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Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations

https://doi.org/10.1101/529990
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What this work says

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

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ATAC‐seq: A Method for Assaying Chromatin Accessibility Genome‐Wide
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Compatibility between enhancers and promoters determines the transcriptional specificity of gooseberry and gooseberry neuro in the Drosophila embryo.
inferredcites →https://doi.org/10.1016/0168-9525(90)90182-6openalex-snapshot
Human globin locus activation region (LAR): role in temporal control
inferredcites →https://doi.org/10.1016/j.ajhg.2017.06.010openalex-snapshot
CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions
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Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells
inferredcites →https://doi.org/10.1016/j.cell.2009.06.001openalex-snapshot
CTCF: Master Weaver of the Genome
inferredcites →https://doi.org/10.1016/j.cell.2011.01.024openalex-snapshot
Functional and Mechanistic Diversity of Distal Transcription Enhancers
inferredcites →https://doi.org/10.1016/j.cell.2011.12.014openalex-snapshot
Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
inferredcites →https://doi.org/10.1016/j.cell.2012.03.051openalex-snapshot
Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor
inferredcites →https://doi.org/10.1016/j.cell.2013.06.044openalex-snapshot
CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes
inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.cell.2015.02.040openalex-snapshot
The Role of Chromosome Domains in Shaping the Functional Genome
inferredcites →https://doi.org/10.1016/j.cell.2016.04.027openalex-snapshot
Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay
inferredcites →https://doi.org/10.1016/j.cell.2016.04.048openalex-snapshot
Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits
inferredcites →https://doi.org/10.1016/j.cell.2016.11.038openalex-snapshot
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens
inferredcites →https://doi.org/10.1016/j.cell.2016.11.039openalex-snapshot
Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq
inferredcites →https://doi.org/10.1016/j.cell.2016.11.048openalex-snapshot
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response
inferredcites →https://doi.org/10.1016/j.cell.2018.03.068openalex-snapshot
Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element
inferredcites →https://doi.org/10.1016/j.celrep.2016.09.002openalex-snapshot
Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes
inferredcites →https://doi.org/10.1016/j.cels.2016.07.002openalex-snapshot
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
inferredcites →https://doi.org/10.1016/j.gde.2011.11.001openalex-snapshot
Enhancer and promoter interactions—long distance calls
inferredcites →https://doi.org/10.1016/j.molcel.2014.12.009openalex-snapshot
Developmental Control of Polycomb Subunit Composition by GATA Factors Mediates a Switch to Non-Canonical Functions
inferredcites →https://doi.org/10.1016/j.molcel.2016.02.029openalex-snapshot
Unlinking an lncRNA from Its Associated cis Element
inferredcites →https://doi.org/10.1016/j.molcel.2016.03.007openalex-snapshot
Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping
inferredcites →https://doi.org/10.1016/j.molcel.2017.03.007openalex-snapshot
Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells
inferredcites →https://doi.org/10.1016/j.tig.2005.04.009openalex-snapshot
Transcriptional interference – a crash course
inferredcites →https://doi.org/10.1016/j.tig.2013.05.010openalex-snapshot
Human housekeeping genes, revisited
inferredcites →https://doi.org/10.1016/s0959-437x(96)80072-4openalex-snapshot
Regulation of β-globin gene expression: straightening out the locus
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/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature13182openalex-snapshot
A promoter-level mammalian expression atlas
inferredcites →https://doi.org/10.1038/nature13994openalex-snapshot
Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation
inferredcites →https://doi.org/10.1038/nature15521openalex-snapshot
BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis
inferredcites →https://doi.org/10.1038/nature20149openalex-snapshot
Local regulation of gene expression by lncRNA promoters, transcription and splicing
inferredcites →https://doi.org/10.1038/nbt.3468openalex-snapshot
High-throughput mapping of regulatory DNA
inferredcites →https://doi.org/10.1038/nbt.3519openalex-snapshot
Near-optimal probabilistic RNA-seq quantification
inferredcites →https://doi.org/10.1038/nbt.3853openalex-snapshot
CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome
inferredcites →https://doi.org/10.1038/ncomms15993openalex-snapshot
Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping
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.3539openalex-snapshot
Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin
inferredcites →https://doi.org/10.1038/ng.3646openalex-snapshot
Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
inferredcites →https://doi.org/10.1038/ng.3793openalex-snapshot
Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci
inferredcites →https://doi.org/10.1038/ng.3884openalex-snapshot
Genome-wide characterization of mammalian promoters with distal enhancer functions
inferredcites →https://doi.org/10.1038/ng.3950openalex-snapshot
Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines
inferredcites →https://doi.org/10.1038/ng.3963openalex-snapshot
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
inferredcites →https://doi.org/10.1038/nm.3975openalex-snapshot
CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants
inferredcites →https://doi.org/10.1038/nmeth.3630openalex-snapshot
Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements
inferredcites →https://doi.org/10.1038/nmeth.4177openalex-snapshot
Pooled CRISPR screening with single-cell transcriptome readout
inferredcites →https://doi.org/10.1038/nmeth.4264openalex-snapshot
A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
inferredcites →https://doi.org/10.1038/nprot.2012.101openalex-snapshot
Identifying ChIP-seq enrichment using MACS
inferredcites →https://doi.org/10.1038/nrg3207openalex-snapshot
Transcription factors: from enhancer binding to developmental control
inferredcites →https://doi.org/10.1038/nrg3682openalex-snapshot
Transcriptional enhancers: from properties to genome-wide predictions
inferredcites →https://doi.org/10.1038/s41467-018-03279-9openalex-snapshot
Dissecting super-enhancer hierarchy based on chromatin interactions
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/10.1073/pnas.1320308111openalex-snapshot
Global view of enhancer–promoter interactome in human cells
inferredcites →https://doi.org/10.1073/pnas.1518552112openalex-snapshot
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
inferredcites →https://doi.org/10.1073/pnas.1521754113openalex-snapshot
Insight into GATA1 transcriptional activity through interrogation of cis elements disrupted in human erythroid disorders
inferredcites →https://doi.org/10.1093/nar/8.7.1521openalex-snapshot
Physical mapping of the globin gene deletion in hereditary persistence of foetal haemoglobin (HPFH)
inferredcites →https://doi.org/10.1093/nar/gkr253openalex-snapshot
The distinctive roles of erythroid specific activator GATA-1 and NF-E2 in transcription of the human fetal γ-globin genes
inferredcites →https://doi.org/10.1101/188755openalex-snapshot
Measuring the reproducibility and quality of Hi-C data
inferredcites →https://doi.org/10.1101/gad.10.10.1260openalex-snapshot
Promoter specificity mediates the independent regulation of neighboring genes.
inferredcites →https://doi.org/10.1101/gad.248526.114openalex-snapshot
A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential
inferredcites →https://doi.org/10.1101/gad.5.5.820openalex-snapshot
DNA looping between sites for transcriptional activation: self-association of DNA-bound Sp1.
inferredcites →https://doi.org/10.1101/gad.924301openalex-snapshot
Enhancer–promoter specificity mediated by DPE or TATA core promoter motifs
inferredcites →https://doi.org/10.1101/gr.210930.116openalex-snapshot
Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple 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.aaf7613openalex-snapshot
High-resolution interrogation of functional elements in the noncoding genome
inferredcites →https://doi.org/10.1126/science.aag2445openalex-snapshot
Systematic mapping of functional enhancer–promoter connections with CRISPR interference
inferredcites →https://doi.org/10.1126/science.aah7111openalex-snapshot
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells
inferredcites →https://doi.org/10.1128/mcb.13.2.911openalex-snapshot
Enhancer-dependent transcription of the epsilon-globin promoter requires promoter-bound GATA-1 and enhancer-bound AP-1/NF-E2.
inferredcites →https://doi.org/10.1128/mcb.13.2.911-917.1993openalex-snapshot
Enhancer-Dependent Transcription of the ε-Globin Promoter Requires Promoter-Bound GATA-1 and Enhancer-Bound AP-1/NF-E2
inferredcites →https://doi.org/10.1128/mcb.23.14.5031-5042.2003openalex-snapshot
GATA-1-Mediated Proliferation Arrest during Erythroid Maturation
inferredcites →https://doi.org/10.1161/atvbaha.117.310103openalex-snapshot
Interrogation of the Atherosclerosis-Associated SORT1 (Sortilin 1) Locus With Primary Human Hepatocytes, Induced Pluripotent Stem Cell-Hepatocytes, and Locus-Humanized Mice
inferredcites →https://doi.org/10.1186/1471-2164-9-172openalex-snapshot
How many human genes can be defined as housekeeping with current expression data?
