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    An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II
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    1. scibot 19 Jul 2024
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    sciencedirect.com/science/article/pii/S1097276524004842
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    Implications of noncoding regulatory functions in the development of insulinomas
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    sciencedirect.com/science/article/pii/S2666979X24001988
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    BPS Publications
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      DOI: 10.1111/bph.16431

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    bpspubs.onlinelibrary.wiley.com/doi/10.1111/bph.16431
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    Epigenomic signatures of sarcomatoid differentiation to guide the treatment of renal cell carcinoma
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    cell.com/cell-reports/abstract/S2211-1247(24)00678-8
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    YY1-mediated enhancer-promoter communication in the immunoglobulin μ locus is regulated by MSL/MOF recruitment
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    cell.com/cell-reports/abstract/S2211-1247(24)00785-X
  7. Jun 2024
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    Hypoxia-induced CTCF promotes EMT in breast cancer
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    sciencedirect.com/science/article/pii/S2211124724006958
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    An enhancer RNA recruits KMT2A to regulate transcription of Myb
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    sciencedirect.com/science/article/pii/S221112472400706X
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    LEUTX regulates porcine embryonic genome activation in somatic cell nuclear transfer embryos
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    sciencedirect.com/science/article/pii/S2211124724007009
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    A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma
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      DOI: 10.7554/eLife.83527

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    ncbi.nlm.nih.gov/pmc/articles/PMC11178360/
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    CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex
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    ncbi.nlm.nih.gov/pmc/articles/PMC11163479/
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    An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors
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    ncbi.nlm.nih.gov/pmc/articles/PMC11148061/
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    The roles of nuclear orphan receptor NR2F6 in anti-viral innate immunity
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    ncbi.nlm.nih.gov/pmc/articles/PMC11175508/
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    Collaboration between distinct SWI/SNF chromatin remodeling complexes directs enhancer selection and activation of macrophage inflammatory genes
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    sciencedirect.com/science/article/pii/S1074761324002620
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    A cis-regulatory module underlies retinal ganglion cell genesis and axonogenesis
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    sciencedirect.com/science/article/pii/S2211124724006193
  17. May 2024
  18. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    XIST and MUC1-C form an auto-regulatory pathway in driving cancer progression
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    ncbi.nlm.nih.gov/pmc/articles/PMC11091074/
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    Mecp2 fine-tunes quiescence exit by targeting nuclear receptors
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    ncbi.nlm.nih.gov/pmc/articles/PMC11095939/
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    Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements
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      DOI: 10.1101/2024.04.12.589208

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    ncbi.nlm.nih.gov/pmc/articles/PMC11042195/
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    A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification
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    sciencedirect.com/science/article/pii/S1074761324002127
  22. Apr 2024
  23. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    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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    ncbi.nlm.nih.gov/pmc/articles/PMC11035368/
  24. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Cis-regulatory control of transcriptional timing and noise in response to estrogen
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    ncbi.nlm.nih.gov/pmc/articles/PMC11099348/
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    Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction
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    sciencedirect.com/science/article/pii/S1074761324001390
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    Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans
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    sciencedirect.com/science/article/pii/S2666979X24000922
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    Tumor cell-intrinsic epigenetic dysregulation shapes cancer-associated fibroblasts heterogeneity to metabolically support pancreatic cancer
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    sciencedirect.com/science/article/pii/S1535610824000904
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    STAT3 couples activated tyrosine kinase signaling to the oncogenic core transcriptional regulatory circuitry of anaplastic large cell lymphoma
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    ncbi.nlm.nih.gov/pmc/articles/PMC10983107/
  29. Mar 2024
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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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    sciencedirect.com/science/article/pii/S2666379124001149
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    Epigenomic tomography for probing spatially defined chromatin state in the brain
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      DOI: 10.1016/j.crmeth.2024.100738

