Histone H3K27ac separates active from poised enhancers and predicts developmental state.
paper
Cited
Public
Unavailable
- Authors
- Creyghton, Menno P; Cheng, Albert W; Welstead, G Grant; Kooistra, Tristan; Carey, Bryce W; Steine, Eveline J; Hanna, Jacob; Lodato, Michael A; Frampton, Garrett M; Sharp, Phillip A; Boyer, Laurie A; Young, Richard A; Jaenisch, Rudolf
- Year
- 2010
- Journal
- Proceedings of the National Academy of Sciences of the United States of America
- PMID
- 21106759
- DOI
- 10.1073/pnas.1016071107
- PMCID
- PMC3003124
Developmental programs are controlled by transcription factors and chromatin regulators, which maintain specific gene expression programs through epigenetic modification of the genome. These regulatory events at enhancers contribute to the specific gene expression programs that determine cell state and the potential for differentiation into new cell types. Although enhancer elements are known to be associated with certain histone modifications and transcription factors, the relationship of these modifications to gene expression and developmental state has not been clearly defined. Here we interrogate the epigenetic landscape of enhancer elements in embryonic stem cells and several adult tissues in the mouse. We find that histone H3K27ac distinguishes active enhancers from inactive/poised enhancer elements containing H3K4me1 alone. This indicates that the amount of actively used enhancers is lower than previously anticipated. Furthermore, poised enhancer networks provide clues to unrealized developmental programs. Finally, we show that enhancers are reset during nuclear reprogramming.
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| SMARCD1 is a dual regulator of PD-L1 expression and cell proliferation facilitating tumor evasion. | Fu G et al. | β | 2025 | β |
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| BRD9-SMAD2/3 Orchestrates Stemness and Tumorigenesis in Pancreatic Ductal Adenocarcinoma. | Feng Y et al. | β | 2024 | β |
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| cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers. | Nocente MC et al. | β | 2024 | β |
| CBP/P300 Inhibition Impairs CD4+ T Cell Activation: Implications for Autoimmune Disorders. | Picavet LW et al. | β | 2024 | β |
| CHHM: a Manually Curated Catalogue of Human Histone Modifications Revealing Hotspot Regions and Unique Distribution Patterns. | Ma W et al. | β | 2024 | β |
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| Chromatin profiling reveals TFAP4 as a critical transcriptional regulator of bovine satellite cell differentiation. | Lyu P et al. | β | 2024 | β |
| Chromatin structure and 3D architecture define the differential functions of PU.1 regulatory elements in blood cell lineages. | Qiu K et al. | β | 2024 | β |
| Coming of age in venom research. | RodrΓguez de la Vega RC | β | 2024 | β |
| CRISPR Activation Reverses Haploinsufficiency and Functional Deficits Caused by <i>TTN</i> Truncation Variants. | Ghahremani S et al. | β | 2024 | β |
| Crispr-Cas9-based long non-coding RNA interference and activation identified that the aberrant expression of Myc-regulated ST8SIA6 antisense RNA 1 promotes tumorigenesis and metastasis in hepatocellular carcinoma. | Liu X et al. | β | 2024 | β |
| CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant. | Kaplan SJ et al. | β | 2024 | β |
| Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage. | Mancheno-Ferris A et al. | β | 2024 | β |
| dCas9 Tells Tales: Probing Gene Function and Transcription Regulation in Cancer. | Mohamad Zamberi NN et al. | β | 2024 | β |
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| DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements. | Chandrashekar PB et al. | β | 2024 | β |
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| Electroacupuncture ameliorates blood-brain barrier disruption after ischemic stroke through histone acetylation regulation at the matrix metalloproteinase 9 and tissue inhibitor of metalloproteinase 2 genes. | Yonglin C et al. | β | 2024 | β |
| Electroacupuncture regulates histone acetylation of Bcl-2 and Caspase-3 genes to improve ischemic stroke injury. | Meng L et al. | β | 2024 | β |
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| Emerging Roles of Vitamin B<sub>12</sub> in Aging and Inflammation. | Simonenko SY et al. | β | 2024 | β |
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| Engineered uterine primary myometrial cells with high-mobility group AT-hook 2 overexpression display a leiomyoma-like transcriptional and epigenomic phenotype. | Saini P et al. | β | 2024 | β |
| EnhancerNet: a predictive model of cell identity dynamics through enhancer selection. | Karin O | β | 2024 | β |
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| Enhancers associated with unstable RNAs are rare in plants. | McDonald BR et al. | β | 2024 | β |
| Enhancers in T Cell development and malignant lesions. | Zhang T et al. | β | 2024 | β |
| Entangled and non-modular enhancer sequences producing independent spatial activities. | Museridze M et al. | β | 2024 | β |
| Epigenetic and Metabolic Reprogramming of Fibroblasts in Crohn's Disease Strictures Reveals Histone Deacetylases as Therapeutic Targets. | Lewis A et al. | β | 2024 | β |
| Epigenetic Approaches to Identifying Asthma Endotypes. | Kelly A et al. | β | 2024 | β |
| Epigenetic characterization of adult rhesus monkey spermatogonial stem cells identifies key regulators of stem cell homeostasis. | Bi R et al. | β | 2024 | β |
| Epigenetic dissection of human blood group genes reveals regulatory elements and detailed characteristics of KEL and four other loci. | Wu PC et al. | β | 2024 | β |
| Epigenetic Effects of Resveratrol on Oncogenic Signaling in Breast Cancer. | Kurzava Kendall L et al. | β | 2024 | β |
| Epigenetic inheritance and gene expression regulation in early Drosophila embryos. | Ciabrelli F et al. | β | 2024 | β |
| Epigenetic regulation and factors that influence the effect of iPSCs-derived neural stem/progenitor cells (NS/PCs) in the treatment of spinal cord injury. | Yang Y et al. | β | 2024 | β |
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| Epigenetics of Fear, Anxiety and Stress - Focus on Histone Modifications. | Ell MA et al. | β | 2024 | β |
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| Extracellular putrescine can augment the epithelial-mesenchymal transition of gastric cancer cells by promoting MAL2 expression by elevating H3K27ac in its promoter region. | Bi C et al. | β | 2024 | β |
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| Impaired bone morphogenetic protein (BMP) signaling pathways disrupt decidualization in endometriosis. | Liao Z et al. | β | 2024 | β |
| Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State. | Smith JP et al. | β | 2024 | β |
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| Intrinsic Epigenetic State of Primary Osteosarcoma Drives Metastasis. | Singh I et al. | β | 2024 | β |
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| Knockdown of PROX1 promotes milk fatty acid synthesis by targeting PPARGC1A in dairy goat mammary gland. | He Q et al. | β | 2024 | β |
| Leveraging Tissue-Specific Enhancer-Target Gene Regulatory Networks Identifies Enhancer Somatic Mutations That Functionally Impact Lung Cancer. | Hariprakash JM et al. | β | 2024 | β |
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| LINC00887 Acts as an Enhancer RNA to Promote Medullary Thyroid Carcinoma Progression by Binding with FOXQ1. | Liu D et al. | β | 2024 | β |
| LncRNA <i>PSMB8-AS1</i> Instigates Vascular Inflammation to Aggravate Atherosclerosis. | Li S et al. | β | 2024 | β |
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| MAE-seq refines regulatory elements across the genome. | Zhu X et al. | β | 2024 | β |
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| Mediator MED23 controls oligodendrogenesis and myelination by modulating Sp1/P300-directed gene programs. | Zhang S et al. | β | 2024 | β |
