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Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1006/viro.1994.1574openalex-snapshot
An NF1 Motif Plays a Central Role in Hepatitis B Virus Enhancer
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ggplot2: Elegant Graphics for Data Analysis
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Tests for Positive Selection on Immune and Reproductive Genes in Closely Related Species of the Murine Genus Mus
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Genome-wide Identification and Characterization of Fixed Human-Specific Regulatory Regions
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A Population-Specific Uncommon Variant in GRIN3A Associated with Schizophrenia
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Functional consequences of genetic variation in primates on tyrosine hydroxylase (TH) expression in vitro
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Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
inferredcites →https://doi.org/10.1016/j.cell.2013.05.056openalex-snapshot
The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb
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.2015.08.036openalex-snapshot
Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest
inferredcites →https://doi.org/10.1016/j.celrep.2014.12.052openalex-snapshot
Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy
inferredcites →https://doi.org/10.1016/j.celrep.2016.08.042openalex-snapshot
ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera
inferredcites →https://doi.org/10.1016/j.cub.2015.01.041openalex-snapshot
Human-Chimpanzee Differences in a FZD8 Enhancer Alter Cell-Cycle Dynamics in the Developing Neocortex
inferredcites →https://doi.org/10.1016/j.gene.2009.06.020openalex-snapshot
Endogenous retroviral LTRs as promoters for human genes: A critical assessment
inferredcites →https://doi.org/10.1016/j.molcel.2013.11.012openalex-snapshot
Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin
inferredcites →https://doi.org/10.1016/j.molcel.2015.09.018openalex-snapshot
Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination
inferredcites →https://doi.org/10.1016/j.semcancer.2010.04.001openalex-snapshot
SVA retrotransposons: Evolution and genetic instability
inferredcites →https://doi.org/10.1016/j.semcdb.2016.05.004openalex-snapshot
Massive contribution of transposable elements to mammalian regulatory sequences
inferredcites →https://doi.org/10.1016/j.ydbio.2014.08.031openalex-snapshot
Wnt signaling underlies evolution and development of the butterfly wing pattern symmetry systems
inferredcites →https://doi.org/10.1016/s0168-9525(02)00006-9openalex-snapshot
Origin of a substantial fraction of human regulatory sequences from transposable elements
inferredcites →https://doi.org/10.1038/nature04696openalex-snapshot
A distal enhancer and an ultraconserved exon are derived from a novel retroposon
inferredcites →https://doi.org/10.1038/nature08454openalex-snapshot
Molecular networks as sensors and drivers of common human diseases
inferredcites →https://doi.org/10.1038/nature09266openalex-snapshot
From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus
inferredcites →https://doi.org/10.1038/nature10532openalex-snapshot
The evolution of gene expression levels in mammalian organs
inferredcites →https://doi.org/10.1038/nature10808openalex-snapshot
DNase I sensitivity QTLs are a major determinant of human expression variation
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/nature13182openalex-snapshot
A promoter-level mammalian expression atlas
inferredcites →https://doi.org/10.1038/nature13668openalex-snapshot
Comparative analysis of regulatory information and circuits across distant species
inferredcites →https://doi.org/10.1038/nbt.2136openalex-snapshot
Massively parallel functional dissection of mammalian enhancers in vivo
inferredcites →https://doi.org/10.1038/nbt.2137openalex-snapshot
Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay
inferredcites →https://doi.org/10.1038/nbt.2205openalex-snapshot
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
inferredcites →https://doi.org/10.1038/ncomms11769openalex-snapshot
