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The Sheep and the Goats: Distinguishing transcriptional enhancers in a complex chromatin landscape

https://doi.org/10.1101/324582
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Spurious transcription factor binding: Non‐functional or genetically redundant?
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Unsupervised Learning of Multiple Motifs in Biopolymers Using Expectation Maximization
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The origin of pattern and polarity in the Drosophila embryo
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Sparkling Insights into Enhancer Structure, Function, and Evolution
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Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
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A Regulatory Archipelago Controls Hox Genes Transcription in Digits
inferredcites →https://doi.org/10.1016/j.cell.2012.01.030openalex-snapshot
A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History
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Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells
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The Wisdom of Crowds: Can Mathematical Models Crack the cis Regulatory Code?
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Shadow Enhancers Foster Robustness of Drosophila Gastrulation
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BLOC-1 Brings Together the Actin and Microtubule Cytoskeletons to Generate Recycling Endosomes
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Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks
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Variable reproducibility in genome‐scale public data: A case study using ENCODE ChIP sequencing resource
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Computational methods for transcriptional regulation
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Computational Identification of Active Enhancers in Model Organisms
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A Universal Framework for Regulatory Element Discovery across All Genomes and Data Types
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Enhancer identification through comparative genomics
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Computational schemes for the prediction and annotation of enhancers from epigenomic assays
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Whole-Genome Analysis of Dorsal-Ventral Patterning in the Drosophila Embryo
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Threshold responses to the dorsal regulatory gradient and the subdivision of primary tissue territories in the Drosophila embryo
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Genetics of gene expression and its effect on disease
inferredcites →https://doi.org/10.1038/nature08531openalex-snapshot
Combinatorial binding predicts spatio-temporal cis-regulatory activity
inferredcites →https://doi.org/10.1038/nature09158openalex-snapshot
Phenotypic robustness conferred by apparently redundant transcriptional enhancers
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A map of the cis-regulatory sequences in the mouse genome
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The long-range interaction landscape of gene promoters
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Genome-scale functional characterization of Drosophila developmental enhancers in vivo
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Enhancer loops appear stable during development and are associated with paused polymerase
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Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation
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Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution
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Absence of canonical marks of active chromatin in developmentally regulated genes
inferredcites →https://doi.org/10.1038/ng.3539openalex-snapshot
Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin
inferredcites →https://doi.org/10.1038/ng.808openalex-snapshot
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
inferredcites →https://doi.org/10.1038/nmeth.1906openalex-snapshot
ChromHMM: automating chromatin-state discovery and characterization
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ChIP–seq: advantages and challenges of a maturing technology
inferredcites →https://doi.org/10.1038/nrg3095openalex-snapshot
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence
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Genomic approaches towards finding cis-regulatory modules in animals
inferredcites →https://doi.org/10.1038/nrg3458openalex-snapshot
Enhancers: five essential questions
inferredcites →https://doi.org/10.1038/nrg3682openalex-snapshot
Transcriptional enhancers: from properties to genome-wide predictions
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The resolution of inflammation
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FTO Obesity Variant Circuitry and Adipocyte Browning in Humans
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.1209589110openalex-snapshot
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila
inferredcites →https://doi.org/10.1073/pnas.1320308111openalex-snapshot
Global view of enhancer–promoter interactome in human cells
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Identifying regulatory elements in eukaryotic genomes
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Cis-regulatory mutations in human disease
inferredcites →https://doi.org/10.1093/bib/bbv097openalex-snapshot
In the loop: promoter–enhancer interactions and bioinformatics
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Progress and challenges in bioinformatics approaches for enhancer identification
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Combining evidence using p-values: application to sequence homology searches.