inferredcites →https://doi.org/10.1186/gb-2004-5-10-r80openalex-snapshot
Bioconductor: open software development for computational biology and bioinformatics
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/s13059-019-1671-xopenalex-snapshot
BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing
inferredcites →https://doi.org/10.1371/journal.pgen.1004102openalex-snapshot
Comprehensive Functional Annotation of 77 Prostate Cancer Risk Loci
inferredcites →https://doi.org/10.1371/journal.pone.0114485openalex-snapshot
CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells
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.35989openalex-snapshot
Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.cell.2021.10.024openalex-snapshot
A single-cell atlas of chromatin accessibility in the human genome
inferred← citeshttps://doi.org/10.1016/j.molcel.2019.08.010openalex-snapshot
Mechanisms of Interplay between Transcription Factors and the 3D Genome
inferred← citeshttps://doi.org/10.1038/s41467-023-40658-3openalex-snapshot
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
inferred← citeshttps://doi.org/10.1038/s41576-019-0128-0openalex-snapshot
Long-range enhancer–promoter contacts in gene expression control
inferred← citeshttps://doi.org/10.1093/hmg/ddaa097openalex-snapshot
Functional genomics in autoimmune diseases
inferred← citeshttps://doi.org/10.1093/nar/gkab547openalex-snapshot
Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer–target gene regulatory interactions
inferred← citeshttps://doi.org/10.1093/nar/gkab598openalex-snapshot
ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination
inferred← citeshttps://doi.org/10.1093/nar/gkac130openalex-snapshot
GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants from whole-genome sequencing data
inferred← citeshttps://doi.org/10.1098/rstb.2019.0347openalex-snapshot
Transposable elements as a potent source of diverse cis -regulatory sequences in mammalian genomes
inferred← citeshttps://doi.org/10.1101/2021.04.19.21255650openalex-snapshot
Genetic determinants of interventricular septal anatomy and the risk of ventricular septal defects and hypertrophic cardiomyopathy
inferred← citeshttps://doi.org/10.1101/2022.10.09.510609openalex-snapshot
ASCL1 interacts with the mSWI/SNF at distal regulatory elements to regulate neural differentiation
inferred← citeshttps://doi.org/10.1101/2022.12.16.520793openalex-snapshot
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
inferred← citeshttps://doi.org/10.1101/2023.06.30.547290openalex-snapshot
Machine learning of enhancer-promoter specificity based on enhancer perturbation studies reveals a distinct class of enhancers
inferred← citeshttps://doi.org/10.1101/782748openalex-snapshot
Inherited Causes of Clonal Hematopoiesis of Indeterminate Potential in TOPMed Whole Genomes
inferred← citeshttps://doi.org/10.1101/gr.249367.119openalex-snapshot
Quantitative prediction of enhancer–promoter interactions
inferred← citeshttps://doi.org/10.1146/annurev-biochem-011420-095916openalex-snapshot
Evaluating Enhancer Function and Transcription
inferred← citeshttps://doi.org/10.1186/s12896-020-00626-xopenalex-snapshot
Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system
inferred← citeshttps://doi.org/10.1186/s13059-020-02046-8openalex-snapshot
MAUDE: inferring expression changes in sorting-based CRISPR screens
inferred← citeshttps://doi.org/10.3389/fimmu.2021.651254openalex-snapshot
High Dose IFN-β Activates GAF to Enhance Expression of ISGF3 Target Genes in MLE12 Epithelial Cells
inferred← citeshttps://doi.org/10.5204/thesis.eprints.248736openalex-snapshot
Identification of multi-cancer risk genes
inferred← citeshttps://doi.org/10.64898/2026.03.03.708783openalex-snapshot
Genome-wide maps of transcription factor footprints identify noncoding variants rewiring gene regulatory networks
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