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    sciencedirect.com/science/article/pii/S2667237524000638
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    The sirtuin-associated human senescence program converges on the activation of placenta-specific gene PAPPA
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    sciencedirect.com/science/article/pii/S1534580724001072
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    PRMT1 promotes pancreatic cancer development and resistance to chemotherapy
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    sciencedirect.com/science/article/pii/S2666379124001058
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    IκBζ is a dual-use coactivator of NF-κB and POU transcription factors
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    sciencedirect.com/science/article/pii/S109727652400008X
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    Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide
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    sciencedirect.com/science/article/pii/S1097276523010791
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    SWI/SNF-dependent genes are defined by their chromatin landscape
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    sciencedirect.com/science/article/pii/S2211124724001839
  37. Feb 2024
  38. 52.53.155.43 52.53.155.43
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    Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer
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    sciencedirect.com/science/article/pii/S1535610824000369
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    Sphingolipid metabolism controls mammalian heart regeneration
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    sciencedirect.com/science/article/pii/S1550413124000172
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    BPS Publications
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      DOI: 10.1111/bph.16299

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    bpspubs.onlinelibrary.wiley.com/doi/10.1111/bph.16299
  42. onlinelibrary.wiley.com onlinelibrary.wiley.com
    H3K27ac modification and transcription characteristics of adipose and muscle tissues in Chuxiang Black pig
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      DOI: 10.1111/age.13400

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    onlinelibrary.wiley.com/doi/10.1111/age.13400
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    The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer
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      DOI: 10.1186/s13059-023-03161-y

