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Endogenous fine-mapping and prioritization of functional regulatory elements in complex genetic loci

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cell.com/cell-genomics/abstract/S2666-979X(25)00238-1
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Preventing CpG hypermethylation in oocytes safeguards mouse development

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  DOI: 10.1016/j.devcel.2025.08.005
  
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sciencedirect.com/science/article/pii/S1534580725005052
Aug 2025
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SKP1A bound to Polycomb-silenced genes mediates degradation of PRC2 and preconditions their activation

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1. scibot 26 Aug 2025
  
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Distinct specificity and functions of PRC2 subcomplexes in human stem cells and cardiac differentiation

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  DOI: 10.1016/j.molcel.2025.07.014
  
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The transcription factor BATF pioneers the differentiation program of effector CD8+ T cells through the interaction with IRF4

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  DOI: 10.1016/j.celrep.2025.116129
  
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sciencedirect.com/science/article/pii/S2211124725009003
Jul 2025
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1-s2.0-S2589004225014555-main-html.html

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  DOI: 10.1016/j.isci.2025.113194
  
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Epigenome profiling identifies H3K27me3 regulation of extracellular matrix composition in human corticogenesis

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1. scibot 23 Jul 2025
  
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  DOI: 10.1016/j.neuron.2025.06.016
  
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CRISPR-based screening identifies the role of KRAB-containing transcription factors ZIM3 and ZNF394 in human major zygotic genome activation

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1. scibot 22 Jul 2025
  
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cell.com/cell-reports/fulltext/S2211-1247(25)00786-7
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Estradiol (E2) concentration shapes the chromatin binding landscape of estrogen receptor alpha

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  DOI: 10.1016/j.jbc.2025.108499
  
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pmc.ncbi.nlm.nih.gov/articles/PMC12256316/
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Antibody-Mediated Protein A-APEX2 Labeling (AMAPEX) for Proximity Proteome Exploration

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1. scibot 15 Jul 2025
  
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  DOI: 10.1007/978-1-0716-4694-6_19
  
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link.springer.com/protocol/10.1007/978-1-0716-4694-6_19
Jun 2025
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Bivalent chromatin instructs lineage specification during hematopoiesis

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  DOI: 10.1016/j.cell.2025.05.011
  
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Non-canonical PRC1.1 licenses transcriptional response to enable Treg plasticity in immune adaptation

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  DOI: 10.1016/j.molcel.2025.05.029
  
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Regulation of epigenetics and chromosome structure by human ORC2

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1. scibot 11 Jun 2025
  
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  DOI: 10.1016/j.celrep.2025.115816
  
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Calcium-responsive phosphorylation of SlLHP1b epigenetically suppresses auxin synthesis to control drought-induced flower drop in tomato

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  DOI: 10.1016/j.devcel.2025.05.006
  
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sciencedirect.com/science/article/pii/S1534580725002965
May 2025
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A specific form of cPRC1 containing CBX4 is co-opted to mediate oncogenic gene repression in diffuse midline glioma

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  DOI: 10.1016/j.molcel.2025.04.026
  
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Chromatin modification abnormalities by CHD7 and KMT2C loss promote medulloblastoma progression

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  DOI: 10.1016/j.celrep.2025.115673
  
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sciencedirect.com/science/article/pii/S2211124725004449
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Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq

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1. scibot 19 May 2025
  
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  DOI: 10.1038/s41596-025-01145-9
  
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nature.com/articles/s41596-025-01145-9
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Super RNA Pol II domains enhance minor ZGA through 3D interaction to ensure the integrity of major transcriptional waves in late-ZGA mammals

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1. scibot 19 May 2025
  
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  DOI: 10.1016/j.xgen.2025.100856
  
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sciencedirect.com/science/article/pii/S2666979X25001120
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Isocitrate dehydrogenase 1 primes group-3 medulloblastomas for cuproptosis

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  DOI: 10.1016/j.ccell.2025.04.013
  
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sciencedirect.com/science/article/pii/S1535610825001722
Mar 2025
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Antagonistic roles for MITF and TFE3 in melanoma plasticity

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  DOI: 10.1016/j.celrep.2025.115474
  
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sciencedirect.com/science/article/pii/S2211124725002451
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Dynamic regulation of murine RNA polymerase III transcription during heat shock stress

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  DOI: 10.1093/genetics/iyaf042
  
