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Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants

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What this work says

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

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Position-independent, high-level expression of the human β-globin gene in transgenic mice

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Cohesin at active genes: a unifying theme for cohesin and gene expression from model organisms to humans

inferredcites →https://doi.org/10.1016/j.cell.2006.02.041openalex-snapshot

A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells

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.2012.12.033openalex-snapshot

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

inferredcites →https://doi.org/10.1016/j.cell.2013.03.035openalex-snapshot

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

inferredcites →https://doi.org/10.1016/j.cell.2013.03.036openalex-snapshot

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

inferredcites →https://doi.org/10.1016/j.cell.2013.07.034openalex-snapshot

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

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Unsupervised pattern discovery in human chromatin structure through genomic segmentation

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Integrative annotation of chromatin elements from ENCODE data

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Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

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Mice Lacking a Myc Enhancer That Includes Human SNP rs6983267 Are Resistant to Intestinal Tumors

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Locus control regions

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A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

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inferred← citeshttps://doi.org/10.1016/j.gendis.2020.12.012openalex-snapshot

BET bromodomain inhibitor JQ1 regulates spermatid development by changing chromatin conformation in mouse spermatogenesis

inferred← citeshttps://doi.org/10.1016/j.gendis.2025.101652openalex-snapshot

Unveiling the regulatory potential of the non-coding genome: Insights from the human genome project to precision medicine

inferred← citeshttps://doi.org/10.1016/j.immuni.2019.03.028openalex-snapshot

The γc Family of Cytokines: Basic Biology to Therapeutic Ramifications

inferred← citeshttps://doi.org/10.1016/j.immuni.2025.10.020openalex-snapshot

FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry

inferred← citeshttps://doi.org/10.1016/j.it.2015.07.005openalex-snapshot

Super-enhancers: Asset management in immune cell genomes

inferred← citeshttps://doi.org/10.1016/j.it.2015.07.006openalex-snapshot

Exploiting genomics and natural genetic variation to decode macrophage enhancers

inferred← citeshttps://doi.org/10.1016/j.jaci.2017.12.1006openalex-snapshot

Epigenome analysis links gene regulatory elements in group 2 innate lymphocytes to asthma susceptibility

inferred← citeshttps://doi.org/10.1016/j.jbc.2021.101559openalex-snapshot

Unraveling three-dimensional chromatin structural dynamics during spermatogonial differentiation

inferred← citeshttps://doi.org/10.1016/j.jgg.2020.11.010openalex-snapshot

Fine genetic mapping of the chromosome 11q23.3 region in a Han Chinese population: insights into the apolipoprotein genes underlying the blood lipid-lipoprotein variances

inferred← citeshttps://doi.org/10.1016/j.jmb.2019.12.045openalex-snapshot

From Genetic Association to Molecular Mechanisms for Islet-cell Dysfunction in Type 2 Diabetes

inferred← citeshttps://doi.org/10.1016/j.jmb.2020.07.023openalex-snapshot

Visualization and Sequencing of Accessible Chromatin Reveals Cell Cycle and Post-HDAC inhibitor Treatment Dynamics

inferred← citeshttps://doi.org/10.1016/j.mex.2020.101165openalex-snapshot

High-performance method for identification of super enhancers from ChIP-Seq data with configurable cloud virtual machines

inferred← citeshttps://doi.org/10.1016/j.molcel.2014.05.016openalex-snapshot

The Mechanisms behind the Therapeutic Activity of BET Bromodomain Inhibition

inferred← citeshttps://doi.org/10.1016/j.molcel.2014.08.024openalex-snapshot

NF-κB Directs Dynamic Super Enhancer Formation in Inflammation and Atherogenesis

inferred← citeshttps://doi.org/10.1016/j.molcel.2015.02.014openalex-snapshot

Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers

inferred← citeshttps://doi.org/10.1016/j.molcel.2016.03.033openalex-snapshot

Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers

inferred← citeshttps://doi.org/10.1016/j.molcel.2017.09.016openalex-snapshot

The Elongation Factor Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Proteins

inferred← citeshttps://doi.org/10.1016/j.molcel.2018.04.025openalex-snapshot

Shaping Gene Expression by Landscaping Chromatin Architecture: Lessons from a Master

inferred← citeshttps://doi.org/10.1016/j.molcel.2020.12.047openalex-snapshot

Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements

inferred← citeshttps://doi.org/10.1016/j.molcel.2022.12.032openalex-snapshot

Deciphering the multi-scale, quantitative cis-regulatory code

inferred← citeshttps://doi.org/10.1016/j.molmed.2016.10.004openalex-snapshot

Genomic Alterations of Non-Coding Regions Underlie Human Cancer: Lessons from T-ALL