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| PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during development. | Bamgbose G et al. | β | 2024 | β |
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| Progress in multifactorial single-cell chromatin profiling methods. | Stuart T | β | 2024 | β |
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| Regulation of MicroRNA-4697-3p by Parkinson's disease-associated SNP rs329648 and its impact on SNCA112 mRNA. | Yoo M et al. | β | 2024 | β |
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| Reprogramming of the LXRΞ± Transcriptome Sustains Macrophage Secondary Inflammatory Responses. | Vladimir de la Rosa J et al. | β | 2024 | β |
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| Roles and Regulation of H3K4 Methylation During Mammalian Early Embryogenesis and Embryonic Stem Cell Differentiation. | Terzi ΓizmecioΔlu N | β | 2024 | β |
| Salinity-responsive histone PTMs identified in the gills and gonads of Mozambique tilapia (Oreochromis mossambicus). | Mojica EA et al. | β | 2024 | β |
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| Single-cell joint profiling of multiple epigenetic proteins and gene transcription. | Xiong H et al. | β | 2024 | β |
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| Small-molecule-induced epigenetic rejuvenation promotes SREBP condensation and overcomes barriers to CNS myelin regeneration. | Liu X et al. | β | 2024 | β |
| SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion. | Leuzzi G et al. | β | 2024 | β |
| SP1 undergoes phase separation and activates RGS20 expression through super-enhancers to promote lung adenocarcinoma progression. | Shan L et al. | β | 2024 | β |
| STAT3 drives the expression of HIF1alpha in cancer cells through a novel super-enhancer. | Dai Y et al. | β | 2024 | β |
| Stromal Pbrm1 mediates chromatin remodeling necessary for embryo implantation in the mouse uterus. | Xin Q et al. | β | 2024 | β |
| Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions. | Zhang Y et al. | β | 2024 | β |
| Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma. | Xiong S et al. | β | 2024 | β |
| Suppression of interferon Ξ± and Ξ³ response by Huwe1-mediated Miz1 degradation promotes SARS-CoV-2 replication. | Arunagiri V et al. | β | 2024 | β |
| Targeting BRD4 mitigates hepatocellular lipotoxicity by suppressing the NLRP3 inflammasome activation and GSDMD-mediated hepatocyte pyroptosis. | Chen F et al. | β | 2024 | β |
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| TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms. | Li Y et al. | β | 2024 | β |
| T-follicular helper cells are epigenetically poised to transdifferentiate into T-regulatory type 1 cells. | Garnica J et al. | β | 2024 | β |
| The DNA loop release factor WAPL suppresses Epstein-Barr virus latent membrane protein expression to maintain the highly restricted latency I program. | Murray-Nerger LA et al. | β | 2024 | β |
| The genetic regulatory architecture and epigenomic basis for age-related changes in rattlesnake venom. | Hogan MP et al. | β | 2024 | β |
| The Human Accelerated Region HAR202 Controls NPAS3 Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences. | Caporale AL et al. | β | 2024 | β |
| The human milk oligosaccharide 3'sialyllactose reduces low-grade inflammation and atherosclerosis development in mice. | Pessentheiner AR et al. | β | 2024 | β |
| The impact of retrotransposons on zygotic genome activation and the chromatin landscape of early embryos. | Solberg T et al. | β | 2024 | β |
| The importance of functional genomics studies in precision rheumatology. | Piedade AP et al. | β | 2024 | β |
| The Long Non-Coding RNA Obesity-Related (Obr) Contributes To Lipid Metabolism Through Epigenetic Regulation. | Kaimala S et al. | β | 2024 | β |
| The pleiotropic enhancer enh9 promotes cell proliferation and migration in non-small cell lung cancer via ERMP1 and PD-L1. | Wang Q et al. | β | 2024 | β |
| The primitive endoderm supports lineage plasticity to enable regulative development. | Linneberg-Agerholm M et al. | β | 2024 | β |
| The RP11-417E7.1/THBS2 signaling pathway promotes colorectal cancer metastasis by activating the Wnt/Ξ²-catenin pathway and facilitating exosome-mediated M2 macrophage polarization. | Liu Y et al. | β | 2024 | β |
| The transcriptional activator Klf5 recruits p300-mediated H3K27ac for maintaining trophoblast stem cell pluripotency. | Dou C et al. | β | 2024 | β |
| The transcriptional regulatory network modulating human trophoblast stem cells to extravillous trophoblast differentiation. | Kim M et al. | β | 2024 | β |
| The transcription factor NF-ΞΊB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling. | Feng AC et al. | β | 2024 | β |
| Three-Dimensional Chromosomal Landscape Revealing miR-146a Dysfunctional Enhancer in Lupus and Establishing a CRISPR-Mediated Approach to Inhibit the Interferon Pathway. | Zhu X et al. | β | 2024 | β |
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| Towards functional maps of non-coding variants in cancer. | Wang Y et al. | β | 2024 | β |
| Transcriptional Regulation of the Lineage-Determining Gene <i>PU.1</i> in Normal and Malignant Hematopoiesis: Current Understanding and Therapeutic Perspective. | Korczmar EA et al. | β | 2024 | β |
| Transcriptional re-programming of liver-resident iNKT cells into T-regulatory type-1-like liver iNKT cells involves extensive gene de-methylation. | MontaΓ±o J et al. | β | 2024 | β |
| Transcriptome-Wide Profiling of Nascent RNA in Neurons with Enriched H3K27ac Signal Elevates eRNA Identification Efficiency. | Jiang J et al. | β | 2024 | β |
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| Translation of genome-wide association study: from genomic signals to biological insights. | Bruner WS et al. | β | 2024 | β |
| Transposable elements contribute to tissue-specific gene regulation in humans. | Ali A et al. | β | 2024 | β |
| TRIM33 plays a critical role in regulating dendritic cell differentiation and homeostasis by modulating Irf8 and Bcl2l11 transcription. | Shen X et al. | β | 2024 | β |
| ULI-ssDRIP-seq revealed R-loop dynamics during vertebrate early embryogenesis. | Xu W et al. | β | 2024 | β |
| Unveiling Novel Mechanism of CIDEB in Fatty Acid Synthesis Through ChIP-Seq and Functional Analysis in Dairy Goat. | He Q et al. | β | 2024 | β |
| ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency. | Hossain I et al. | β | 2024 | β |
| 5-Azacytidine- and retinoic-acid-induced reprogramming of DCCs into dormancy suppresses metastasis via restored TGF-Ξ²-SMAD4 signaling. | Singh DK et al. | β | 2023 | β |
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| Acetyltransferases CBP/p300 Control Transcriptional Switch of Ξ²-Catenin and Stat1 Promoting Osteoblast Differentiation. | Zhang L et al. | β | 2023 | β |
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| Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1. | Sreekar N et al. | β | 2023 | β |
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| Bromodomain Protein Inhibitors Reorganize the Chromatin of Synovial Fibroblasts. | KroΕ‘el M et al. | β | 2023 | β |
| Cancer-Associated Fibroblast-Derived miR-146a-5p Generates a Niche That Promotes Bladder Cancer Stemness and Chemoresistance. | Zhuang J et al. | β | 2023 | β |
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| Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays. | Koesterich J et al. | β | 2023 | β |
| Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells. | Moyers BA et al. | β | 2023 | β |
| Characterization of network hierarchy reflects cell state specificity in genome organization. | Wang J et al. | β | 2023 | β |
| Chromatin accessibility differences between alpha, beta, and delta cells identifies common and cell type-specific enhancers. | Mawla AM et al. | β | 2023 | β |
| Chromatin control of human cytomegalovirus infection. | Matthews SM et al. | β | 2023 | β |
| Chromatin regulation of transcriptional enhancers and cell fate by the Sotos syndrome gene NSD1. | Sun Z et al. | β | 2023 | β |
