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    ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF
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    1. scibot 21 Dec 2024
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  3. Dec 2024
  4. pmc.ncbi.nlm.nih.gov pmc.ncbi.nlm.nih.gov
    PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination
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    Epigenetic and Oncogenic Inhibitors Cooperatively Drive Differentiation and Kill KRAS-Mutant Colorectal Cancers
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  6. Nov 2024
  7. 52.53.155.43 52.53.155.43
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  8. Oct 2024
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    HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding
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  10. Sep 2024
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    Streamlined regulation of chloroplast development in the liverwort Marchantia polymorpha
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    Detecting Small Cell Transformation in Patients with Advanced EGFR Mutant Lung Adenocarcinoma through Epigenomic cfDNA Profiling
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  13. Aug 2024
  14. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Characterizing Relationships between T-cell Inflammation and Outcomes in Patients with High-Risk Neuroblastoma According to Mesenchymal and Adrenergic Signatures
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    CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant
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    Members of an array of zinc-finger proteins specify distinct Hox chromatin boundaries
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    HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability
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    A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance
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    1. scibot 18 Aug 2024
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  19. Jul 2024
  20. www.cell.com www.cell.com
    Innate immune training restores pro-reparative myeloid functions to promote remyelination in the aged central nervous system
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    MYB-related transcription factors control chloroplast biogenesis
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    Rapid Dynamics of Signal-Dependent Transcriptional Repression by Capicua
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    1. scibot 13 Jul 2024
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  23. Jun 2024
  24. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    The TERT Promoter is Polycomb-Repressed in Neuroblastoma Cells with Long Telomeres
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    A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma
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  26. molecular-cancer.biomedcentral.com molecular-cancer.biomedcentral.com
    Diversifying the anthracycline class of anti-cancer drugs identifies aclarubicin for superior survival of acute myeloid leukemia patients
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  27. May 2024
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    Heterochromatic 3D genome organization is directed by HP1a- and H3K9-dependent and independent mechanisms
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    Reciprocal conversion between annual and polycarpic perennial flowering behavior in the Brassicaceae
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    1. scibot 30 May 2024
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  30. 52.53.155.43 52.53.155.43
    ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF
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  31. 52.53.155.43 52.53.155.43
    mcr-23-0295-html.html
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    T-bet deficiency and Hic1 induction override TGF-β-dependency in the formation of CD103+ intestine-resident memory CD8+ T cells
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    Osr2 functions as a biomechanical checkpoint to aggravate CD8+ T cell exhaustion in tumor
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    Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation
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    sciencedirect.com/science/article/pii/S1934590924001425
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    The MYCN oncoprotein is an RNA-binding accessory factor of the nuclear exosome targeting complex
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    MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons
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    sciencedirect.com/science/article/pii/S0896627324002459
  37. Apr 2024
  38. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Enhanced bovine genome annotation through integration of transcriptomics and epi-transcriptomics datasets facilitates genomic biology
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      DOI: 10.1093/gigascience/giae019

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    Class I HDAC inhibitors enhance antitumor efficacy and persistence of CAR-T cells by activation of the Wnt pathway
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    A senescence restriction point acting on chromatin integrates oncogenic signals
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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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      DOI: 10.1016/j.xcrm.2024.101472

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    ncbi.nlm.nih.gov/pmc/articles/PMC10983107/
  42. Mar 2024
  43. link.springer.com link.springer.com
    From degraded to deciphered: ATAC-seq’s application potential in forensic diagnosis
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      DOI: 10.1007/s00414-024-03206-2