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academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyaf042/8085024
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Isogenic comparison of Airn and Xist reveals core principles of Polycomb recruitment by lncRNAs

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cell.com/molecular-cell/fulltext/S1097-2765(25)00145-5
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Dual targeting of CXCR4 and EZH2 in endometriosis

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  DOI: 10.1016/j.isci.2025.112143
  
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Lipoylation inhibition enhances radiation control of lung cancer by suppressing homologous recombination DNA damage repair

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  DOI: 10.1126/sciadv.adt1241
  
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Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag

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  DOI: 10.1016/j.molcel.2025.02.012
  
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Feb 2025
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Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia

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1. scibot 27 Feb 2025
  
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  DOI: 10.1101/2025.01.21.25320683
  
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EZH1/EZH2 inhibition enhances adoptive T cell immunotherapy against multiple cancer models

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  DOI: 10.1016/j.ccell.2025.01.013
  
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cell.com/cancer-cell/abstract/S1535-6108(25)00031-5
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CCN6 suppresses metaplastic breast carcinoma by antagonizing WNT/β-catenin signaling to inhibit EZH2-driven EMT

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1. scibot 13 Feb 2025
  
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  DOI: 10.1158/0008-5472.CAN-23-4054
  
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aacrjournals.org/cancerres/article/84/19/3235/748708/CCN6-Suppresses-Metaplastic-Breast-Carcinoma-by
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Dynamic regulation of RNA Polymerase III transcription in mouse embryonic stem cells during heat shock stress

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  DOI: 10.1101/2024.11.28.625959
  
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52.53.155.43/036271772ffeeb8f5a4cfd38744d991b76301855/2024.11.28.625959.full-html.html
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KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition

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  DOI: 10.1016/j.celrep.2025.115272
  
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Jan 2025
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KDM6B-dependent epigenetic programming of uterine fibroblasts in early pregnancy regulates parturition timing in mice

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  DOI: 10.1016/j.cell.2024.12.019
  
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Chromosome mis-segregation triggers cell cycle arrest through a mechanosensitive nuclear envelope checkpoint

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  DOI: 10.1038/s41556-024-01565-x
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11735390/
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Single-cell RNA-seq identifies protracted mouse germline X chromosome reactivation dynamics directed by a PRC2-dependent mechanism

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  DOI: 10.1016/j.devcel.2024.12.028
  
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Pan-inhibition of super-enhancer-driven oncogenic transcription by next-generation synthetic ecteinascidins yields potent anti-cancer activity

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1. scibot 15 Jan 2025
  
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  DOI: 10.1038/s41467-024-55667-z
  
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pmc.ncbi.nlm.nih.gov/articles/PMC11711318/
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Nucleosomal asymmetry shapes histone mark binding and promotes poising at bivalent domains

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  DOI: 10.1016/j.molcel.2024.12.002
  
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sciencedirect.com/science/article/pii/S1097276524009973
Dec 2024
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The histone H3.3 K27M mutation suppresses Ser31phosphorylation and mitotic fidelity, which can directly drive gliomagenesis

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Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesis

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Actin-based deformations of the nucleus control mouse multiciliated ependymal cell differentiation

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Enforced activation of the CREB/KDM2B axis prevents alcohol-induced embryonic developmental delay

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Epigenetic and Oncogenic Inhibitors Cooperatively Drive Differentiation and Kill KRAS-Mutant Colorectal Cancers

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EZH2 inhibition enhances T cell immunotherapies by inducing lymphoma immunogenicity and improving T cell function

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DNA hypomethylation promotes UHRF1-and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states

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Acute multi-level response to defective de novo chromatin assembly in S-phase

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BRG1 programs PRC2-complex repression and controls oligodendrocyte differentiation and remyelination

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HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding

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Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors

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H3.3 G34W Promotes Growth and Impedes Differentiation of Osteoblast-Like Mesenchymal Progenitors in Giant Cell Tumor of Bone

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Epigenetic alternations in the SYP and DLG4 genes due to low-level methylmercury exposure during neuronal differentiation in vitro

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Reduction of Global H3K27me3 Enhances HER2/ErbB2 Targeted Therapy

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Hyperactivating EZH2 to augment H3K27me3 levels in regulatory T cells enhances immune suppression by driving early effector differentiation

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Sex-dependent effects in the aged melanoma tumor microenvironment influence invasion and resistance to targeted therapy