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    link.springer.com/article/10.1186/s13059-023-03161-y
  44. Jan 2024
  45. www.sciencedirect.com www.sciencedirect.com
    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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    FK506 bypasses the effect of erythroferrone in cancer cachexia skeletal muscle atrophy
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    Elimination of oncogenic KRAS in genetic mouse models eradicates pancreatic cancer by inducing FAS-dependent apoptosis by CD8+ T cells
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    A histone deacetylase network regulates epigenetic reprogramming and viral silencing in HIV-infected cells
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    Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage
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    ASCL1 characterizes adrenergic neuroblastoma via its pioneer function and cooperation with core regulatory circuit factors
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    YAP targetome reveals activation of SPEM in gastric pre-neoplastic progression and regeneration
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  60. Nov 2023
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    Cooperation of MLL1 and Jun in controlling H3K4me3 on enhancers in colorectal cancer
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    Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits
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    LINC00921 reduces lung cancer radiosensitivity by destabilizing NUDT21 and driving aberrant MED23 alternative polyadenylation
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    Therapeutic targeting of EP300/CBP by bromodomain inhibition in hematologic malignancies
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    Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS
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    Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation
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    Endonucleosis mediates internalization of cytoplasm into the nucleus in senescent cells
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    p57Kip2 acts as a transcriptional corepressor to regulate intestinal stem cell fate and proliferation
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    Systemic and intrinsic functions of ATRX in glial cell fate and CNS myelination in male mice
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    ZNF397 Loss Triggers TET2-driven Epigenetic Rewiring, Lineage Plasticity, and AR-targeted Therapy Resistance in AR-dependent Cancers
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    Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation
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    Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells
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    Oct1 cooperates with the Smad family of transcription factors to promote mesodermal lineage specification
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    End binding-3 inhibitor activates regenerative program in age-related macular degeneration
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    A fluorophore-conjugated reagent enabling rapid detection, isolation and live tracking of senescent cells
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    Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas
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    Integrative analysis of single-cell RNA-seq and ATAC-seq reveals heterogeneity of induced pluripotent stem cell derived hepatic organoids
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  83. Aug 2023
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    Sepsis induces non-classic innate immune memory in granulocytes
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    XAF1 promotes anti-RNA virus immune responses by regulating chromatin accessibility
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    BET Inhibitors Target the SCLC-N subtype of Small Cell Lung Cancer by Blocking NEUROD1 Transactivation
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  90. Jul 2023
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    The default and directed pathways of hepatoblast differentiation involve distinct epigenomic mechanisms
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    Alcohol-sourced acetate impairs T cell function by promoting cortactin acetylation
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    FOXA2 controls the anti-oxidant response in FH-deficient cells
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  94. Jun 2023
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    Removal of epigenetic repressive mark on inflammatory genes in fat liver
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    Single genomic enhancers drive experience-dependent GABAergic plasticity to maintain sensory processing in the adult cortex
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    Antiandrogen treatment induces stromal cell reprogramming to promote castration resistance in prostate cancer
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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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    Nuclear translocation of an aminoacyl-tRNA synthetase may mediate a chronic “integrated stress response”
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    Oct1 cooperates with the Smad family of transcription factors to promote mesodermal lineage specification
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    The circadian clock CRY1 regulates pluripotent stem cell identity and somatic cell reprogramming
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  103. May 2023
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    MYCOBACTERIUM MANRESENSIS INDUCES TRAINED IMMUNITY IN VITRO
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    Chemical-induced epigenome resetting for regeneration program activation in human cells
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    Lactobacillus plantarum-derived indole-3-lactic acid ameliorates colorectal tumorigenesis via epigenetic regulation of CD8+ T cell immunity
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    Histone deacetylase-mediated silencing of PSTPIP2 expression contributes to AAI-induced PANoptosis
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    Reversible transitions between noradrenergic and mesenchymal tumor identities define cell plasticity in neuroblastoma
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  109. Apr 2023
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    Kupffer-cell-derived IL-6 is repurposed for hepatocyte dedifferentiation via activating progenitor genes from injury-specific enhancers
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    NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons
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    Novel enhancers conferring compensatory transcriptional regulation of Nkx2-5 in heart development
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    Systematic fine-mapping and functional studies of prostate cancer risk variants
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    Targeting the mevalonate pathway suppresses ARID1A-inactivated cancers by promoting pyroptosis
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    MeCP2 Represses the Activity of Topoisomerase IIβ in Long Neuronal Genes
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    Restraint of IFN-γ expression through a distal silencer CNS–28 for tissue homeostasis
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    NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons
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    PRC2.1- and PRC2.2-specific accessory proteins drive recruitment of different forms of canonical PRC1
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    Histone phosphorylation integrates the hepatic glucagon-PKA-CREB gluconeogenesis program in response to fasting
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    ERCC6L2 mitigates replication stress and promotes centromere stability
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    Cooperative super-enhancer inactivation caused by heterozygous loss of CREBBP and KMT2D skews B cell fate decisions and yields T cell-depleted lymphomas
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  122. Mar 2023
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    Stepwise activities of mSWI/SNF family chromatin remodeling complexes direct T cell activation and exhaustion
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    Exposure to high-sugar diet induces transgenerational changes in sweet sensitivity and feeding behavior via H3K27me3 reprogramming
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    Aryl hydrocarbon receptor activity downstream of IL-10 signaling is required to promote regulatory functions in human dendritic cells
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  126. Feb 2023
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    Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging
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  128. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging
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    Chromatin immunoprecipitation with mouse adipocytes using hypotonic buffer to enrich nuclear fraction before fixation
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  131. Jan 2023
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    EKLF/Klf1 regulates erythroid transcription by its pioneering activity and selective control of RNA Pol II pause-release
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  133. www.nature.com www.nature.com
    Targeting Menin disrupts the KMT2A/B and polycomb balance to paradoxically activate bivalent genes
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  134. Dec 2022
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    ΔNp63/p73 drive metastatic colonization by controlling a regenerative epithelial stem cell program in quasi-mesenchymal cancer stem cells
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    KMT2D deficiency drives lung squamous cell carcinoma and hypersensitivity to RTK-RAS inhibition
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    Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma
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    Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation
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    PPARγ lipodystrophy mutants reveal intermolecular interactions required for enhancer activation
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    Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes promotes chromatin compaction at promoters
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    Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription
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    Acute depletion of human core nucleoporin reveals direct roles in transcription control but dispensability for 3D genome organization
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    Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer
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    Cross-lineage potential of Ascl1 uncovered by comparing diverse reprogramming regulatomes
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    Dissection of the MEF2D-IRF8 transcriptional circuit dependency in acute myeloid leukemia
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    A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation
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  154. Sep 2022
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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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    Intracellular cholesterol pools regulate oncogenic signaling and epigenetic circuitries in Early T-cell Precursor Acute Lymphoblastic Leukemia
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    The Il6 -39kb enhancer containing clustered GATA2- and PU.1- binding sites is essential for Il6 expression in murine mast cells
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    Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster
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    Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
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    Transcription factors TCF-1 and GATA3 are key factors for the epigenetic priming of early innate lymphoid progenitors toward distinct cell fates
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    Induction of senescence upon loss of the Ash2l core subunit of H3K4 methyltransferase complexes
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    Inhibition of DYRK1A, via histone modification, promotes cardiomyocyte cell cycle activation and cardiac repair after myocardial infarction
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    MacroH2As regulate enhancer-promoter contacts affecting enhancer activity and sensitivity to inflammatory cytokines
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    TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors
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    Dynamic Chromatin States Coupling with Key Transcription Factors in Colitis-Associated Colorectal Cancer
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    Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression
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    Mapping cis-regulatory elements in human neurons links psychiatric disease heritability and activity-regulated transcriptional programs
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    Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging
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    XIST loss impairs mammary stem cell differentiation and increases tumorigenicity through Mediator hyperactivation
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    C/EBPδ-induced epigenetic changes control the dynamic gene transcription of S100a8 and S100a9
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    Transcription activation is enhanced by multivalent interactions independent of phase separation
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    NSD1 mediates antagonism between SWI/SNF and polycomb complexes and is required for transcriptional activation upon EZH2 inhibition
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    ISL2 is a putative tumor suppressor whose epigenetic silencing reprograms the metabolism of pancreatic cancer
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    Selective requirement of MYB for oncogenic hyperactivation of a translocated enhancer in leukemia
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    Functional elements of the cis-regulatory lincRNA-p21
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    An enriched environment reduces hippocampal inflammatory... : Neural Regeneration Research
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    Targeted Therapy of TERT-Rearranged Neuroblastoma with BET Bromodomain Inhibitor and Proteasome Inhibitor Combination Therapy
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      DOI: 10.1158/1078-0432.CCR-20-3044