| Chromatin regulators in the TBX1 network confer risk for conotruncal heart defects in 22q11.2DS. | Zhao Y et al. | β | 2023 | β |
| Chromatin remodeling of prostaglandin signaling in smooth muscle enables mouse embryo passage through the female reproductive tract. | Xin Q et al. | β | 2023 | β |
| Cis-Regulatory Elements in Mammals. | Liu X et al. | β | 2023 | β |
| Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes. | Zhu I et al. | β | 2023 | β |
| Clustered PHD domains in KMT2/MLL proteins are attracted by H3K4me3 and H3 acetylation-rich active promoters and enhancers. | Stroynowska-Czerwinska AM et al. | β | 2023 | β |
| Comprehensive machine learning-generated classifier identifies pro-metastatic characteristics and predicts individual treatment in pancreatic cancer: A multicenter cohort study based on super-enhancer profiling. | Chen D et al. | β | 2023 | β |
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| Conserved and divergent gene regulatory programs of the mammalian neocortex. | Zemke NR et al. | β | 2023 | β |
| Cross-tissue patterns of DNA hypomethylation reveal genetically distinct histories of cell development. | Scott TJ et al. | β | 2023 | β |
| Deciphering the DNA methylome in women with PCOS diagnosed using the new international evidence-based guidelines. | Wang Y et al. | β | 2023 | β |
| Decoding enhancer complexity with machine learning and high-throughput discovery. | Smith GD et al. | β | 2023 | β |
| DeepICSH: a complex deep learning framework for identifying cell-specific silencers and their strength from the human genome. | Zhang T et al. | β | 2023 | β |
| DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome. | Zhang T et al. | β | 2023 | β |
| Defining super-enhancers by highly ranked histone H4 multi-acetylation levels identifies transcription factors associated with glioblastoma stem-like properties. | Das ND et al. | β | 2023 | β |
| Demethylase-independent roles of LSD1 in regulating enhancers and cell fate transition. | Zeng C et al. | β | 2023 | β |
| Detailed molecular and epigenetic characterization of the pig IPEC-J2 and chicken SL-29 cell lines. | de Vos J et al. | β | 2023 | β |
| DEtail-seq is an ultra-efficient and convenient method for meiotic DNA break profiling in multiple organisms. | Xu W et al. | β | 2023 | β |
| Differential exon usage of developmental genes is associated with deregulated epigenetic marks. | Do HTT et al. | β | 2023 | β |
| Differentiated neuroblastoma cells remain epigenetically poised for de-differentiation to an immature state. | Guyer RA et al. | β | 2023 | β |
| Discrimination of cell-intrinsic and environment-dependent effects of natural genetic variation on Kupffer cell epigenomes and transcriptomes. | Bennett H et al. | β | 2023 | β |
| Disruption of the ATXN1-CIC complex reveals the role of additional nuclear ATXN1 interactors in spinocerebellar ataxia type 1. | Coffin SL et al. | β | 2023 | β |
| Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia. | Yashar WM et al. | β | 2023 | β |
| Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. | Beard DC et al. | β | 2023 | β |
| Distinct layers of BRD4-PTEFb reveal bromodomain-independent function in transcriptional regulation. | Zheng B et al. | β | 2023 | β |
| Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function. | Spolski R et al. | β | 2023 | β |
| Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation. | Li J et al. | β | 2023 | β |
| DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle. | Maehara H et al. | β | 2023 | β |
| Dynamic chromatin accessibility during nutritional iron overload reveals a BMP6-independent induction of cell cycle genes. | Radushkevitz-Frishman T et al. | β | 2023 | β |
| Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock. | Bafna A et al. | β | 2023 | β |
| Dynamics of Chromatin Accessibility During Hematopoietic Stem Cell Differentiation Into Progressively Lineage-Committed Progeny. | Martin EW et al. | β | 2023 | β |
| Dynamics of histone acetylation during human early embryogenesis. | Wu K et al. | β | 2023 | β |
| Effects of the omega-3 fatty acid DHA on histone and p53 acetylation in diffuse large B cell lymphoma. | Bakhshi TJ et al. | β | 2023 | β |
| Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development. | Lismer A et al. | β | 2023 | β |
| Emerging insights into enhancer biology and function. | Arnold M et al. | β | 2023 | β |
| Engineered MED12 mutations drive leiomyoma-like transcriptional and metabolic programs by altering the 3D genome compartmentalization. | Buyukcelebi K et al. | β | 2023 | β |
| Enhancer and super-enhancer landscape in polycystic kidney disease. | Lakhia R et al. | β | 2023 | β |
| Enhancer Clusters Drive Type I Interferon-Induced TRAIL Overexpression in Cancer, and Its Intracellular Protein Accumulation Fails to Induce Apoptosis. | Di Benedetto C et al. | β | 2023 | β |
| Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. | Cao J et al. | β | 2023 | β |
| Epigenetic and epitranscriptomic regulation of axon regeneration. | Cheng Y et al. | β | 2023 | β |
| Epigenetic changes in inflammatory arthritis monocytes contribute to disease and can be targeted by JAK inhibition. | Peeters JGC et al. | β | 2023 | β |
| Epigenetic Control of Cell Potency and Fate Determination during Mammalian Gastrulation. | Sullivan AE | β | 2023 | β |
| Epigenetic (De)regulation in Prostate Cancer. | Xu C et al. | β | 2023 | β |
| Epigenetic moonlighting: Catalytic-independent functions of histone modifiers in regulating transcription. | Morgan MAJ et al. | β | 2023 | β |
| Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma. | Abatti LE et al. | β | 2023 | β |
| Epigenetic signals that direct cell type-specific interferon beta response in mouse cells. | Muckenhuber M et al. | β | 2023 | β |
| Epigenome-Driven Strategies for Personalized Cancer Immunotherapy. | Rocha GIY et al. | β | 2023 | β |
| Epigenomic analysis of Alzheimer's disease brains reveals diminished CTCF binding on genes involved in synaptic organization. | Patel PJ et al. | β | 2023 | β |
| Epigenomic mapping reveals distinct B cell acute lymphoblastic leukemia chromatin architectures and regulators. | Barnett KR et al. | β | 2023 | β |
| Epigenomic regulation of macrophage polarization: Where do the nuclear receptors belong? | Czimmerer Z et al. | β | 2023 | β |
| Epromoters are new players in the regulatory landscape with potential pleiotropic roles. | Malfait J et al. | β | 2023 | β |
| eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways. | Ahmed I et al. | β | 2023 | β |
| Experimental Validation and Prediction of Super-Enhancers: Advances and Challenges. | Kravchuk EV et al. | β | 2023 | β |
| Expression of Human Endogenous Retrovirus Group K (HERV-K) HML-2 Correlates with Immune Activation of Macrophages and Type I Interferon Response. | Russ E et al. | β | 2023 | β |
| Ex vivo mapping of enhancer networks that define the transcriptional program driving melanoma metastasis. | Manicardi V et al. | β | 2023 | β |
| FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer. | Guneri-Sozeri PY et al. | β | 2023 | β |
| Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions. | Kim HM et al. | β | 2023 | β |
| FOXA2 controls the anti-oxidant response in FH-deficient cells. | Rogerson C et al. | β | 2023 | β |
| FoxK1 associated gene regulatory network in hepatic insulin action and its relationship to FoxO1 and insulin receptor mediated transcriptional regulation. | Allu PKR et al. | β | 2023 | β |
| From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis. | Mulet-Lazaro R et al. | β | 2023 | β |
| Functional annotation of the animal genomes: An integrated annotation resource for the horse. | Peng S et al. | β | 2023 | β |
| Genome graphs detect human polymorphisms in active epigenomic state during influenza infection. | Groza C et al. | β | 2023 | β |
| Genome-wide analysis of histone modifications that underlie the dynamic changes in gene expression during decidualization in human endometrial stromal cells. | Tamura I et al. | β | 2023 | β |
| Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation. | Jing Y et al. | β | 2023 | β |
| Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function. | Bhat S et al. | β | 2023 | β |
| Genome-wide enhancer identification by massively parallel reporter assay in Arabidopsis. | Tan Y et al. | β | 2023 | β |
| Genome-wide identification of notochord enhancers comprising the regulatory landscape of the brachyury locus in mouse. | Schifferl D et al. | β | 2023 | β |
| Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma. | Koh KD et al. | β | 2023 | β |
| Genomic glucocorticoid action in embryonic mouse neural stem cells. | Berry KJ et al. | β | 2023 | β |
| Genomic targets of the IRE1-XBP1s pathway in mediating metabolic adaptation in epithelial plasticity. | Qiao D et al. | β | 2023 | β |
| Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response. | Pagadala M et al. | β | 2023 | β |
| Globally elevated levels of histone H3 lysine 9 trimethylation in early infancy are associated with poor growth trajectory in Bangladeshi children. | Kupkova K et al. | β | 2023 | β |
| H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development. | Yu Y et al. | β | 2023 | β |
| H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function. | Pal D et al. | β | 2023 | β |
| High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription. | Bressin A et al. | β | 2023 | β |
| HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers. | Morozov VM et al. | β | 2023 | β |
| Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis. | Zhou JJ et al. | β | 2023 | β |
| Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells. | DunjiΔ M et al. | β | 2023 | β |
| Histone Modification Analysis of Low-Mappability Regions. | Yoshizawa-Sugata N et al. | β | 2023 | β |
| Histone modification analysis reveals common regulators of gene expression in liver and blood stage merozoites of Plasmodium parasites. | Reers AB et al. | β | 2023 | β |
| HIV-1 Gag co-localizes with euchromatin histone marks at the nuclear periphery. | Chang J et al. | β | 2023 | β |
| HMGA1 induces FGF19 to drive pancreatic carcinogenesis and stroma formation. | Chia L et al. | β | 2023 | β |
| Human cytomegalovirus pUL97 upregulates SOCS3 expression via transcription factor RFX7 in neural progenitor cells. | Wang XZ et al. | β | 2023 | β |
| Human microglia maturation is underpinned by specific gene regulatory networks. | Han CZ et al. | β | 2023 | β |
| Identification and characterization of enhancer elements controlling cell type-specific and signalling dependent chromatin programming during hematopoietic development. | Maytum A et al. | β | 2023 | β |
| Identification and comprehensive analysis of super-enhancer related genes involved in epithelial-to-mesenchymal transition in lung adenocarcinoma. | Liu Y | β | 2023 | β |
| Identification of non-coding silencer elements and their regulation of gene expression. | Pang B et al. | β | 2023 | β |
| Ikaros family proteins redundantly regulate temporal patterning in the developing mouse retina. | Javed A et al. | β | 2023 | β |
| Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model. | Pierzynska-Mach A et al. | β | 2023 | β |
| Impact of Germline Depletion of Bonus on Chromatin State in <i>Drosophila</i> Ovaries. | Godneeva B et al. | β | 2023 | β |
| Increased chromatin accessibility promotes the evolution of a transcriptional silencer in <i>Drosophila</i>. | Ling L et al. | β | 2023 | β |
| Inducible CRISPR Epigenome Systems Mimic Cocaine Induced Bidirectional Regulation of Nab2 and Egr3. | Choi EY et al. | β | 2023 | β |
| Insights from a 30-year journey: function, regulation and therapeutic modulation of PD1. | Chamoto K et al. | β | 2023 | β |
| In silico enhancer mining reveals SNS-032 and EHMT2 inhibitors as therapeutic candidates in high-grade serous ovarian cancer. | Quintela M et al. | β | 2023 | β |
| Integrated high-throughput analysis identifies super enhancers in metastatic castration-resistant prostate cancer. | Zeng J et al. | β | 2023 | β |
| Integrated multiomics analysis of chromosome 19 miRNA cluster in bladder cancer. | Ware AP et al. | β | 2023 | β |
| Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation. | Collora JA et al. | β | 2023 | β |
| Integrative epigenetic analysis reveals AP-1 promotes activation of tumor-infiltrating regulatory T cells in HCC. | Zhuo B et al. | β | 2023 | β |
| Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies. | Son KH et al. | β | 2023 | β |
| Interactive enhancer hubs (iHUBs) mediate transcriptional reprogramming and adaptive resistance in pancreatic cancer. | Hamdan FH et al. | β | 2023 | β |
| Interpretable predictive models of genome-wide aryl hydrocarbon receptor-DNA binding reveal tissue-specific binding determinants. | Filipovic D et al. | β | 2023 | β |
| Iron Oxide Nanoparticles with and without Cobalt Functionalization Provoke Changes in the Transcription Profile via Epigenetic Modulation of Enhancer Activity. | Gamberoni F et al. | β | 2023 | β |
| JUN-induced super-enhancer RNA forms R-loop to promote nasopharyngeal carcinoma metastasis. | Jia Q et al. | β | 2023 | β |
| Leveraging dominant-negative histone H3 K-to-M mutations to study chromatin during differentiation and development. | Serdyukova K et al. | β | 2023 | β |
| Liquid biopsy epigenomic profiling for cancer subtyping. | Baca SC et al. | β | 2023 | β |
| Live-cell imaging uncovers the relationship between histone acetylation, transcription initiation, and nucleosome mobility. | Saxton MN et al. | β | 2023 | β |
| Long non-coding RNA lncMGC mediates the expression of TGF-Ξ²-induced genes in renal cells via nucleosome remodelers. | Kato M et al. | β | 2023 | β |
| Long-read genome assemblies reveal a <i>cis</i>-regulatory landscape associated with phenotypic divergence in two sister <i>Siniperca</i> fish species. | Tu GX et al. | β | 2023 | β |
| Loss of ANCO1 Expression Regulates Chromatin Accessibility and Drives Progression of Early-Stage Triple-Negative Breast Cancer. | Yuan M et al. | β | 2023 | β |
| Loss of Kmt2c in vivo leads to EMT, mitochondrial dysfunction and improved response to lapatinib in breast cancer. | Simigdala N et al. | β | 2023 | β |
| L-type calcium channels and neuropsychiatric diseases: Insights into genetic risk variant-associated genomic regulation and impact on brain development. | Baker MR et al. | β | 2023 | β |
| Machine learning reveals STAT motifs as predictors for GR-mediated gene repression. | HΓΆllbacher B et al. | β | 2023 | β |
| MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming. | Mohammed Ismail W et al. | β | 2023 | β |
| Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. | Andrews G et al. | β | 2023 | β |
| Mecp2 Fine-tunes Quiescence Exit by Targeting Nuclear Receptors | Yang J et al. | β | 2023 | β |
| Mesenchymal Stromal Cells Facilitate Neutrophil-Trained Immunity by Reprogramming Hematopoietic Stem Cells. | Ng J et al. | β | 2023 | β |
| Methyl-CpG binding domain 2 (Mbd2) is an epigenetic regulator of autism-risk genes and cognition. | Lax E et al. | β | 2023 | β |
| Microglial pattern recognition via IL-33 promotes synaptic refinement in developing corticothalamic circuits in mice. | Han RT et al. | β | 2023 | β |
| MLL3/MLL4 methyltransferase activities control early embryonic development and embryonic stem cell differentiation in a lineage-selective manner. | Xie G et al. | β | 2023 | β |
| MOF-mediated histone H4 Lysine 16 acetylation governs mitochondrial and ciliary functions by controlling gene promoters. | Wang D et al. | β | 2023 | β |
| Molecular Genetics of Abnormal Redox Homeostasis in Type 2 Diabetes Mellitus. | Azarova I et al. | β | 2023 | β |
| Mouse B2 SINE elements function as IFN-inducible enhancers. | Horton I et al. | β | 2023 | β |
| Multi-layered transcriptional control of cranial neural crest development. | Candido-Ferreira IL et al. | β | 2023 | β |
| Multimodal epigenetic changes and altered NEUROD1 chromatin binding in the mouse hippocampus underlie FOXG1 syndrome. | Akol I et al. | β | 2023 | β |
| Multiomic analysis implicates FOXO4 in genetic regulation of chick lens fiber cell differentiation. | Brennan L et al. | β | 2023 | β |
