1 3918 119 LINKING ABERRANT CHROMATIN FEATURES IN CHRONIC LYMPHOCYTIC LEUKEMIA TO TRANSCRIPTION FACTOR NETWORKS. IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), A DIVERSE SET OF GENETIC MUTATIONS IS EMBEDDED IN A DEREGULATED EPIGENETIC LANDSCAPE THAT DRIVES CANCEROGENESIS. TO ELUCIDATE THE ROLE OF ABERRANT CHROMATIN FEATURES, WE MAPPED DNA METHYLATION, SEVEN HISTONE MODIFICATIONS, NUCLEOSOME POSITIONS, CHROMATIN ACCESSIBILITY, BINDING OF EBF1 AND CTCF, AS WELL AS THE TRANSCRIPTOME OF B CELLS FROM CLL PATIENTS AND HEALTHY DONORS. A GLOBALLY INCREASED HISTONE DEACETYLASE ACTIVITY WAS DETECTED AND HALF OF THE GENOME COMPRISED TRANSCRIPTIONALLY DOWNREGULATED PARTIALLY DNA METHYLATED DOMAINS DEMARCATED BY CTCF CLL SAMPLES DISPLAYED A H3K4ME3 REDISTRIBUTION AND NUCLEOSOME GAIN AT PROMOTERS AS WELL AS CHANGES OF ENHANCER ACTIVITY AND ENHANCER LINKAGE TO TARGET GENES. A DNA BINDING MOTIF ANALYSIS IDENTIFIED TRANSCRIPTION FACTORS THAT GAINED OR LOST BINDING IN CLL AT SITES WITH ABERRANT CHROMATIN FEATURES. THESE FINDINGS WERE INTEGRATED INTO A GENE REGULATORY ENHANCER CONTAINING NETWORK ENRICHED FOR B-CELL RECEPTOR SIGNALING PATHWAY COMPONENTS. OUR STUDY PREDICTS NOVEL MOLECULAR LINKS TO TARGETS OF CLL THERAPIES AND PROVIDES A VALUABLE RESOURCE FOR FURTHER STUDIES ON THE EPIGENETIC CONTRIBUTION TO THE DISEASE. 2019 2 3754 33 INTEGRATED ANALYSIS OF OMICS DATA REVEAL AP-1 AS A POTENTIAL REGULATION HUB IN THE INFLAMMATION-INDUCED HYPERALGESIA RAT MODEL. INFLAMMATION-ASSOCIATED CHRONIC PAIN IS A GLOBAL CLINICAL PROBLEM, AFFECTING MILLIONS OF PEOPLE WORLDWIDE. HOWEVER, THE UNDERLYING MECHANISMS THAT MEDIATE INFLAMMATION-ASSOCIATED CHRONIC PAIN REMAIN UNCLEAR. A RAT MODEL OF CUTANEOUS INFLAMMATION INDUCED BY COMPLETE FREUND'S ADJUVANT (CFA) HAS BEEN WIDELY USED AS AN INFLAMMATION-INDUCED PAIN HYPERSENSITIVITY MODEL. WE PRESENT THE TRANSCRIPTOMICS PROFILE OF CFA-INDUCED INFLAMMATION IN THE RAT DORSAL ROOT GANGLION (DRG) VIA AN APPROACH THAT TARGETS GENE EXPRESSION, DNA METHYLATION, AND POST-TRANSCRIPTIONAL REGULATION. WE IDENTIFIED 418 DIFFERENTIALLY EXPRESSED MRNAS, 120 DIFFERENTIALLY EXPRESSED MICRORNAS (MIRNAS), AND 2,670 DIFFERENTIALLY METHYLATED REGIONS (DMRS), WHICH WERE ALL HIGHLY ASSOCIATED WITH MULTIPLE INFLAMMATION-RELATED PATHWAYS, INCLUDING NUCLEAR FACTOR KAPPA B (NF-KAPPAB) AND INTERFERON (IFN) SIGNALING PATHWAYS. AN