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    link.springer.com/article/10.1007/s00414-024-03206-2
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    The transcription factor NF-κB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling
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    sciencedirect.com/science/article/pii/S1074761324000803
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    Mitochondrial isocitrate dehydrogenase impedes CAR T cell function by restraining antioxidant metabolism and histone acetylation
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  46. Feb 2024
  47. 52.53.155.43 52.53.155.43
    can-23-1129-html.html
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    The EstroGene database reveals diverse temporal, context-dependent, and bidirectional estrogen receptor regulomes in breast cancer
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    SLAM-ITseq identifies that Nrf2 induces liver regeneration through the pentose phosphate pathway
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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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    Genome-wide p63-target gene analyses reveal TAp63/NRF2-dependent oxidative stress responses
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    Development of sexual dimorphism of skeletal muscles through the adrenal cortex, caused by androgen-induced global gene suppression
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  64. Dec 2023
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    Pluripotency state transition of embryonic stem cells requires the turnover of histone chaperone FACT on chromatin
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  67. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Blimp-1 and c-Maf regulate  Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells
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  70. Nov 2023
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    Blimp-1 and c-Maf regulate Il10 and negatively regulate common and unique proinflammatory gene networks in IL-12 plus IL-27-driven T helper-1 cells
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    TET2 lesions enhance the aggressiveness of CEBPA-mutant acute myeloid leukemia by rebalancing GATA2 expression
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    Loss of CtBP2 may be a mechanistic link between metabolic derangements and progressive impairment of pancreatic β cell function
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    Pharmacological HDAC inhibition impairs pancreatic β-cell function through an epigenome-wide reprogramming
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    Prenatal Δ9-tetrahydrocannabinol exposure in males leads to motivational disturbances related to striatal epigenetic dysregulation
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    Low-level repressive histone marks fine-tune gene transcription in neural stem cells
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    5-Azacytidine- and retinoic-acid-induced reprogramming of DCCs into dormancy suppresses metastasis via restored TGF-β-SMAD4 signaling
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  93. May 2023
  94. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    Developmental dynamics of chromatin accessibility during post-implantation development of monkey embryos
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  96. Apr 2023
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    Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis
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    Novel enhancers conferring compensatory transcriptional regulation of Nkx2-5 in heart development
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    Complementary gene regulation by NRF1 and NRF2 protects against hepatic cholesterol overload
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    Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia
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    Active maintenance of CD8+ T cell naïvety through regulation of global genome architecture
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  102. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    SWI/SNF Blockade Disrupts PU.1-Directed Enhancer Programs in Normal Hematopoietic Cells and Acute Myeloid Leukemia
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    Asparagine starvation suppresses histone demethylation through iron depletion
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  104. 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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    Jarid2 promotes temporal progression of retinal progenitors via repression of Foxp1
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  107. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
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  108. Feb 2023
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    Genome-wide epigenetic and mRNA-expression profiling followed by CRISPR/Cas9-mediated gene-disruptions corroborate the MIR141/MIR200C-ZEB1/ZEB2-FGFR1 axis in acquired EMT-associated EGFR TKI-resistance in NSCLC cells
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    Loss of PBRM1 alters promoter histone modifications and activates ALDH1A1 to drive renal cell carcinoma
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  111. Jan 2023
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    SMN promotes mitochondrial metabolic maturation during myogenesis by regulating the MYOD-miRNA axis
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  113. Dec 2022
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    Prevalent and dynamic binding of the cell cycle checkpoint kinase Rad53 to gene promoters
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  115. aacrjournals.org aacrjournals.org
    BAF complex maintains glioma stem cells in pediatric H3K27M-glioma
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  116. Nov 2022
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    Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation
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    Essential role of MESP1-RING1A complex in cardiac differentiation
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    Transcription factor antagonism regulates heterogeneity in embryonic stem cell states
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  120. Oct 2022
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    CircIPO7 Promotes Nasopharyngeal Carcinoma Metastasis and Cisplatin Chemoresistance by Facilitating YBX1 Nuclear Localization
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    A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation
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  123. Sep 2022
  124. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    In Vivo Genome-Wide CRISPR Activation Screening Identifies Functionally Important Long Noncoding RNAs in Hepatocellular Carcinoma
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    STAG2 promotes the myelination transcriptional program in oligodendrocytes
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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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  127. Aug 2022
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    Npas3 deficiency impairs cortical astrogenesis and induces autistic-like behaviors
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    SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression
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  130. Jun 2022
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    Inflammaging is driven by upregulation of innate immune receptors and systemic interferon signaling and is ameliorated by dietary restriction
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    Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine
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    JAZF1-SUZ12 dysregulates PRC2 function and gene expression during cell differentiation
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    Mediator recruits the cohesin loader Scc2 to RNA Pol II-transcribed genes and promotes sister chromatid cohesion
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    Oct4 differentially regulates chromatin opening and enhancer transcription in pluripotent stem cells
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  137. Apr 2022
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    An adult-stage transcriptional program for survival of serotonergic connectivity
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    HNF4A modulates glucocorticoid action in the liver
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    Presence of H3K4me3 on Paternally Expressed Genes of the Paternal Genome From Sperm to Implantation
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  141. Mar 2022
  142. elifesciences.org elifesciences.org
    Novel insights from a multiomics dissection of the Hayflick limit
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    Placental uptake and metabolism of 25(OH)vitamin D determine its activity within the fetoplacental unit
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    EP300 Selectively Controls the Enhancer Landscape of MYCN-Amplified Neuroblastoma
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    A test of the pioneer factor hypothesis using ectopic liver gene activation
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    A genetic compensatory mechanism regulated by Jun and Mef2d modulates the expression of distinct class IIa Hdacs to ensure peripheral nerve myelination and repair
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  147. Feb 2022
  148. www.sciencedirect.com www.sciencedirect.com
    HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization
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    EBF1 nuclear repositioning instructs chromatin refolding to promote therapy resistance in T leukemic cells
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    Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration
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    Lymphocyte-Specific Chromatin Accessibility Pre-determines Glucocorticoid Resistance in Acute Lymphoblastic Leukemia
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  198. www.sciencedirect.com www.sciencedirect.com
    Novel cell adhesion/migration pathways are predictive markers of HDAC inhibitor resistance in cutaneous T cell lymphoma
    1
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      MACS2