| Multi-omics approach reveals dysregulated genes during hESCs neuronal differentiation exposure to paracetamol. | Spildrejorde M et al. | β | 2023 | β |
| Multiple lineage-specific epigenetic landscapes at the antigen receptor loci. | Qiu X et al. | β | 2023 | β |
| MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain. | Chen J et al. | β | 2023 | β |
| Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution. | Stuart T et al. | β | 2023 | β |
| Neuroprotective protein ADNP-dependent histone remodeling complex promotes T helper 2 immune cell differentiation. | Ferreira ACF et al. | β | 2023 | β |
| New Insights in Immunometabolism in Neonatal Monocytes and Macrophages in Health and Disease. | de Jong R et al. | β | 2023 | β |
| Noncoding RNA mutations in cancer. | Zhou H et al. | β | 2023 | β |
| Novel enhancers conferring compensatory transcriptional regulation of Nkx2-5 in heart development. | Zhang J et al. | β | 2023 | β |
| Novel rare mutation in a conserved site of PTPRB causes human hypoplastic left heart syndrome. | Jia Y et al. | β | 2023 | β |
| Nuclear condensates of YAP fusion proteins alter transcription to drive ependymoma tumourigenesis. | Hu X et al. | β | 2023 | β |
| Olig1/2-Expressing Intermediate Lineage Progenitors Are Predisposed to PTEN/p53-Loss-Induced Gliomagenesis and Harbor Specific Therapeutic Vulnerabilities. | Verma R et al. | β | 2023 | β |
| ONECUT2 regulates RANKL-dependent enterocyte and microfold cell differentiation in the small intestine; a multi-omics study. | Luna Velez MV et al. | β | 2023 | β |
| OnTarget: in silico design of MiniPromoters for targeted delivery of expression. | Fornes O et al. | β | 2023 | β |
| Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato. | Julian R et al. | β | 2023 | β |
| Ovulatory signal-triggered chromatin remodeling in ovarian granulosa cells by HDAC2 phosphorylation activation-mediated histone deacetylation. | Jin J et al. | β | 2023 | β |
| Palbociclib releases the latent differentiation capacity of neuroblastoma cells. | Ferguson KM et al. | β | 2023 | β |
| PGE<sub>2</sub> alters chromatin through H2A.Z-variant enhancer nucleosome modification to promote hematopoietic stem cell fate. | Sporrij A et al. | β | 2023 | β |
| Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure. | Oka M et al. | β | 2023 | β |
| Phenotypic dimorphism between honeybee queen and worker is regulated by complicated epigenetic modifications. | Jin MJ et al. | β | 2023 | β |
| Pioneer factor ASCL1 cooperates with the mSWI/SNF complex at distal regulatory elements to regulate human neural differentiation. | PΔun O et al. | β | 2023 | β |
| Plasmodium falciparum gametocytes display global chromatin remodelling during sexual differentiation. | Jeninga MD et al. | β | 2023 | β |
| Polymorphisms of the <i>GCLC</i> Gene Are Novel Genetic Markers for Susceptibility to Psoriasis Associated with Alcohol Abuse and Cigarette Smoking. | Efanova E et al. | β | 2023 | β |
| PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks. | Wang J et al. | β | 2023 | β |
| POSTRE: a tool to predict the pathological effects of human structural variants. | SΓ‘nchez-Gaya V et al. | β | 2023 | β |
| Predicting active enhancers with DNA methylation and histone modification. | Luo X et al. | β | 2023 | β |
| Prediction accuracy of regulatory elements from sequence varies by functional sequencing technique. | Nowling RJ et al. | β | 2023 | β |
| Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues. | Zhao X et al. | β | 2023 | β |
| Profiling neuronal methylome and hydroxymethylome of opioid use disorder in the human orbitofrontal cortex. | Rompala G et al. | β | 2023 | β |
| Quantitative Acetylomics Reveals Substrates of Lysine Acetyltransferase GCN5 in Adult and Aging <i>Drosophila</i>. | Li J et al. | β | 2023 | β |
| RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1Ξ²- and RNA-dependent co-activator of osteoclast gene expression. | Abe Y et al. | β | 2023 | β |
| Recapitulation of patient-specific 3D chromatin conformation using machine learning. | Xu D et al. | β | 2023 | β |
| Recycling of parental histones preserves the epigenetic landscape during embryonic development. | MΓΌhlen D et al. | β | 2023 | β |
| Regulation, functions and transmission of bivalent chromatin during mammalian development. | Macrae TA et al. | β | 2023 | β |
| Regulation of HDAC11 gene expression in early myogenic differentiation. | Li Q et al. | β | 2023 | β |
| Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences. | Lindhorst D et al. | β | 2023 | β |
| Reprogramming of cis-regulatory networks during skeletal muscle atrophy in male mice. | Lin H et al. | β | 2023 | β |
| Rewiring cancer drivers to activate apoptosis. | Gourisankar S et al. | β | 2023 | β |
| Rho enhancers play unexpectedly minor roles in Rhodopsin transcription and rod cell integrity. | Sun C et al. | β | 2023 | β |
| Role of epigenetics in pancreatic ductal adenocarcinoma. | Pandey S et al. | β | 2023 | β |
| Role of primary aging hallmarks in AlzheimerΒ΄s disease. | Zhao J et al. | β | 2023 | β |
| RSV replication modifies the XBP1s binding complex on the IRF1 upstream enhancer to potentiate the mucosal anti-viral response. | Qiao D et al. | β | 2023 | β |
| SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity. | Fixsen BR et al. | β | 2023 | β |
| Selective control of transposable element expression during T cell exhaustion and anti-PD-1 treatment. | BontΓ© PE et al. | β | 2023 | β |
| SENIES: DNA Shape Enhanced Two-Layer Deep Learning Predictor for the Identification of Enhancers and Their Strength. | Li Y et al. | β | 2023 | β |
| SET8 is a novel negative regulator of TGF-Ξ² signaling in a methylation-independent manner. | Nagasaka M et al. | β | 2023 | β |
| SETD1A drives stemness by reprogramming the epigenetic landscape in hepatocellular carcinoma stem cells. | Chen J et al. | β | 2023 | β |
| SETD2 regulates chromatin accessibility and transcription to suppress lung tumorigenesis. | Xie Y et al. | β | 2023 | β |
| SETting up the genome: KMT2D and KDM6A genomic function in the Kabuki syndrome craniofacial developmental disorder. | Shpargel KB et al. | β | 2023 | β |
| Shaping faces: genetic and epigenetic control of craniofacial morphogenesis. | Selleri L et al. | β | 2023 | β |
| Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex. | Roethler O et al. | β | 2023 | β |
| Single nucleotide polymorphisms rs148582811 regulates its host gene <i>ARVCF</i> expression to affect nicotine-associated hippocampus-dependent memory. | Yang Z et al. | β | 2023 | β |
| Small-sample learning reveals propionylation in determining global protein homeostasis. | Shui K et al. | β | 2023 | β |
| Smarcd3 is an epigenetic modulator of the metabolic landscape in pancreatic ductal adenocarcinoma. | Ferguson LP et al. | β | 2023 | β |
| Super-enhancer-associated transcription factors collaboratively regulate trophoblast-active gene expression programs in human trophoblast stem cells. | Kim M et al. | β | 2023 | β |
| Super-enhancer landscape rewiring in cancer: The epigenetic control at distal sites. | Di Giorgio E et al. | β | 2023 | β |
| Systemic and intrinsic functions of ATRX in glial cell fate and CNS myelination in male mice. | Rowland ME et al. | β | 2023 | β |
| Targeting the super elongation complex for oncogenic transcription driven tumor malignancies: Progress in structure, mechanisms and small molecular inhibitor discovery. | Wu X et al. | β | 2023 | β |
| The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data. | Hecker D et al. | β | 2023 | β |
| The BAF chromatin complex component SMARCC1 does not mediate GLI transcriptional repression of Hedgehog target genes in limb buds. | Ramachandran J et al. | β | 2023 | β |
| The cholesterol transporter NPC1 is essential for epigenetic regulation and maturation of oligodendrocyte lineage cells. | Kunkel TJ et al. | β | 2023 | β |
| The chromatin signatures of enhancers and their dynamic regulation. | Barral A et al. | β | 2023 | β |