INTEGRATED ANALYSIS FURTHER DEMONSTRATED THAT THE ACTIVATOR PROTEIN 1 (AP-1) NETWORK, WHICH MAY ACT AS A REGULATOR OF THE INFLAMMATORY RESPONSE, IS REGULATED AT BOTH THE TRANSCRIPTOMIC AND EPIGENETIC LEVELS. WE BELIEVE OUR DATA WILL NOT ONLY PROVIDE DRUG SCREENING TARGETS FOR THE TREATMENT OF CHRONIC PAIN AND INFLAMMATION BUT WILL ALSO SHED LIGHT ON THE MOLECULAR NETWORK ASSOCIATED WITH INFLAMMATION-INDUCED HYPERALGESIA. 2021 3 1336 37 DESCRIBING A TRANSCRIPTION FACTOR DEPENDENT REGULATION OF THE MICRORNA TRANSCRIPTOME. WHILE THE TRANSCRIPTION REGULATION OF PROTEIN CODING GENES WAS EXTENSIVELY STUDIED, LITTLE IS KNOWN ON HOW TRANSCRIPTION FACTORS ARE INVOLVED IN TRANSCRIPTION OF NON-CODING RNAS, SPECIFICALLY OF MICRORNAS. HERE, WE PROPOSE A STRATEGY TO STUDY THE POTENTIAL ROLE OF TRANSCRIPTION FACTOR IN REGULATING TRANSCRIPTION OF MICRORNAS USING PUBLICALLY AVAILABLE DATA, COMPUTATIONAL RESOURCES AND HIGH THROUGHPUT DATA. WE USE THE H3K4ME3 EPIGENETIC SIGNATURE TO IDENTIFY MICRORNA PROMOTERS AND CHROMATIN IMMUNOPRECIPITATION (CHIP)-SEQUENCING DATA FROM THE ENCODE PROJECT TO IDENTIFY MICRORNA PROMOTERS THAT ARE ENRICHED WITH TRANSCRIPTION FACTOR BINDING SITES. BY TRANSFECTING CELLS OF INTEREST WITH SHRNA TARGETING A TRANSCRIPTION FACTOR OF INTEREST AND SUBJECTING THE CELLS TO MICRORNA ARRAY, WE STUDY THE EFFECT OF THIS TRANSCRIPTION FACTOR ON THE MICRORNA TRANSCRIPTOME. AS AN ILLUSTRATIVE EXAMPLE WE USE OUR STUDY ON THE EFFECT OF STAT3 ON THE MICRORNA TRANSCRIPTOME OF CHRONIC LYMPHOCYTIC LEUKEMIA (CLL) CELLS. 2016 4 4546 37 MUTANT P53 REGULATES ENHANCER-ASSOCIATED H3K4 MONOMETHYLATION THROUGH INTERACTIONS WITH THE METHYLTRANSFERASE MLL4. MONOMETHYLATION OF HISTONE H3 LYSINE 4 (H3K4ME1) IS ENRICHED AT ENHANCERS THAT ARE PRIMED FOR ACTIVATION AND THE LEVELS OF THIS HISTONE MARK ARE FREQUENTLY ALTERED IN VARIOUS HUMAN CANCERS. YET, HOW ALTERATIONS IN H3K4ME1 ARE ESTABLISHED AND THE CONSEQUENCES OF THESE EPIGENETIC CHANGES IN TUMORIGENESIS ARE NOT WELL UNDERSTOOD. USING CHIP-SEQ IN HUMAN COLON CANCER CELLS, WE DEMONSTRATE THAT MUTANT P53 DEPLETION RESULTS IN DECREASED H3K4ME1 LEVELS AT ACTIVE ENHANCERS THAT REVEAL A STRIKING COLOCALIZATION OF MUTANT P53 AND THE H3K4 MONOMETHYLTRANSFERASE MLL4 FOLLOWING CHRONIC TUMOR NECROSIS FACTOR ALPHA (TNFALPHA) SIGNALING. WE FURTHER REVEAL THAT MUTANT P53 FORMS PHYSIOLOGICAL ASSOCIATIONS