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DNA binding sites: representation and discovery
inferredcites →https://doi.org/10.1093/bioinformatics/bti623openalex-snapshot
ROCR: visualizing classifier performance in R
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On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE
inferredcites →https://doi.org/10.1093/hmg/ddw216openalex-snapshot
Identification and function of enhancers in the human genome
inferredcites →https://doi.org/10.1093/molbev/msw001openalex-snapshot
“Reverse Genomics” Predicts Function of Human Conserved Noncoding Elements
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MEME SUITE: tools for motif discovery and searching
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FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
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The UCSC Genome Browser database: update 2011
inferredcites →https://doi.org/10.1093/nar/gkq999openalex-snapshot
REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila
inferredcites →https://doi.org/10.1093/nar/gkr621openalex-snapshot
Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison
inferredcites →https://doi.org/10.1093/nar/gkt519openalex-snapshot
kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets
inferredcites →https://doi.org/10.1093/nar/gku1058openalex-snapshot
DEEP: a general computational framework for predicting enhancers
inferredcites →https://doi.org/10.1093/nar/gku1177openalex-snapshot
The UCSC Genome Browser database: 2015 update
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Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape
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EMERGE: a flexible modelling framework to predict genomic regulatory elements from genomic signatures
inferredcites →https://doi.org/10.1101/gad.1509607openalex-snapshot
Whole-genome ChIP–chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
inferredcites →https://doi.org/10.1101/gad.230953.113openalex-snapshot
A conserved role for Snail as a potentiator of active transcription
inferredcites →https://doi.org/10.1101/gad.251694.114openalex-snapshot
Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
inferredcites →https://doi.org/10.1101/gr.164079.113openalex-snapshot
Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
inferredcites →https://doi.org/10.1101/gr.192542.115openalex-snapshot
Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation
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.228902openalex-snapshot
Computation-Based Discovery of Related Transcriptional Regulatory Modules and Motifs Using an Experimentally Validated Combinatorial Model
inferredcites →https://doi.org/10.1101/gr.3545105openalex-snapshot
Ultraconserved elements in insect genomes: A highly conserved intronic sequence implicated in the control of homothorax mRNA splicing
inferredcites →https://doi.org/10.1101/gr.5022906openalex-snapshot
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
inferredcites →https://doi.org/10.1111/j.1365-313x.2006.02697.xopenalex-snapshot
Conservation and divergence of plant microRNA genes
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.1198374openalex-snapshot
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
inferredcites →https://doi.org/10.1126/science.1232542openalex-snapshot
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
inferredcites →https://doi.org/10.1186/1471-2105-4-57openalex-snapshot
Conservation of regulatory elements between two species of Drosophila
inferredcites →https://doi.org/10.1186/1471-2105-5-170openalex-snapshot
PhyME: A probabilistic algorithm for finding motifs in sets of orthologous sequences
inferredcites →https://doi.org/10.1186/gb-2009-10-7-r80openalex-snapshot
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
inferredcites →https://doi.org/10.1186/gb-2010-11-2-r22openalex-snapshot
ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
inferredcites →https://doi.org/10.1186/s12859-015-0656-3openalex-snapshot
groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data
inferredcites →https://doi.org/10.1186/s12859-018-2187-1openalex-snapshot
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods
inferredcites →https://doi.org/10.1186/s12861-016-0106-0openalex-snapshot
Computational prediction and experimental validation of novel Hedgehog-responsive enhancers linked to genes of the Hedgehog pathway
inferredcites →https://doi.org/10.1186/s12864-015-1264-3openalex-snapshot
Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study
inferredcites →https://doi.org/10.1242/dev.01124openalex-snapshot
A regulatory code for neurogenic gene expression in theDrosophilaembryo
inferredcites →https://doi.org/10.1242/dev.015826openalex-snapshot
Multiple modular promoter elements drive gradedbrinkerexpression in response to the Dpp morphogen gradient
inferredcites →https://doi.org/10.1242/dev.119.3.767openalex-snapshot
Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter
inferredcites →https://doi.org/10.1242/dev.125.15.2943openalex-snapshot
shaven and sparkling are mutations in separate enhancers of the Drosophila Pax2 homolog
inferredcites →https://doi.org/10.1371/journal.pbio.0050234openalex-snapshot
Deletion of Ultraconserved Elements Yields Viable Mice
inferredcites →https://doi.org/10.1371/journal.pbio.1000343openalex-snapshot
Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species
inferredcites →https://doi.org/10.1371/journal.pcbi.1000299openalex-snapshot
Alignment and Prediction of cis-Regulatory Modules Based on a Probabilistic Model of Evolution
inferredcites →https://doi.org/10.1371/journal.pcbi.1002798openalex-snapshot
Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State
inferredcites →https://doi.org/10.1371/journal.pcbi.1003677openalex-snapshot
Integrating Diverse Datasets Improves Developmental Enhancer Prediction
inferredcites →https://doi.org/10.1371/journal.pgen.1000106openalex-snapshot
Sepsid even-skipped Enhancers Are Functionally Conserved in Drosophila Despite Lack of Sequence Conservation
inferredcites →https://doi.org/10.1371/journal.pgen.1002266openalex-snapshot
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition
inferredcites →https://doi.org/10.1371/journal.pgen.1003748openalex-snapshot
Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression
inferredcites →https://doi.org/10.1534/genetics.107.070425openalex-snapshot
Phylogenetic Footprinting Analysis in the Upstream Regulatory Regions of the DrosophilaEnhancer of splitGenes
inferredcites →https://doi.org/10.7554/elife.06394openalex-snapshot
Genome-wide errant targeting by Hairy
inferredcites →https://doi.org/10.7554/elife.08445openalex-snapshot
Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo

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inferred← citeshttps://doi.org/10.1101/468405openalex-snapshot
Unbiased genome-scale identification of cis -regulatory modules in the human genome by GRAMc
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