      DOI: 10.1016/j.ebiom.2019.07.053

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  199. academic.oup.com academic.oup.com
    HUMAN TROPHOBLAST DIFFERENTIATION IS ASSOCIATED WITH PROFOUND GENE REGULATORY AND EPIGENETIC CHANGES
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      MACS

      DOI: 10.1210/en.2019-00144

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    Targeting CDK9 Reactivates Epigenetically Silenced Genes in Cancer
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      RRID:SCR_013291

      DOI: 10.1016/j.cell.2018.09.051

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    Chromatin Environment and Cellular Context Specify Compensatory Activity of Paralogous MEF2 Transcription Factors
    1
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    Mapping the Global Chromatin Connectivity Network for Sox2 Function in Neural Stem Cell Maintenance
    2
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      MACS2 (for H3K27ac/H3K4me1 ChIPseq)

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    Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation
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    Enhancer Architecture and Essential Core Regulatory Circuitry of Chronic Lymphocytic Leukemia
    1
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    Ezh2 and Runx1 Mutations Collaborate to Initiate Lympho-Myeloid Leukemia in Early Thymic Progenitors
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    Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
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    Acetylation of Cytidine in mRNA Promotes Translation Efficiency
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    Widespread Enhancer Dememorization and Promoter Priming during Parental-to-Zygotic Transition
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    A CHAF1B-Dependent Molecular Switch in Hematopoiesis and Leukemia Pathogenesis
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    MYC Protein Interactome Profiling Reveals Functionally Distinct Regions that Cooperate to Drive Tumorigenesis
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    N6-methyladenine DNA Modification in Glioblastoma
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    SUMO Safeguards Somatic and Pluripotent Cell Identities by Enforcing Distinct Chromatin States
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      MACS

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    ORY-1001, a Potent and Selective Covalent KDM1A Inhibitor, for the Treatment of Acute Leukemia
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    BRD4 Inhibition Is Synthetic Lethal with PARP Inhibitors through the Induction of Homologous Recombination Deficiency
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    Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis
    2
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      MACS2

      DOI: 10.1016/j.cell.2017.02.015

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      DOI: 10.1016/j.cell.2017.02.015

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    sciencedirect.com/science/article/pii/S0092867417301939
  216. academic.oup.com academic.oup.com
    Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa
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      RRID:SRC_013291

      DOI: 10.1093/gigascience/giz147

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    academic.oup.com/gigascience/article/8/12/giz147/5652252
  217. f1000research.com f1000research.com
    F1000Research Article: PEGS: An efficient tool for gene set enrichment within defined sets of genomic intervals.
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      RRID:SCR_013291

      DOI: 10.12688/f1000research.53926.1

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    f1000research.com/articles/10-570
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    Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination
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      DOI: 10.1016/j.molcel.2021.06.016

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    sciencedirect.com/science/article/pii/S1097276521004962
  219. Jun 2021
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    Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation
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      RRID:SCR_013291

      DOI: 10.1016/j.xpro.2021.100609

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    sciencedirect.com/science/article/pii/S2666166721003166
  221. May 2021
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    ZC3H4 restricts non-coding transcription in human cells
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      SCR_013291

      DOI: 10.7554/eLife.67305

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    ncbi.nlm.nih.gov/pmc/articles/PMC8137146/
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    Morphological and genomic shifts in mole-rat ‘queens’ increase fecundity but reduce skeletal integrity
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      RRID:SCR_013291

      DOI: 10.7554/eLife.65760

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    ncbi.nlm.nih.gov/pmc/articles/PMC8104968/
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    Sequential CRISPR gene editing in human iPSCs charts the clonal evolution of myeloid leukemia and identifies early disease targets
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      RRID:SCR_013291

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    Non-canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function
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      RRID:SCR_013291

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    Derivation of Intermediate Pluripotent Stem Cells Amenable to Primordial Germ Cell Specification
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      RRID:SCR_013291

      DOI: 10.1016/j.stem.2020.11.003

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    sciencedirect.com/science/article/pii/S1934590920305415
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    Neural Stem Cells Direct Axon Guidance via Their Radial Fiber Scaffold
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      SCR_013291

      DOI: 10.1016/j.neuron.2020.06.035

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    sciencedirect.com/science/article/pii/S089662732030489X
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    A Prion-like Domain in Transcription Factor EBF1 Promotes Phase Separation and Enables B Cell Programming of Progenitor Chromatin
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      RRID:SCR_013291

      DOI: 10.1016/j.immuni.2020.10.009

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    sciencedirect.com/science/article/pii/S1074761320304507
  229. Apr 2021
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    5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer’s disease
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      RRID:SCR_013291

      DOI: 10.1016/j.celrep.2021.109042

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    sciencedirect.com/science/article/pii/S2211124721003582
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    Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells
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      SCR_013291

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    sciencedirect.com/science/article/pii/S009286742030814X
  232. www.cell.com www.cell.com
    IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis
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      RRID:SCR_013291

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    cell.com/cancer-cell/fulltext/S1535-6108(20)30311-1