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Feedforward cysteine regulation maintains melanoma differentiation state and limits metastatic spread

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Thyroid hormone suppresses medulloblastoma progression through promoting terminal differentiation of tumor cells

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The fork protection complex promotes parental histone recycling and epigenetic memory

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The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening

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H3 K27M and EZHIP Impede H3K27-Methylation Spreading by Inhibiting Allosterically Stimulated PRC2

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Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue

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The TERT Promoter is Polycomb-Repressed in Neuroblastoma Cells with Long Telomeres

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DOT1L maintains NK cell phenotype and function for optimal tumor control

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Lineage specification in glioblastoma is regulated by METTL7B

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Defining cis-regulatory elements and transcription factors that control human cortical interneuron development

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Deletion of the mRNA endonuclease Regnase-1 promotes NK cell anti-tumor activity via OCT2-dependent transcription of Ifng

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Enhanced ApcMin/+ adenoma formation after epithelial CUL4B deletion by recruitment of myeloid-derived suppressor cells

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2024.02.25.581951v1.full-html.html

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Identification of WNK1 as a therapeutic target to suppress IgH/MYC expression in multiple myeloma

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Protein degradation of Lysine-specific demethylase 1 is mediated by Bre1 yet opposed by Lsd1-interacting lncRNAs during fly follicle development

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The Drosophila Hippo pathway transcription factor Scalloped and its co-factors alter each other’s chromatin binding dynamics and transcription in vivo

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The growth factor EPIREGULIN promotes basal progenitor cell proliferation in the developing neocortex

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Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization

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The growth factor EPIREGULIN promotes basal progenitor cell proliferation in the developing neocortex

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miR-217 regulates normal and tumor cell fate following induction of Endoplasmic Reticulum Stress

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Nucleation and spreading maintain Polycomb domains every cell cycle

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H2AK119ub1 differentially fine-tunes gene expression by modulating canonical PRC1- and H1-dependent chromatin compaction

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SP6 controls human cytotrophoblast fate decisions and trophoblast stem cell establishment by targeting MSX2 regulatory elements

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EZH2 as a major histone methyltransferase in PDGF-BB-activated orbital fibroblast in the pathogenesis of Graves’ ophthalmopathy

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Select EZH2 inhibitors enhance viral mimicry effects of DNMT inhibition through a mechanism involving NFAT:AP-1 signaling

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Histone lysine demethylase 4 family proteins maintain the transcriptional program and adrenergic cellular state of MYCN-amplified neuroblastoma

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Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape

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DNMT3B PWWP mutations cause hypermethylation of heterochromatin

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The sirtuin-associated human senescence program converges on the activation of placenta-specific gene PAPPA

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Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders

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ARID1A orchestrates SWI/SNF-mediated sequential binding of transcription factors with ARID1A loss driving pre-memory B cell fate and lymphomagenesis

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MTOR modulation induces selective perturbations in histone methylation which influence the anti-proliferative effects of mTOR inhibitors

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Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis

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Hepatic Snai1 and Snai2 promote liver regeneration and suppress liver fibrosis in mice

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Enhancer-promoter activation by the Kaposi sarcoma-associated herpesvirus episome maintenance protein LANA

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l-Methionine potentiates anticancer activity of Sorafenib by epigenetically altering DUSP3/ERK pathway in hepatocellular carcinoma

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CircUSP1 as a novel marker promotes gastric cancer progression via stabilizing HuR to upregulate USP1 and Vimentin

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The iron chelator and OXPHOS inhibitor VLX600 induces mitophagy and an autophagy-dependent type of cell death in glioblastoma cells

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Selection of epigenetically privileged HIV-1 proviruses during treatment with panobinostat and interferon-α2a

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The iron chelator and OXPHOS inhibitor VLX600 induces mitophagy and an autophagy-dependent type of cell death in glioblastoma cells

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EZH2 Inhibition Promotes Tumor Immunogenicity in Lung Squamous Cell Carcinomas

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A fluorescence-based protocol to quantitatively titrate CUT&RUN buffer components

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EZH2/G9a interact to mediate drug resistance in non-small-cell lung cancer by regulating the SMAD4/ERK/c-Myc signaling axis

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Lactic acid induces transcriptional repression of macrophage inflammatory response via histone acetylation

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Mapping chromatin state and transcriptional response in CIC-DUX4 undifferentiated round cell sarcoma