| The enhancer landscape predetermines the skeletal regeneration capacity of stromal cells. | Hochmann S et al. | β | 2023 | β |
| The Hdc GC box is critical for Hdc gene transcription and histamine-mediated anaphylaxis. | Li Y et al. | β | 2023 | β |
| The histone demethylase KDM5C functions as a tumor suppressor in AML by repression of bivalently marked immature genes. | Trempenau ML et al. | β | 2023 | β |
| The Interplay between Dysregulated Metabolism and Epigenetics in Cancer. | Bassal MA | β | 2023 | β |
| The miR-430 locus with extreme promoter density forms a transcription body during the minor wave of zygotic genome activation. | Hadzhiev Y et al. | β | 2023 | β |
| The paracaspase MALT1 is a downstream target of Smad3 and potentiates the crosstalk between TGF-Ξ² and NF-kB signaling pathways in cancer cells. | Mazi FA et al. | β | 2023 | β |
| Therapeutic Efficacy of YM155 to Regulate an Epigenetic Enzyme in Major Subtypes of RCC. | Hong SH et al. | β | 2023 | β |
| The super-enhancer repertoire in porcine liver. | Zhang Y et al. | β | 2023 | β |
| The suppressive efficacy of THZ1 depends on KRAS mutation subtype and is associated with super-enhancer activity and the PI3K/AKT/mTOR signalling in pancreatic ductal adenocarcinoma: A hypothesis-generating study. | Huang L et al. | β | 2023 | β |
| Three-Dimensional Gene Regulation Network in Glioblastoma Ferroptosis. | Liu M et al. | β | 2023 | β |
| Titration-based normalization of antibody amount improves consistency of ChIP-seq experiments. | Caride A et al. | β | 2023 | β |
| Toward a comprehensive catalog of regulatory elements. | Fan K et al. | β | 2023 | β |
| Toward Identification of Functional Sequences and Variants in Noncoding DNA. | Monti R et al. | β | 2023 | β |
| Toxic PARP trapping upon cAMP-induced DNA damage reinstates the efficacy of endocrine therapy and CDK4/6 inhibitors in treatment-refractory ER+ breast cancer. | Saatci O et al. | β | 2023 | β |
| TP63 fusions drive multicomplex enhancer rewiring, lymphomagenesis, and EZH2 dependence. | Wu G et al. | β | 2023 | β |
| Tracking Targets of Dynamic Super-Enhancers <i>in Vitro</i> to Better Characterize Osteoclastogenesis and to Evaluate the Effect of Diuron on the Maturation of Human Bone Cells. | Tesfaye RA et al. | β | 2023 | β |
| Transcriptional metabolic reprogramming implements meiotic fate decision in mouse testicular germ cells. | Zhang X et al. | β | 2023 | β |
| Translating non-coding genetic associations into a better understanding of immune-mediated disease. | Stankey CT et al. | β | 2023 | β |
| Transmission of stimulus-induced epigenetic changes through cell division is coupled to continuous transcription factor activity. | Sun S et al. | β | 2023 | β |
| Transposable elements as tissue-specific enhancers in cancers of endodermal lineage. | Karttunen K et al. | β | 2023 | β |
| TWIST2-mediated chromatin remodeling promotes fusion-negative rhabdomyosarcoma. | Shah AM et al. | β | 2023 | β |
| Uncovering oligodendrocyte enhancers that control Cnp expression. | Fan C et al. | β | 2023 | β |
| Variation in histone configurations correlates with gene expression across nine inbred strains of mice. | Tyler AL et al. | β | 2023 | β |
| Vitamin D inhibits osteosarcoma by reprogramming nonsense-mediated RNA decay and SNAI2-mediated epithelial-to-mesenchymal transition. | Capobianco E et al. | β | 2023 | β |
| Widespread regulatory specificities between transcriptional co-repressors and enhancers in <i>Drosophila</i>. | Jacobs J et al. | β | 2023 | β |
| Ypel5 regulates liver development and function in zebrafish. | Deng Y et al. | β | 2023 | β |
| Zebrafish ELL-associated factors Eaf1/2 modulate erythropoiesis via regulating gata1a expression and WNT signaling to facilitate hypoxia tolerance. | Liu W et al. | β | 2023 | β |
| 3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells. | Papadogkonas G et al. | β | 2022 | β |
| 3D genome organization links non-coding disease-associated variants to genes. | Orozco G et al. | β | 2022 | β |
| Abnormal transcriptome-wide DNA demethylation induced by folate deficiency causes neural tube defects. | Wang S et al. | β | 2022 | β |
| Adrenergic receptor signaling induced by Klf15, a regulator of regeneration enhancer, promotes kidney reconstruction. | Suzuki N et al. | β | 2022 | β |
| Advances in Single-Cell Multi-Omics and Application in Cardiovascular Research. | Zhang X et al. | β | 2022 | β |
| Alcohol induced increases in sperm Histone H3 lysine 4 trimethylation correlate with increased placental CTCF occupancy and altered developmental programming. | Bedi YS et al. | β | 2022 | β |
| Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage. | Balasooriya GI et al. | β | 2022 | β |
| A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome. | Ni P et al. | β | 2022 | β |
| Analysis of the landscape of human enhancer sequences in biological databases. | Mulero HernΓ‘ndez J et al. | β | 2022 | β |
| Ancestry- and sex-specific effects underlying inguinal hernia susceptibility identified in a multiethnic genome-wide association study meta-analysis. | Choquet H et al. | β | 2022 | β |
| An Epigenetic Role of Mitochondria in Cancer. | Liu Y et al. | β | 2022 | β |
| An inhibitor of BRD4, GNE987, inhibits the growth of glioblastoma cells by targeting C-Myc and S100A16. | Ma L et al. | β | 2022 | β |
| A quantitative metric of pioneer activity reveals that HNF4A has stronger in vivo pioneer activity than FOXA1. | Hansen JL et al. | β | 2022 | β |
| Arc Regulates Transcription of Genes for Plasticity, Excitability and Alzheimer's Disease. | Leung HW et al. | β | 2022 | β |
| Asymmetric subgenomic chromatin architecture impacts on gene expression in resynthesized and natural allopolyploid Brassica napus. | Li Z et al. | β | 2022 | β |
| Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis. | Aylon Y et al. | β | 2022 | β |
| Bridging between Mouse and Human Enhancer-Promoter Long-Range Interactions in Neural Stem Cells, to Understand Enhancer Function in Neurodevelopmental Disease. | D'Aurizio R et al. | β | 2022 | β |
| CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos. | Wang M et al. | β | 2022 | β |
| Cell type-specific histone acetylation profiling of Alzheimer's disease subjects and integration with genetics. | Ramamurthy E et al. | β | 2022 | β |
| Characterisation of ethnic differences in DNA methylation between UK-resident South Asians and Europeans. | Elliott HR et al. | β | 2022 | β |
| Characterization of sequence determinants of enhancer function using natural genetic variation. | Yang MG et al. | β | 2022 | β |
| Chromatin accessibility analysis reveals distinct functions for HDAC and EZH2 activities in early appendage regeneration. | Arbach HE et al. | β | 2022 | β |
| Chromatin accessibility-based characterisation of brain gene regulatory networks in three distinct honey bee polyphenisms. | Lowe R et al. | β | 2022 | β |
| Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants. | Xiao Y et al. | β | 2022 | β |
| Chromatin interaction maps identify Wnt responsive cis-regulatory elements coordinating Paupar-Pax6 expression in neuronal cells. | Pavlaki I et al. | β | 2022 | β |
| Chromatin state distribution of residue-specific histone acetylation in early myoblast differentiation. | Li Y et al. | β | 2022 | β |
| Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states. | Jaber M et al. | β | 2022 | β |
| Context-dependant enhancers as a reservoir of functional polymorphisms and epigenetic markers linked to alcohol use disorders and comorbidities. | MacKenzie A et al. | β | 2022 | β |
| Cross-species enhancer prediction using machine learning. | MacPhillamy C et al. | β | 2022 | β |
| Cysteinyl-tRNA Synthetase 1 Promotes Ferroptosis-Induced Cell Death via Regulating GPX4 Expression. | Zhang W et al. | β | 2022 | β |
| Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken. | Hintermann A et al. | β | 2022 | β |
| Differentiation-related epigenomic changes define clinically distinct keratinocyte cancer subclasses. | SolΓ©-Boldo L et al. | β | 2022 | β |