inferred← citeshttps://doi.org/10.1016/j.molmet.2019.06.002openalex-snapshot

(Epi)genomic heterogeneity of pancreatic islet function and failure in type 2 diabetes

inferred← citeshttps://doi.org/10.1016/j.molmet.2019.12.006openalex-snapshot

Single-cell ATAC-Seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

inferred← citeshttps://doi.org/10.1016/j.mrrev.2024.108489openalex-snapshot

Super-enhancers: Implications in gastric cancer

inferred← citeshttps://doi.org/10.1016/j.nbd.2018.02.007openalex-snapshot

Parkinson's disease genetic risk in a midbrain neuronal cell line

inferred← citeshttps://doi.org/10.1016/j.neuron.2014.11.011openalex-snapshot

Genomic Perspectives of Transcriptional Regulation in Forebrain Development

inferred← citeshttps://doi.org/10.1016/j.neuron.2022.06.004openalex-snapshot

3D spatial genome organization in the nervous system: From development and plasticity to disease

inferred← citeshttps://doi.org/10.1016/j.pharmthera.2015.07.004openalex-snapshot

Histone profiles in cancer

inferred← citeshttps://doi.org/10.1016/j.phrs.2023.106940openalex-snapshot

Super-enhancer-associated SNHG15 cooperating with FOSL1 contributes to bladder cancer progression through the WNT pathway

inferred← citeshttps://doi.org/10.1016/j.phrs.2026.108275openalex-snapshot

Targeting the transcriptional coactivator p300/CBP in cancer: Mechanistic insights and translational implications for osteosarcoma

inferred← citeshttps://doi.org/10.1016/j.semcdb.2018.07.008openalex-snapshot

Modeling three-dimensional genomic organization in evolution and pathogenesis

inferred← citeshttps://doi.org/10.1016/j.semcdb.2019.05.007openalex-snapshot

CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases

inferred← citeshttps://doi.org/10.1016/j.stem.2014.05.004openalex-snapshot

Lost in Transition: Dynamic Enhancer Organization across Naive and Primed Stem Cell States

inferred← citeshttps://doi.org/10.1016/j.stem.2014.05.005openalex-snapshot

Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency

inferred← citeshttps://doi.org/10.1016/j.stem.2019.11.011openalex-snapshot

Circadian Entrainment Triggers Maturation of Human In Vitro Islets

inferred← citeshttps://doi.org/10.1016/j.stemcr.2015.09.016openalex-snapshot

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

inferred← citeshttps://doi.org/10.1016/j.stemcr.2019.04.004openalex-snapshot

Enhancer Chromatin and 3D Genome Architecture Changes from Naive to Primed Human Embryonic Stem Cell States

inferred← citeshttps://doi.org/10.1016/j.stemcr.2026.102930openalex-snapshot

ZFHX4 is necessary for dopaminergic neuron differentiation and controls cell cycle by regulating LIN28A

inferred← citeshttps://doi.org/10.1016/j.tcb.2013.10.008openalex-snapshot

Distal enhancers: new insights into heart development and disease

inferred← citeshttps://doi.org/10.1016/j.tcb.2018.04.003openalex-snapshot

Enhancer Logic and Mechanics in Development and Disease

inferred← citeshttps://doi.org/10.1016/j.tcm.2015.01.014openalex-snapshot

The promise of enhancer-associated long noncoding RNAs in cardiac regeneration

inferred← citeshttps://doi.org/10.1016/j.tem.2014.05.001openalex-snapshot

The pancreatic β cell: recent insights from human genetics

inferred← citeshttps://doi.org/10.1016/j.tem.2016.11.005openalex-snapshot

Genome-Wide Insights into the Development and Function of Thermogenic Adipocytes

inferred← citeshttps://doi.org/10.1016/j.tibs.2022.01.002openalex-snapshot

The Mediator kinase module: an interface between cell signaling and transcription

inferred← citeshttps://doi.org/10.1016/j.tig.2014.02.006openalex-snapshot

Laying a solid foundation for Manhattan – ‘setting the functional basis for the post-GWAS era’

inferred← citeshttps://doi.org/10.1016/j.tig.2015.02.008openalex-snapshot

Epigenetic modifications and long noncoding RNAs influence pancreas development and function

