheria

(2009) M.G. Elliot et al.   PLACENTA

Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves

(2009) Ling Li et al.   PLANT JOURNAL

A Rice Gene of De Novo Origin Negatively Regulates Pathogen-Induced Defense Response

(2009) Wenfei Xiao et al.   PLoS One

Wolbachia-Mediated Cytoplasmic Incompatibility Is Associated with Impaired Histone Deposition in the Male Pronucleus

(2009) Frédéric Landmann et al.   PLoS Pathogens

De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae

(2008) J. Cai et al.   GENETICS

On the origin and evolution of new genes—a genomic and experimental perspective

(2008) Qi Zhou et al.   Journal of Genetics and Genomics

An Ancient Evolutionary Origin of Genes Associated with Human Genetic Diseases

(2008) T. Domazet-Loso et al.   MOLECULAR BIOLOGY AND EVOLUTION

Origin of Primate Orphan Genes: A Comparative Genomics Approach

(2008) M. Toll-Riera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Translational control of intron splicing in eukaryotes

(2008) Olivier Jaillon et al.   NATURE

Ripples from neighbouring transcription

(2008) Miki Ebisuya et al.   NATURE CELL BIOLOGY

A novel transcript from theKLKP1 gene is androgen regulated, down-regulated during prostate cancer progression and encodes the first non-serine protease identified from the human kallikrein gene locus

(2008) Aneel Kaushal et al.   PROSTATE

A Single Gene Causes Both Male Sterility and Segregation Distortion in Drosophila Hybrids

(2008) N. Phadnis et al.   SCIENCE

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

(2008) Nicolas Galtier et al.   TRENDS IN GENETICS

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics

Integration of Horizontally Transferred Genes into Regulatory Interaction Networks Takes Many Million Years

(2007) M. J. Lercher et al.   MOLECULAR BIOLOGY AND EVOLUTION