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Enhancers facilitate the birth of de novo genes and their integration into regulatory networks
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.cell.2008.06.030openalex-snapshot
Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
inferredcites →https://doi.org/10.1016/j.cell.2011.02.017openalex-snapshot
Evolution of Gene Regulatory Networks Controlling Body Plan Development
inferredcites →https://doi.org/10.1016/j.cell.2013.10.048openalex-snapshot
Divergent Transcription: A Driving Force for New Gene Origination?
inferredcites →https://doi.org/10.1016/j.cell.2014.02.009openalex-snapshot
Looping Back to Leap Forward: Transcription Enters a New Era
inferredcites →https://doi.org/10.1016/j.cell.2015.01.006openalex-snapshot
Enhancer Evolution across 20 Mammalian Species
inferredcites →https://doi.org/10.1016/j.cell.2016.09.028openalex-snapshot
Progressive Loss of Function in a Limb Enhancer during Snake Evolution
inferredcites →https://doi.org/10.1016/j.cell.2018.05.019openalex-snapshot
Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq
inferredcites →https://doi.org/10.1016/j.cell.2018.06.052openalex-snapshot
A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
inferredcites →https://doi.org/10.1016/j.celrep.2014.07.045openalex-snapshot
Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes
inferredcites →https://doi.org/10.1016/j.molcel.2018.06.044openalex-snapshot
Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data
inferredcites →https://doi.org/10.1016/j.tibs.2018.03.004openalex-snapshot
Widespread Enhancer Activity from Core Promoters
inferredcites →https://doi.org/10.1016/j.tig.2007.08.014openalex-snapshot
A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages
inferredcites →https://doi.org/10.1016/j.tig.2018.12.003openalex-snapshot
Translation of Small Open Reading Frames: Roles in Regulation and Evolutionary Innovation
inferredcites →https://doi.org/10.1038/35059227openalex-snapshot
Chance and necessity: the evolution of morphological complexity and diversity
inferredcites →https://doi.org/10.1038/nature09033openalex-snapshot
Widespread transcription at neuronal activity-regulated enhancers
inferredcites →https://doi.org/10.1038/nature11184openalex-snapshot
Proto-genes and de novo gene birth
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature12787openalex-snapshot
An atlas of active enhancers across human cell types and tissues
inferredcites →https://doi.org/10.1038/nature13395openalex-snapshot
Genome-scale functional characterization of Drosophila developmental enhancers in vivo
inferredcites →https://doi.org/10.1038/nature19813openalex-snapshot
Evolution of Hoxa11 regulation in vertebrates is linked to the pentadactyl state
inferredcites →https://doi.org/10.1038/nature25461openalex-snapshot
Enhancer redundancy provides phenotypic robustness in mammalian development
inferredcites →https://doi.org/10.1038/ng1340openalex-snapshot
Gene regulatory network growth by duplication
inferredcites →https://doi.org/10.1038/ng1966openalex-snapshot
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
inferredcites →https://doi.org/10.1038/nrg.2016.4openalex-snapshot
Enhancers as non-coding RNA transcription units: recent insights and future perspectives
inferredcites →https://doi.org/10.1038/nrg.2016.78openalex-snapshot
Open questions in the study of de novo genes: what, how and why
inferredcites →https://doi.org/10.1038/nrg2083openalex-snapshot
Genome-wide transcription and the implications for genomic organization
inferredcites →https://doi.org/10.1038/nrg3053openalex-snapshot
The evolutionary origin of orphan genes
inferredcites →https://doi.org/10.1038/nrg3207openalex-snapshot
Transcription factors: from enhancer binding to developmental control
inferredcites →https://doi.org/10.1038/nrg3645openalex-snapshot
Ribosome profiling: new views of translation, from single codons to genome scale
inferredcites →https://doi.org/10.1038/s41467-018-06544-zopenalex-snapshot
Repurposing of promoters and enhancers during mammalian evolution
inferredcites →https://doi.org/10.1038/s41467-018-07122-zopenalex-snapshot
Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution
inferredcites →https://doi.org/10.1038/s41559-017-0377-2openalex-snapshot
Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression
inferredcites →https://doi.org/10.1038/s41559-018-0506-6openalex-snapshot
Translation of neutrally evolving peptides provides a basis for de novo gene evolution
inferredcites →https://doi.org/10.1038/s41559-018-0575-6openalex-snapshot
Early metazoan cell type diversity and the evolution of multicellular gene regulation
inferredcites →https://doi.org/10.1038/s41559-018-0639-7openalex-snapshot
Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover
inferredcites →https://doi.org/10.1038/s41559-019-0822-5openalex-snapshot