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Targeting EMSY-mediated methionine metabolism is a potential therapeutic strategy for triple-negative breast cancer

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Spatiotemporal role of SETD2-H3K36me3 in murine pancreatic organogenesis

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PCGF6 controls murine Tuft cell differentiation via H3K9me2 modification independently of Polycomb repression

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IL-15-dependent immune crosstalk between natural killer cells and dendritic cells in HIV-1 elite controllers

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ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry

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Pioneer and PRDM transcription factors coordinate bivalent epigenetic states to safeguard cell fate

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Metabolic switch regulates lineage plasticity and induces synthetic lethality in triple-negative breast cancer

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XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells

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Cell stretching activates an ATM mechano-transduction pathway that remodels cytoskeleton and chromatin

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Mof plays distinct roles in hepatic lipid metabolism under healthy or non-alcoholic fatty liver conditions

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Chromosome-specific maturation of the epigenome in the Drosophila male germline

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KDM6B drives epigenetic reprogramming associated with lymphoid stromal cell early commitment and immune properties

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Alternative splicing of histone demethylase Kdm6bb mediates temperature-induced sex reversal in the Nile tilapia

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Scalable single-cell profiling of chromatin modifications with sciCUT&Tag

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Recruitment of FBXO22 for Targeted Degradation of NSD2

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The anaphase-promoting complex controls a ubiquitination-phosphoprotein axis in chromatin during neurodevelopment

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mTORC1 stimulates cell growth through SAM synthesis and m6A mRNA-dependent control of protein synthesis

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Discordant interactions between YAP1 and polycomb group protein SCML2 determine cell fate

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Ethanol changes Nestin-promoter induced neural stem cells to disturb newborn dendritic spine remodeling in the hippocampus of mice

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Histone bivalency regulates the timing of cerebellar granule cell development

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Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma

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Activation of AKT induces EZH2-mediated β-catenin trimethylation in colorectal cancer

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The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr

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The two enantiomers of 2-hydroxyglutarate differentially regulate cytotoxic T cell function

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Spermine is a natural suppressor of AR signaling in castration-resistant prostate cancer

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Proximity-dependent recruitment of Polycomb repressive complexes by the lncRNA Airn

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Chromatin regulation of transcriptional enhancers and cell fate by the Sotos syndrome gene NSD1

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Uterine-specific Ezh2 deletion enhances stromal cell senescence and impairs placentation, resulting in pregnancy loss

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Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin

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Canonical BAF complex activity shapes the enhancer landscape that licenses CD8+ T cell effector and memory fates

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METTL14 regulates chromatin bivalent domains in mouse embryonic stem cells

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DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs

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Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas

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SAM-Competitive EZH2-Inhibitors Induce Platinum Resistance by EZH2-Independent Induction of ABC-Transporters

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Targeted deprivation of methionine with engineered Salmonella leads to oncolysis and suppression of metastasis in broad types of animal tumor models

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Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus

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Methionine restriction promotes cGAS activation and chromatin untethering through demethylation to enhance antitumor immunity

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Depletion of CUL4B in macrophages ameliorates diabetic kidney disease via miR-194-5p/ITGA9 axis

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Exercise improves homeostasis of the intestinal epithelium by activation of APJ-AMPK signaling

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Methylated histones on mitotic chromosomes promote Topoisomerase IIα function for high fidelity chromosome segregation.

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Combating castration-resistant prostate cancer by co-targeting the epigenetic regulators EZH2 and HDAC

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Fusobacterium nucleatum-derived succinic acid induces tumor resistance to immunotherapy in colorectal cancer

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A hyper-quiescent chromatin state formed during aging is reversed by regeneration

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Changes in nascent chromatin structure regulate activation of the pro-fibrotic transcriptome and myofibroblast emergence in organ fibrosis

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Transcriptional-translational conflict is a barrier to cellular transformation and cancer progression

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Asparagine starvation suppresses histone demethylation through iron depletion

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PRC2.1- and PRC2.2-specific accessory proteins drive recruitment of different forms of canonical PRC1

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Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers

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Single substitution in H3.3G34 alters DNMT3A recruitment to cause progressive neurodegeneration

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Mutant NPM1 Hijacks Transcriptional Hubs to Maintain Pathogenic Gene Programs in Acute Myeloid Leukemia

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MeCP2 regulates Gdf11, a dosage-sensitive gene critical for neurological function