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    Altered BAF occupancy and transcription factor dynamics in PBAF-deficient melanoma
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    The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma
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  188. aacrjournals.org aacrjournals.org
    MUC1-C Dictates JUN and BAF-mediated Chromatin Remodeling at Enhancer Signatures in Cancer Stem Cells
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      DOI: 10.1158/1541-7786.MCR-21-0672

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  189. Mar 2022
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    Mucus sialylation determines intestinal host-commensal homeostasis
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    The mTOR chromatin-bound interactome in prostate cancer
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    The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes
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    EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma
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  194. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    STAT3-mediated allelic imbalance of novel genetic variant rs1047643 and B cell specific super-enhancer in association with systemic lupus erythematosus
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      DOI: 10.7554/eLife.72837

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  195. Feb 2022
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    The landscape of pioneer factor activity reveals the mechanisms of chromatin reprogramming and genome activation
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    Histone marks regulate the epithelial-to-mesenchymal transition via alternative splicing
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    Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth
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    Chemical-induced chromatin remodeling reprograms mouse ESCs to totipotent-like stem cells
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    In vivo CRISPR screening identifies BAZ2 chromatin remodelers as druggable regulators of mammalian liver regeneration
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    An oncogenic enhancer encodes selective selenium dependency in AML
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  202. Jan 2022
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    ASH1L haploinsufficiency results in autistic-like phenotypes in mice and links Eph receptor gene to autism spectrum disorder
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      DOI: 10.1016/j.neuron.2021.12.035

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    Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response
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    SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers
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    Multi-CUT&Tag to simultaneously profile multiple chromatin factors
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    Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos
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    Chromatin alterations during the epididymal maturation of mouse sperm refine the paternally inherited epigenome
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      DOI: 10.1186/s13072-021-00433-4

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    YAP1 and PRDM14 converge to promote cell survival and tumorigenesis
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  210. Dec 2021
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    SUMOylation of linker histone H1 drives chromatin condensation and restriction of embryonic cell fate identity
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  212. Nov 2021
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    Differentiation of fetal hematopoietic stem cells requires ARID4B to restrict autocrine KITLG/KIT-Src signaling
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    Reprogramming of H3K9bhb at regulatory elements is a key feature of fasting in the small intestine
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    An epigenetic mechanism underlying chromosome 17p deletion-driven tumorigenesis
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    Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers
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    1-deoxysphingolipids bind to COUP-TF to modulate lymphatic and cardiac cell development
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    Global characterization of macrophage polarization mechanisms and identification of M2-type polarization inhibitors
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    Impaired glucocorticoid receptor expression in liver disrupts feeding-induced gene expression, glucose uptake, and glycogen storage
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    Acute depletion of the ARID1A subunit of SWI/SNF complexes reveals distinct pathways for activation and repression of transcription
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    An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity
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  222. Oct 2021
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    Reprogramming CBX8-PRC1 function with a positive allosteric modulator
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    A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus
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    Increased ACTL6A occupancy within mSWI/SNF chromatin remodelers drives human squamous cell carcinoma
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    The Parkinson’s-disease-associated mutation LRRK2-G2019S alters dopaminergic differentiation dynamics via NR2F1
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