inferred← citeshttps://doi.org/10.1016/j.tig.2015.11.004openalex-snapshot

Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases

inferred← citeshttps://doi.org/10.1016/j.tig.2016.02.003openalex-snapshot

Understanding Celiac Disease by Genomics

inferred← citeshttps://doi.org/10.1016/j.tig.2017.01.010openalex-snapshot

Genomics of Islet (Dys)function and Type 2 Diabetes

inferred← citeshttps://doi.org/10.1016/j.tig.2022.05.011openalex-snapshot

Interplay between regulatory elements and chromatin topology in cellular lineage determination

inferred← citeshttps://doi.org/10.1016/j.tig.2022.05.015openalex-snapshot

Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures

inferred← citeshttps://doi.org/10.1016/j.tma.2019.12.003openalex-snapshot

Remodeling of the H3 nucleosomal landscape during mouse aging

inferred← citeshttps://doi.org/10.1016/j.trecan.2016.09.002openalex-snapshot

Epigenomic Consequences of Coding and Noncoding Driver Mutations

inferred← citeshttps://doi.org/10.1016/j.trecan.2017.03.006openalex-snapshot

Super-Enhancer-Driven Transcriptional Dependencies in Cancer

inferred← citeshttps://doi.org/10.1016/j.xcrm.2022.100632openalex-snapshot

Intrinsic transcriptional heterogeneity in neuroblastoma guides mechanistic and therapeutic insights

inferred← citeshttps://doi.org/10.1016/j.xcrm.2024.101472openalex-snapshot

STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma

inferred← citeshttps://doi.org/10.1016/j.xgen.2024.100604openalex-snapshot

Implications of noncoding regulatory functions in the development of insulinomas

inferred← citeshttps://doi.org/10.1016/j.xgen.2025.100850openalex-snapshot

Incorporating multiple functional annotations to improve polygenic risk prediction accuracy

inferred← citeshttps://doi.org/10.1016/j.xgen.2025.101040openalex-snapshot

Predictive prioritization of enhancers associated with pancreatic disease risk

inferred← citeshttps://doi.org/10.1016/j.xhgg.2022.100158openalex-snapshot

CFDP1 is a neuroblastoma susceptibility gene that regulates transcription factors of the noradrenergic cell identity

inferred← citeshttps://doi.org/10.1016/j.xhgg.2026.100674openalex-snapshot

Massively parallel functional profiling prioritizes breast cancer risk variants and implicates CCDC88C in ER-positive breast cancer

inferred← citeshttps://doi.org/10.1016/j.ygeno.2014.04.006openalex-snapshot

Strategies to fine-map genetic associations with lipid levels by combining epigenomic annotations and liver-specific transcription profiles

inferred← citeshttps://doi.org/10.1016/j.yjmcc.2019.04.012openalex-snapshot

Epigenetic therapies in heart failure

inferred← citeshttps://doi.org/10.1016/j.ymeth.2017.03.012openalex-snapshot

Mining the topography and dynamics of the 4D Nucleome to identify novel CNS drug pathways

inferred← citeshttps://doi.org/10.1017/s001667231600001xopenalex-snapshot

The future of iPS cells in advancing regenerative medicine

inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c01100openalex-snapshot

Discovery of a Highly Potent PROTAC Degrader of p300/CBP Proteins for the Treatment of Enzalutamide-Resistant Prostate Cancer

inferred← citeshttps://doi.org/10.1021/acssynbio.4c00244openalex-snapshot

Enhancers: A Focus on Synthetic Biology and Correlated Gene Expression

inferred← citeshttps://doi.org/10.1038/leu.2014.70openalex-snapshot

Promiscuous MYC locus rearrangements hijack enhancers but mostly super-enhancers to dysregulate MYC expression in multiple myeloma

inferred← citeshttps://doi.org/10.1038/nature13835openalex-snapshot

Genetic and epigenetic fine mapping of causal autoimmune disease variants

inferred← citeshttps://doi.org/10.1038/nature14154openalex-snapshot

Super-enhancers delineate disease-associated regulatory nodes in T cells

inferred← citeshttps://doi.org/10.1038/nature15521openalex-snapshot

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

inferred← citeshttps://doi.org/10.1038/nature15540openalex-snapshot

Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism

inferred← citeshttps://doi.org/10.1038/nature18642openalex-snapshot

The genetic architecture of type 2 diabetes

inferred← citeshttps://doi.org/10.1038/nbt.3863openalex-snapshot

Characterization of noncoding regulatory DNA in the human genome

inferred← citeshttps://doi.org/10.1038/ncomms11764openalex-snapshot

The genetic regulatory signature of type 2 diabetes in human skeletal muscle

inferred← citeshttps://doi.org/10.1038/ncomms12092openalex-snapshot

Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci

inferred← citeshttps://doi.org/10.1038/ncomms12983openalex-snapshot

Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity

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