Genome editing in butterflies reveals that spalt promotes and Distal-less represses eyespot colour patterns
inferredcites →https://doi.org/10.1038/ncomms7069openalex-snapshot
Coordinated regulatory variation associated with gestational hyperglycaemia regulates expression of the novel hexokinase HKDC1
inferredcites →https://doi.org/10.1038/ng.2007.60openalex-snapshot
Dynamic evolution of the innate immune system in Drosophila
inferredcites →https://doi.org/10.1038/ng.2553openalex-snapshot
Endogenous retroviruses function as species-specific enhancer elements in the placenta
inferredcites →https://doi.org/10.1038/ng.2649openalex-snapshot
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
inferredcites →https://doi.org/10.1038/ng.3142openalex-snapshot
Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
inferredcites →https://doi.org/10.1038/ng.3591openalex-snapshot
Parallel evolution of male germline epigenetic poising and somatic development in animals
inferredcites →https://doi.org/10.1038/ng.600openalex-snapshot
Transposable elements have rewired the core regulatory network of human embryonic stem cells
inferredcites →https://doi.org/10.1038/ng.917openalex-snapshot
Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals
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/nrg2063openalex-snapshot
The evolutionary significance of cis-regulatory mutations
inferredcites →https://doi.org/10.1038/nrg3905openalex-snapshot
Evolutionary insights into host–pathogen interactions from mammalian sequence data
inferredcites →https://doi.org/10.1038/sj.onc.1206572openalex-snapshot
FEV acts as a transcriptional repressor through its DNA-binding ETS domain and alanine-rich domain
inferredcites →https://doi.org/10.1073/pnas.0607662103openalex-snapshot
Ancient polymorphism and functional variation in the primate MHC- DQA1 5′ cis-regulatory region
inferredcites →https://doi.org/10.1073/pnas.0703637104openalex-snapshot
Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53
inferredcites →https://doi.org/10.1073/pnas.0709398105openalex-snapshot
Possible involvement of SINEs in mammalian-specific brain formation
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.1204800109openalex-snapshot
Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand
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.1609997113openalex-snapshot
Regulatory evolution of Tbx5 and the origin of paired appendages
inferredcites →https://doi.org/10.1073/pnas.36.6.344openalex-snapshot
The origin and behavior of mutable loci in maize
inferredcites →https://doi.org/10.1073/pnas.89.22.10706openalex-snapshot
On "genomenclature": a comprehensive (and respectful) taxonomy for pseudogenes and other "junk DNA".
inferredcites →https://doi.org/10.1074/jbc.272.33.20684openalex-snapshot
The Hepatitis B Virus X Protein Enhances the DNA Binding Potential and Transcription Efficacy of bZip Transcription Factors
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/btr261openalex-snapshot
DREME: motif discovery in transcription factor ChIP-seq data
inferredcites →https://doi.org/10.1093/bioinformatics/btr354openalex-snapshot
False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btu613openalex-snapshot
The Ensembl REST API: Ensembl Data for Any Language
inferredcites →https://doi.org/10.1093/database/bav096openalex-snapshot
Ensembl comparative genomics resources
inferredcites →https://doi.org/10.1093/database/baw053openalex-snapshot
Ensembl comparative genomics resources
inferredcites →https://doi.org/10.1093/database/baw093openalex-snapshot
The Ensembl gene annotation system
inferredcites →https://doi.org/10.1093/gbe/evq002openalex-snapshot
Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain
inferredcites →https://doi.org/10.1093/gbe/evu012openalex-snapshot
Evolution of a Cellular Immune Response in Drosophila: A Phenotypic and Genomic Comparative Analysis
inferredcites →https://doi.org/10.1093/hmg/ddh253openalex-snapshot
Positive selection on the human genome
inferredcites →https://doi.org/10.1093/molbev/mst045openalex-snapshot
Exaptation of Transposable Elements into Novel Cis-Regulatory Elements: Is the Evidence Always Strong?