| Distinctive functional regime of endogenous lncRNAs in dark regions of human genome. | Wang A | β | 2022 | β |
| DLX1 and the NuRD complex cooperate in enhancer decommissioning and transcriptional repression. | Price JD et al. | β | 2022 | β |
| DOT1L regulates chamber-specific transcriptional networks during cardiogenesis and mediates postnatal cell cycle withdrawal. | Cattaneo P et al. | β | 2022 | β |
| Double-strand break toxicity is chromatin context independent. | Friskes A et al. | β | 2022 | β |
| Dynamic enhancer transcription associates with reprogramming of immune genes during pattern triggered immunity in Arabidopsis. | Zhang Y et al. | β | 2022 | β |
| DYT6 mutated THAP1 is a cell type dependent regulator of the SP1 family. | Cheng F et al. | β | 2022 | β |
| Effective Quality Breeding Directions-Comparison and Conservative Analysis of Hepatic Super-Enhancers between Chinese and Western Pig Breeds. | Zhang Y et al. | β | 2022 | β |
| EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release. | Mukherjee K et al. | β | 2022 | β |
| Emerging Role of Enhancer RNAs as Potential Diagnostic and Prognostic Biomarkers in Cancer. | Panahi-Moghadam S et al. | β | 2022 | β |
| Enhancer decommissioning by MLL4 ablation elicits dsRNA-interferon signaling and GSDMD-mediated pyroptosis to potentiate anti-tumor immunity. | Ning H et al. | β | 2022 | β |
| Enhancer RNAs step forward: new insights into enhancer function. | Harrison LJ et al. | β | 2022 | β |
| Enhancers regulate 3' end processing activity to control expression of alternative 3'UTR isoforms. | Kwon B et al. | β | 2022 | β |
| Epigenetic reactivation of transcriptional programs orchestrating fetal lung development in human pulmonary hypertension. | Chelladurai P et al. | β | 2022 | β |
| Epigenetic regulation in cardiovascular disease: mechanisms and advances in clinical trials. | Shi Y et al. | β | 2022 | β |
| Epigenetic regulation of innate immune memory in microglia. | Zhang X et al. | β | 2022 | β |
| Epigenetics and environment in breast cancer: New paradigms for anti-cancer therapies. | Thakur C et al. | β | 2022 | β |
| Epigenetics of neural differentiation: Spotlight on enhancers. | Giacoman-Lozano M et al. | β | 2022 | β |
| Epigenomic dynamics of early Xenopus Embryos. | Zhou JJ et al. | β | 2022 | β |
| Epigenomic profiling of glucocorticoid responses identifies cis-regulatory disruptions impacting steroid resistance in childhood acute lymphoblastic leukemia. | Bergeron BP et al. | β | 2022 | β |
| Epigenomics of conventional type-I dendritic cells depicted preferential control of TLR9 versus TLR3 response by NCoR1 through differential IRF3 activation. | Mishra GP et al. | β | 2022 | β |
| Exploring high-resolution chromatin interaction changes and functional enhancers of myogenic marker genes during myogenic differentiation. | Long K et al. | β | 2022 | β |
| Extracellular vesicle expansion of PMIS-miR-210 expression inhibits colorectal tumour growth via apoptosis and an XIST/NME1 regulatory mechanism. | Eliason S et al. | β | 2022 | β |
| Factors and Mechanisms That Influence Chromatin-Mediated Enhancer-Promoter Interactions and Transcriptional Regulation. | Ito S et al. | β | 2022 | β |
| FOXA1 repression drives lineage plasticity and immune heterogeneity in bladder cancers with squamous differentiation. | Warrick JI et al. | β | 2022 | β |
| Functional characterization of 5p15.33 risk locus in uveal melanoma reveals rs452384 as a functional variant and NKX2.4 as an allele-specific interactor. | Derrien AC et al. | β | 2022 | β |
| Functional genomic analysis delineates regulatory mechanisms of GWAS-identified bipolar disorder risk variants. | Chen R et al. | β | 2022 | β |
| GATA4 and estrogen receptor alpha bind at SNPs rs9921222 and rs10794639 to regulate AXIN1 expression in osteoblasts. | Suthon S et al. | β | 2022 | β |
| Generation of functional hepatocytes by forward programming with nuclear receptors. | Tomaz RA et al. | β | 2022 | β |
| Gene regulation on extrachromosomal DNA. | Hung KL et al. | β | 2022 | β |
| Genetic variants associated with psychiatric disorders are enriched at epigenetically active sites in lymphoid cells. | Lynall ME et al. | β | 2022 | β |
| Genome-wide association study of cerebellar volume provides insights into heritable mechanisms underlying brain development and mental health. | Tissink E et al. | β | 2022 | β |
| Genome-Wide Super-Enhancer-Based Analysis: Identification of Prognostic Genes in Oral Squamous Cell Carcinoma. | Saito T et al. | β | 2022 | β |
| GoPeaks: histone modification peak calling for CUT&Tag. | Yashar WM et al. | β | 2022 | β |
| GREAP: a comprehensive enrichment analysis software for human genomic regions. | Yang Y et al. | β | 2022 | β |
| H3K18 lactylation marks tissue-specific active enhancers. | Galle E et al. | β | 2022 | β |
| Haplotype-specific chromatin looping reveals genetic interactions of regulatory regions modulating gene expression in 8p23.1. | Saint Just Ribeiro M et al. | β | 2022 | β |
| Hedgehog signaling activates a mammalian heterochronic gene regulatory network controlling differentiation timing across lineages. | Rowton M et al. | β | 2022 | β |
| Hepatic GATA4 regulates cholesterol and triglyceride homeostasis in collaboration with LXRs. | Bideyan L et al. | β | 2022 | β |
| High enhancer activity is an epigenetic feature of HPV negative atypical head and neck squamous cell carcinoma. | Callahan SC et al. | β | 2022 | β |
| Histone editing elucidates the functional roles of H3K27 methylation and acetylation in mammals. | Sankar A et al. | β | 2022 | β |
| Histone H3.3 K27M chromatin functions implicate a network of neurodevelopmental factors including ASCL1 and NEUROD1 in DIPG. | Lewis NA et al. | β | 2022 | β |
| Histone methyltransferase Smyd2 drives vascular aging by its enhancer-dependent activity. | Su Z et al. | β | 2022 | β |
| Histone modification and histone modification-targeted anti-cancer drugs in breast cancer: Fundamentals and beyond. | Feng J et al. | β | 2022 | β |
| Hormone-controlled cooperative binding of transcription factors drives synergistic induction of fasting-regulated genes. | Goldberg D et al. | β | 2022 | β |
| HSFs drive transcription of distinct genes and enhancers during oxidative stress and heat shock. | Himanen SV et al. | β | 2022 | β |
| Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis. | Luo Z et al. | β | 2022 | β |
| Hydroxamic Acid-Modified Peptide Library Provides Insights into the Molecular Basis for the Substrate Selectivity of HDAC Corepressor Complexes. | Archibald LJ et al. | β | 2022 | β |
| Identification and functional validation of super-enhancers in <i>Arabidopsis thaliana</i>. | Zhao H et al. | β | 2022 | β |
| Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle. | Long K et al. | β | 2022 | β |
| Identification of putative enhancer-like elements predicts regulatory networks active in planarian adult stem cells. | Neiro J et al. | β | 2022 | β |
| Identification of risk loci for primary aldosteronism in genome-wide association studies. | Le Floch E et al. | β | 2022 | β |
| Identification of super-enhancer-driven peptidyl arginine deiminases as potential biomarkers and therapeutic targets for osimertinib-resistant non-small cell lung cancer. | Li H et al. | β | 2022 | β |
| Identifying enhancer-driven subtype-specific prognostic markers in breast cancer based on multi-omics data. | Zhao H et al. | β | 2022 | β |
| Impact of Multiple Sclerosis Risk Polymorphism rs7665090 on MANBA Activity, Lysosomal Endocytosis, and Lymphocyte Activation. | GonzΓ‘lez-JimΓ©nez A et al. | β | 2022 | β |
| Integrated genomic analysis identifies novel low-frequency <i>cis</i>-regulatory variant rs2279658 associated with VSD risk in Chinese children. | Jin L et al. | β | 2022 | β |
| Integrating extrusion complex-associated pattern to predict cell type-specific long-range chromatin loops. | Deng Y et al. | β | 2022 | β |
| Interleukin-7 receptor signaling is crucial for enhancer-dependent TCRΞ΄ germline transcription mediated through STAT5 recruitment. | RodrΓguez-CaparrΓ³s A et al. | β | 2022 | β |