Rapid evolution of protein diversity by de novo origination in Oryza
inferredcites →https://doi.org/10.1038/s41580-018-0028-8openalex-snapshot
Eukaryotic core promoters and the functional basis of transcription initiation
inferredcites →https://doi.org/10.1038/s41586-018-0590-4openalex-snapshot
Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris
inferredcites →https://doi.org/10.1038/s41586-018-0734-6openalex-snapshot
Amphioxus functional genomics and the origins of vertebrate gene regulation
inferredcites →https://doi.org/10.1038/s41598-017-04520-zopenalex-snapshot
A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq
inferredcites →https://doi.org/10.1038/srep07280openalex-snapshot
Pleiotropy of the de novo-originated gene MDF1
inferredcites →https://doi.org/10.1073/pnas.0700488104openalex-snapshot
Emerging principles of regulatory evolution
inferredcites →https://doi.org/10.1073/pnas.0806007105openalex-snapshot
Properties of developmental gene regulatory networks
inferredcites →https://doi.org/10.1073/pnas.1016071107openalex-snapshot
Histone H3K27ac separates active from poised enhancers and predicts developmental state
inferredcites →https://doi.org/10.1073/pnas.1320308111openalex-snapshot
Global view of enhancer–promoter interactome in human cells
inferredcites →https://doi.org/10.1073/pnas.1603718113openalex-snapshot
Origin and evolution of developmental enhancers in the mammalian neocortex
inferredcites →https://doi.org/10.1073/pnas.2136655100openalex-snapshot
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/gbe/evr019openalex-snapshot
The Accumulation of Gene Regulation Through Time
inferredcites →https://doi.org/10.1093/gbe/evr099openalex-snapshot
Putatively Noncoding Transcripts Show Extensive Association with Ribosomes
inferredcites →https://doi.org/10.1093/gbe/evz095openalex-snapshot
Genome Plasticity in Papillomaviruses and De Novo Emergence of E5 Oncogenes
inferredcites →https://doi.org/10.1093/nar/gkt1035openalex-snapshot
GWIPS-viz: development of a ribo-seq genome browser
inferredcites →https://doi.org/10.1101/gad.310367.117openalex-snapshot
Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation
inferredcites →https://doi.org/10.1101/gr.101386.109openalex-snapshot
Origins, evolution, and phenotypic impact of new genes
inferredcites →https://doi.org/10.1101/gr.162529.113openalex-snapshot
Evolutionary conservation of the eumetazoan gene regulatory landscape
inferredcites →https://doi.org/10.1101/gr.234872.118openalex-snapshot
Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation
inferredcites →https://doi.org/10.1126/science.aao6809openalex-snapshot
Agouti-related peptide 2 facilitates convergent evolution of stripe patterns across cichlid fish radiations
inferredcites →https://doi.org/10.1186/1471-2164-14-117openalex-snapshot
Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution
inferredcites →https://doi.org/10.1186/gb-2010-11-12-r127openalex-snapshot
Novel genes exhibit distinct patterns of function acquisition and network integration
inferredcites →https://doi.org/10.1186/s13059-014-0560-6openalex-snapshot
Gateways to the FANTOM5 promoter level mammalian expression atlas
inferredcites →https://doi.org/10.1371/journal.pbio.1000384openalex-snapshot
A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers
inferredcites →https://doi.org/10.1371/journal.pbio.1000625openalex-snapshot
The Reality of Pervasive Transcription
inferredcites →https://doi.org/10.1371/journal.pbio.1002353openalex-snapshot
Evolutionary Novelty in a Butterfly Wing Pattern through Enhancer Shuffling
inferredcites →https://doi.org/10.1371/journal.pgen.1003860openalex-snapshot
De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences
inferredcites →https://doi.org/10.1371/journal.pgen.1005146openalex-snapshot
The Orphan Gene dauerless Regulates Dauer Development and Intraspecific Competition in Nematodes by Copy Number Variation
inferredcites →https://doi.org/10.1371/journal.pone.0131673openalex-snapshot
Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse
inferredcites →https://doi.org/10.1534/genetics.113.152256openalex-snapshot
Integration of New Genes into Cellular Networks, and Their Structural Maturation
inferredcites →https://doi.org/10.7554/elife.03523openalex-snapshot
Long non-coding RNAs as a source of new peptides
inferredcites →https://doi.org/10.7554/elife.09977openalex-snapshot
Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence
inferredcites →https://doi.org/10.7554/elife.22194openalex-snapshot
Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity
inferredcites →https://doi.org/10.7554/elife.47138openalex-snapshot
Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/j.gpb.2020.06.010openalex-snapshot
Profiling Chromatin Accessibility at Single-Cell Resolution
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