inferredcites →https://doi.org/10.1093/molbev/msv344openalex-snapshot
Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor
inferredcites →https://doi.org/10.1093/molbev/msw128openalex-snapshot
Genome-Wide Identification of Regulatory Sequences Undergoing Accelerated Evolution in the Human Genome
inferredcites →https://doi.org/10.1093/nar/gkj144openalex-snapshot
The UCSC Genome Browser Database: update 2006
inferredcites →https://doi.org/10.1093/nar/gkp335openalex-snapshot
MEME SUITE: tools for motif discovery and searching
inferredcites →https://doi.org/10.1093/nar/gkp823openalex-snapshot
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing
inferredcites →https://doi.org/10.1093/nar/gkv1272openalex-snapshot
The Dfam database of repetitive DNA families
inferredcites →https://doi.org/10.1093/nar/gkv350openalex-snapshot
The BioMart community portal: an innovative alternative to large, centralized data repositories
inferredcites →https://doi.org/10.1093/nar/gkv637openalex-snapshot
Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments
inferredcites →https://doi.org/10.1101/gr.080663.108openalex-snapshot
Evolution of the mammalian transcription factor binding repertoire via transposable elements
inferredcites →https://doi.org/10.1101/gr.097857.109openalex-snapshot
Detection of nonneutral substitution rates on mammalian phylogenies
inferredcites →https://doi.org/10.1101/gr.136184.111openalex-snapshot
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
inferredcites →https://doi.org/10.1101/gr.152306.112openalex-snapshot
Enhancer transcripts mark active estrogen receptor binding sites
inferredcites →https://doi.org/10.1101/gr.163014.113openalex-snapshot
Tempo and mode of regulatory evolution in Drosophila
inferredcites →https://doi.org/10.1101/gr.168872.113openalex-snapshot
Widespread contribution of transposable elements to the innovation of gene regulatory networks
inferredcites →https://doi.org/10.1101/gr.168963.113openalex-snapshot
Noncoding origins of anthropoid traits and a new null model of transposon functionalization
inferredcites →https://doi.org/10.1101/gr.192591.115openalex-snapshot
Comprehensive identification and analysis of human accelerated regulatory DNA
inferredcites →https://doi.org/10.1101/gr.3715005openalex-snapshot
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
inferredcites →https://doi.org/10.1101/gr.7205808openalex-snapshot
Qualifying the relationship between sequence conservation and molecular function
inferredcites →https://doi.org/10.1126/science.1090005openalex-snapshot
Evolution at Two Levels in Humans and Chimpanzees
inferredcites →https://doi.org/10.1126/science.1145893openalex-snapshot
Functional Architecture and Evolution of Transcriptional Elements That Drive Gene Coexpression
inferredcites →https://doi.org/10.1126/science.1159974openalex-snapshot
Human-Specific Gain of Function in a Developmental Enhancer
inferredcites →https://doi.org/10.1126/science.1186176openalex-snapshot
Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding
inferredcites →https://doi.org/10.1126/science.1222794openalex-snapshot
Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
inferredcites →https://doi.org/10.1126/science.1260943openalex-snapshot
Evolutionary changes in promoter and enhancer activity during human corticogenesis
inferredcites →https://doi.org/10.1126/science.15739260openalex-snapshot
The Significance of Responses of the Genome to Challenge
inferredcites →https://doi.org/10.1126/science.165.3891.349openalex-snapshot
Gene Regulation for Higher Cells: A Theory
inferredcites →https://doi.org/10.1126/science.451548openalex-snapshot
Regulation of Gene Expression: Possible Role of Repetitive Sequences
inferredcites →https://doi.org/10.1126/science.aad5497openalex-snapshot
Regulatory evolution of innate immunity through co-option of endogenous retroviruses
inferredcites →https://doi.org/10.1128/mcb.00690-09openalex-snapshot
A New Role for Sterol Regulatory Element Binding Protein 1 Transcription Factors in the Regulation of Muscle Mass and Muscle Cell Differentiation
inferredcites →https://doi.org/10.1146/annurev-immunol-032713-120254openalex-snapshot
Systems-Level Analysis of Innate Immunity
inferredcites →https://doi.org/10.1158/0008-5472.can-07-2778openalex-snapshot
PAX5/TEL Acts as a Transcriptional Repressor Causing Down-modulation of CD19, Enhances Migration to CXCL12, and Confers Survival Advantage in pre-BI Cells
inferredcites →https://doi.org/10.1186/1471-2105-10-1openalex-snapshot
Regularized gene selection in cancer microarray meta-analysis
inferredcites →https://doi.org/10.1186/1471-2105-10-48openalex-snapshot
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
inferredcites →https://doi.org/10.1186/1471-2105-11-1openalex-snapshot
Detection of gene pathways with predictive power for breast cancer prognosis
inferredcites →https://doi.org/10.1186/1471-2105-11-165openalex-snapshot
Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data
inferredcites →https://doi.org/10.1186/1471-2164-16-1openalex-snapshot
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing
inferredcites →https://doi.org/10.1186/gb-2007-8-2-r24openalex-snapshot
Quantifying similarity between motifs
inferredcites →https://doi.org/10.1186/gb-2008-9-1-r7openalex-snapshot
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/gb-2014-15-1-r1openalex-snapshot
Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis
inferredcites →https://doi.org/10.1186/preaccept-2025469919139083openalex-snapshot
Epigenetic modifications are associated with inter-species gene expression variation in primates
inferredcites →https://doi.org/10.1186/s12864-015-2070-7openalex-snapshot
Functionally conserved enhancers with divergent sequences in distant vertebrates
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1186/s13059-015-0866-zopenalex-snapshot
Ancient DNA and the rewriting of human history: be sparing with Occam’s razor
inferredcites →https://doi.org/10.1186/s13059-016-1008-yopenalex-snapshot
Gene-specific patterns of expression variation across organs and species
inferredcites →https://doi.org/10.1186/s13059-017-1379-8openalex-snapshot
Bidirectional transcription initiation marks accessible chromatin and is not specific to enhancers
inferredcites →https://doi.org/10.1186/s13072-016-0078-0openalex-snapshot
Chromatin variation associated with liver metabolism is mediated by transposable elements
inferredcites →https://doi.org/10.1242/dev.062547openalex-snapshot
HNF4A is essential for specification of hepatic progenitors from human pluripotent stem cells
inferredcites →https://doi.org/10.1371/journal.pbio.0030417openalex-snapshot
Selection on a Neural Gene Regulator Sheds Light on Human Evolution
inferredcites →https://doi.org/10.1371/journal.pbio.1000256openalex-snapshot
ZBED6, a Novel Transcription Factor Derived from a Domesticated DNA Transposon Regulates IGF2 Expression and Muscle Growth
inferredcites →https://doi.org/10.1371/journal.pbio.1000414openalex-snapshot
The Role of Nucleosome Positioning in the Evolution of Gene Regulation
inferredcites →https://doi.org/10.1371/journal.pbio.1002499openalex-snapshot
Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline
inferredcites →https://doi.org/10.1371/journal.pcbi.0030039openalex-snapshot
Discovering Motifs in Ranked Lists of DNA Sequences
inferredcites →https://doi.org/10.1371/journal.pgen.0020168openalex-snapshot
Forces Shaping the Fastest Evolving Regions in the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.1000698openalex-snapshot
Quantifying Adaptive Evolution in the Drosophila Immune System
inferredcites →https://doi.org/10.1371/journal.pgen.1000709openalex-snapshot
Functional Evolution of cis-Regulatory Modules at a Homeotic Gene in Drosophila
inferredcites →https://doi.org/10.1371/journal.pgen.1001342openalex-snapshot
A Molecular Phylogeny of Living Primates
inferredcites →https://doi.org/10.1371/journal.pgen.1002078openalex-snapshot
Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue
inferredcites →https://doi.org/10.1371/journal.pgen.1003470openalex-snapshot
Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs
inferredcites →https://doi.org/10.1371/journal.pgen.1003649openalex-snapshot
Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs
inferredcites →https://doi.org/10.1371/journal.pgen.1004226openalex-snapshot
The Functional Consequences of Variation in Transcription Factor Binding
inferredcites →https://doi.org/10.1371/journal.pone.0089632openalex-snapshot
Episodic Positive Selection in the Evolution of Avian Toll-Like Receptor Innate Immunity Genes
inferredcites →https://doi.org/10.1534/genetics.110.126177openalex-snapshot
Gene Expression Differences Among Primates Are Associated With Changes in a Histone Epigenetic Modification
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3389/fgene.2015.00222openalex-snapshot
Genomic basis of evolutionary change: evolving immunity
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM
inferredcites →https://doi.org/10.7554/elife.02626openalex-snapshot
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/jez.b.23131openalex-snapshot
Evolution of modular and pleiotropic enhancers
inferred← citeshttps://doi.org/10.1093/molbev/msx219openalex-snapshot
Transposable Element Exaptation into Regulatory Regions Is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints
inferred← citeshttps://doi.org/10.1101/295329openalex-snapshot
The impact of endogenous retroviruses on nuclear organization and gene expression
inferred← citeshttps://doi.org/10.1186/s13059-018-1473-6openalex-snapshot
Functional characterization of enhancer evolution in the primate lineage
inferred← citeshttps://doi.org/10.1242/dev.200413openalex-snapshot
Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors
inferred← citeshttps://doi.org/10.70675/245170ecz8b20z47e3z808ezc3fdc8a60a33openalex-snapshot
Is the differential expression of genes and transposable element between testes and ovaries of Drosophila mojavensis and D. arizonae hybrids associated with Postzygotic reproductive isolation?
inferred← citeshttps://doi.org/10.7554/elife.33084openalex-snapshot
Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs
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