| Intrinsic epigenetic control of angiogenesis in induced pluripotent stem cell-derived endothelium regulates vascular regeneration. | Macklin BL et al. | β | 2022 | β |
| Intronic enhancers of the human <i>SNCA</i> gene predominantly regulate its expression in brain in vivo. | Cheng F et al. | β | 2022 | β |
| JUN Regulation of Injury-Induced Enhancers in Schwann Cells. | Ramesh R et al. | β | 2022 | β |
| Lineage-selective super enhancers mediate core regulatory circuitry during adipogenic and osteogenic differentiation of human mesenchymal stem cells. | Wang C et al. | β | 2022 | β |
| Lipolysis regulates major transcriptional programs in brown adipocytes. | Markussen LK et al. | β | 2022 | β |
| Loss of Monoallelic Expression of <i>IGF2</i> in the Adult Liver <i>Via</i> Alternative Promoter Usage and Chromatin Reorganization. | Ahn J et al. | β | 2022 | β |
| <i>Olig2</i> Ablation in Immature Oligodendrocytes Does Not Enhance CNS Myelination and Remyelination. | Wang J et al. | β | 2022 | β |
| Maternal high-fat diet modifies epigenetic marks H3K27me3 and H3K27ac in bone to regulate offspring osteoblastogenesis in mice. | Chen JR et al. | β | 2022 | β |
| Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors. | Lin X et al. | β | 2022 | β |
| Modulation of the high-order chromatin structure by Polycomb complexes. | Guo Y et al. | β | 2022 | β |
| Molecular Crosstalk between Chromatin Remodeling and Tumor Microenvironment in Multiple Myeloma. | Chakraborty C et al. | β | 2022 | β |
| Multiomics analysis reveals that hepatocyte nuclear factor 1Ξ² regulates axon guidance genes in the developing mouse kidney. | Shao A et al. | β | 2022 | β |
| NetTIME: a multitask and base-pair resolution framework for improved transcription factor binding site prediction. | Yi R et al. | β | 2022 | β |
| Neuronal survival factor VGF promotes chemoresistance and predicts poor prognosis in lung cancers with neuroendocrine feature. | Yang LH et al. | β | 2022 | β |
| Non-coding genetic variation in regulatory elements determines thrombosis and hemostasis phenotypes. | Stefanucci L et al. | β | 2022 | β |
| NSMCE2, a novel super-enhancer-regulated gene, is linked to poor prognosis and therapy resistance in breast cancer. | Di Benedetto C et al. | β | 2022 | β |
| Nuclear RIPK1 promotes chromatin remodeling to mediate inflammatory response. | Li W et al. | β | 2022 | β |
| Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages. | Arnan C et al. | β | 2022 | β |
| PHF20 is crucial for epigenetic control of starvation-induced autophagy through enhancer activation. | Park SW et al. | β | 2022 | β |
| Placental sex-dependent spermine synthesis regulates trophoblast gene expression through acetyl-coA metabolism and histone acetylation. | Aye ILMH et al. | β | 2022 | β |
| Polycomb contraction differentially regulates terminal human hematopoietic differentiation programs. | Lorzadeh A et al. | β | 2022 | β |
| PRC2, Chromatin Regulation, and Human Disease: Insights From Molecular Structure and Function. | Liu X et al. | β | 2022 | β |
| PRMT3 drives glioblastoma progression by enhancing HIF1A and glycolytic metabolism. | Liao Y et al. | β | 2022 | β |
| Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer. | Cheng J et al. | β | 2022 | β |
| RELAβ8-Oxoguanine DNA Glycosylase1 Is an Epigenetic Regulatory Complex Coordinating the Hexosamine Biosynthetic Pathway in RSV Infection. | Xu X et al. | β | 2022 | β |
| Role of CNSs Conserved Distal Cis-Regulatory Elements in CD4 + T Cell Development and Differentiation. | Long X et al. | β | 2022 | β |
| SAFA facilitates chromatin opening of immune genes through interacting with anti-viral host RNAs. | Cao L et al. | β | 2022 | β |
| scEpiLock: A Weakly Supervised Learning Framework for <i>cis</i>-Regulatory Element Localization and Variant Impact Quantification for Single-Cell Epigenetic Data. | Gong Y et al. | β | 2022 | β |
| Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases. | Wang SK et al. | β | 2022 | β |
| Single-cell multi-omics sequencing and its applications in studying the nervous system. | Wang C et al. | β | 2022 | β |
| SMARCB1-Deficient Cancers: Novel Molecular Insights and Therapeutic Vulnerabilities. | Cooper GW et al. | β | 2022 | β |
| SOX2 is essential for astrocyte maturation and its deletion leads to hyperactive behavior in mice. | Wang Y et al. | β | 2022 | β |
| Sox8 remodels the cranial ectoderm to generate the ear. | Buzzi AL et al. | β | 2022 | β |
| SOX transcription factors direct TCF-independent WNT/Ξ²-catenin responsive transcription to govern cell fate in human pluripotent stem cells. | Mukherjee S et al. | β | 2022 | β |
| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu T et al. | β | 2022 | β |
| Structural insight into ASH1L PHD finger recognizing methylated histone H3K4 and promoting cell growth in prostate cancer. | Yu M et al. | β | 2022 | β |
| Structural insights into p300 regulation and acetylation-dependent genome organisation. | Ibrahim Z et al. | β | 2022 | β |
| Super-enhancers conserved within placental mammals maintain stem cell pluripotency. | Zhang J et al. | β | 2022 | β |
| Super-enhancers in esophageal carcinoma: Transcriptional addictions and therapeutic strategies. | Shi Y et al. | β | 2022 | β |
| Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions. | Wang K et al. | β | 2022 | β |
| Temporal analysis of enhancers during mouse cerebellar development reveals dynamic and novel regulatory functions. | Ramirez M et al. | β | 2022 | β |
| Tetrandrine, an immunosuppressive alkaloid isolated from Steohania tetrandra S. Moore, induces the generation of Treg cells through enhancing fatty acid oxidation. | Fang Y et al. | β | 2022 | β |
| TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes. | Kenny C et al. | β | 2022 | β |
| TGFΞ² reprograms TNF stimulation of macrophages towards a non-canonical pathway driving inflammatory osteoclastogenesis. | Xia Y et al. | β | 2022 | β |
| The Chromatin Structure at the <i>MECP2</i> Gene and In Silico Prediction of Potential Coding and Non-Coding <i>MECP2</i> Splice Variants. | Shevkoplyas D et al. | β | 2022 | β |
| The Divergent Pluripotent States in Mouse and Human Cells. | Wang X et al. | β | 2022 | β |
| The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intracellular communication after learning. | Burns AM et al. | β | 2022 | β |
| The lysine deacetylase activity of histone deacetylases 1 and 2 is required to safeguard zygotic genome activation in mice and cattle. | Dang Y et al. | β | 2022 | β |
| Time makes histone H3 modifications drift in mouse liver. | Hillje R et al. | β | 2022 | β |
| Timing is everything: Transcriptional repression is not the default mode for regulating Hedgehog signaling. | Lex RK et al. | β | 2022 | β |
| Transcriptional Activation of Ecdysone-Responsive Genes Requires H3K27 Acetylation at Enhancers. | Cheng D et al. | β | 2022 | β |
| Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures. | Nair SJ et al. | β | 2022 | β |
| Transcription factor antagonism regulates heterogeneity in embryonic stem cell states. | Hu S et al. | β | 2022 | β |
| Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep. | Bilbao-Arribas M et al. | β | 2022 | β |
| Trypanosoma brucei histones are heavily modified with combinatorial post-translational modifications and mark Pol II transcription start regions with hyperacetylated H2A. | Maree JP et al. | β | 2022 | β |
| Vascular Regulation by Super Enhancer-Derived LINC00607. | Sriram K et al. | β | 2022 | β |
| Viewing AML through a New Lens: Technological Advances in the Study of Epigenetic Regulation. | Godfrey LC et al. | β | 2022 | β |
| Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis. | Yang T et al. | β | 2022 | β |
| YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency. | Dong X et al. | β | 2022 | β |
| Zebrafish cox17 modulates primitive erythropoiesis via regulation of mitochondrial metabolism to facilitate hypoxia tolerance. | Li L et al. | β | 2022 | β |
| ZFP281-BRCA2 prevents R-loop accumulation during DNA replication. | Wang Y et al. | β | 2022 | β |