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Gene silencing dynamics are modulated by transiently active regulatory elements

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Histone bivalency regulates the timing of cerebellar granule cell development

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FAK-mediated phosphorylation at Y464 regulates p85β nuclear translocation to promote tumorigenesis of ccRCC by repressing RB1 expression

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Recycling of modified H2A-H2B provides short-term memory of chromatin states

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Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication

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RNA mis-splicing drives viral mimicry response after DNMTi therapy in SETD2-mutant kidney cancer

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Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes

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Genetic screens reveal new targetable vulnerabilities in BAP1-deficient mesothelioma

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Human SMARCA5 is continuously required to maintain nucleosome spacing

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EZH2/hSULF1 axis mediates receptor tyrosine kinase signaling to shape cartilage tumor progression

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Dual-specificity RNA aptamers enable manipulation of target-specific O-GlcNAcylation and unveil functions of O-GlcNAc on β-catenin

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Decreased expression of EZH2 in granulosa cells contributes to endometriosis-associated infertility by targeting IL-1R2

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Remarkable Synergy When Combining EZH2 Inhibitors with YM155 Is H3K27me3-Independent

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ΔNp63 drives dysplastic alveolar remodeling and restricts epithelial plasticity upon severe lung injury

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Dynamic chromosomal interactions and control of heterochromatin positioning by Ki‐67

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PALI1 promotes tumor growth through competitive recruitment of PRC2 to G9A-target chromatin for dual epigenetic silencing

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Dual Acting Peptides Target EZH2 and AR: a New Paradigm for Effective Treatment of Castration-Resistant Prostate Cancer

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BAF complex maintains glioma stem cells in pediatric H3K27M-glioma

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Mcm2 promotes stem cell differentiation via its ability to bind H3-H4

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De-erosion of X chromosome dosage compensation by the editing of XIST regulatory regions restores the differentiation potential in hPSCs

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  DOI: 10.1016/j.crmeth.2022.100352
  
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Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia

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  DOI: 10.1016/j.ccell.2022.10.002
  
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Oct 2022
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Spatially resolved epigenomic profiling of single cells in complex tissues

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1. scibot 23 Oct 2022
  
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  DOI: 10.1016/j.cell.2022.09.035
  
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Spatial epitope barcoding reveals clonal tumor patch behaviors

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  DOI: 10.1016/j.ccell.2022.09.014
  
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BCOR and BCORL1 Mutations Drive Epigenetic Reprogramming and Oncogenic Signaling by Unlinking PRC1.1 from Target Genes

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  DOI: 10.1158/2643-3230.BCD-21-0115
  
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Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas

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  DOI: 10.1016/j.molcel.2022.09.007
  
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Inhibition of the CtBP complex and FBXO11 enhances MHC class II expression and anti-cancer immune responses

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Single-cell sequencing reveals activation of core transcription factors in PRC2-deficient malignant peripheral nerve sheath tumor

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  DOI: 10.1016/j.celrep.2022.111363
  
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Multiplexed protein profiling reveals spatial subcellular signaling networks

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  DOI: 10.1016/j.isci.2022.104980
  
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Targeting histone methylation to reprogram the transcriptional state that drives survival of drug-tolerant myeloid leukemia persisters

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Reversible epigenetic alterations regulate class I HLA loss in prostate cancer

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  DOI: 10.1038/s42003-022-03843-6
  
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Androgen-mediated perturbation of the hepatic circadian system through epigenetic modulation promotes NAFLD in PCOS mice

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  DOI: 10.1210/endocr/bqac127
  
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EZH2 T367 phosphorylation activates p38 signaling through lysine methylation to promote breast cancer progression

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  DOI: 10.1016/j.isci.2022.104827
  
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Jul 2022
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Reciprocal SOX2 regulation by SMAD1-SMAD3 is critical for anoikis resistance and metastasis in cancer

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  DOI: 10.1016/j.celrep.2022.111066
  
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RPA1 controls chromatin architecture and maintains lipid metabolic homeostasis

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  DOI: 10.1016/j.celrep.2022.111071
  
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Targeting miR-30d reverses pathological cardiac hypertrophy

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Dynamic Chromatin States Coupling with Key Transcription Factors in Colitis-Associated Colorectal Cancer

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1. scibot 18 Jun 2022
  
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  DOI: 10.1002/advs.202200536
  
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pmc.ncbi.nlm.nih.gov/articles/PMC9376751/

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