AND DIRECT INTERACTIONS WITH MLL4 AND PROMOTES THE ENHANCER BINDING OF MLL4, WHICH IS REQUIRED FOR TNFALPHA-INDUCIBLE H3K4ME1 AND HISTONE H3 LYSINE 27 ACETYLATION (H3K27AC) LEVELS, ENHANCER-DERIVED TRANSCRIPT (ERNA) SYNTHESIS, AND MUTANT P53-DEPENDENT TARGET GENE ACTIVATION. COMPLEMENTARY IN VITRO STUDIES WITH RECOMBINANT CHROMATIN AND PURIFIED PROTEINS DEMONSTRATE THAT BINDING OF THE MLL3/4 COMPLEX AND H3K4ME1 DEPOSITION IS ENHANCED BY MUTANT P53 AND P300-MEDIATED ACETYLATION, WHICH IN TURN REFLECTS A MLL3/4-DEPENDENT ENHANCEMENT OF MUTANT P53 AND P300-DEPENDENT TRANSCRIPTIONAL ACTIVATION. COLLECTIVELY, OUR FINDINGS ESTABLISH A MECHANISM IN WHICH MUTANT P53 COOPERATES WITH MLL4 TO REGULATE ABERRANT ENHANCER ACTIVITY AND TUMOR-PROMOTING GENE EXPRESSION IN RESPONSE TO CHRONIC IMMUNE SIGNALING. 2018 5 775 38 CELL TYPE-SPECIFIC WHOLE-GENOME LANDSCAPE OF DELTAFOSB BINDING IN THE NUCLEUS ACCUMBENS AFTER CHRONIC COCAINE EXPOSURE. BACKGROUND: THE ABILITY OF NEURONS TO RESPOND TO EXTERNAL STIMULI INVOLVES ADAPTATIONS OF GENE EXPRESSION. INDUCTION OF THE TRANSCRIPTION FACTOR DELTAFOSB IN THE NUCLEUS ACCUMBENS, A KEY BRAIN REWARD REGION, IS IMPORTANT FOR THE DEVELOPMENT OF DRUG ADDICTION. HOWEVER, A COMPREHENSIVE MAP OF DELTAFOSB'S GENE TARGETS HAS NOT YET BEEN GENERATED. METHODS: WE USED CUT&RUN (CLEAVAGE UNDER TARGETS AND RELEASE USING NUCLEASE) TO MAP THE GENOME-WIDE CHANGES IN DELTAFOSB BINDING IN THE 2 MAIN TYPES OF NUCLEUS ACCUMBENS NEURONS-D1 OR D2 MEDIUM SPINY NEURONS-AFTER CHRONIC COCAINE EXPOSURE. TO ANNOTATE GENOMIC REGIONS OF DELTAFOSB BINDING SITES, WE ALSO EXAMINED THE DISTRIBUTIONS OF SEVERAL HISTONE MODIFICATIONS. RESULTING DATASETS WERE LEVERAGED FOR MULTIPLE BIOINFORMATIC ANALYSES. RESULTS: THE MAJORITY OF DELTAFOSB PEAKS OCCUR OUTSIDE PROMOTER REGIONS, INCLUDING INTERGENIC REGIONS, AND ARE SURROUNDED BY EPIGENETIC MARKS INDICATIVE OF ACTIVE ENHANCERS. BRG1, THE CORE SUBUNIT OF THE SWI/SNF CHROMATIN REMODELING COMPLEX, OVERLAPS WITH DELTAFOSB PEAKS, A FINDING CONSISTENT WITH EARLIER STUDIES OF DELTAFOSB'S INTERACTING PROTEINS. CHRONIC COCAINE USE INDUCES BROAD CHANGES IN DELTAFOSB BINDING IN BOTH D1 AND D2 NUCLEUS ACCUMBENS MEDIUM SPINY NEURONS OF MALE AND FEMALE MICE. IN ADDITION, IN SILICO ANALYSES PREDICT THAT DELTAFOSB COOPERATIVELY REGULATES GENE EXPRESSION WITH HOMEOBOX AND T-BOX TRANSCRIPTION FACTORS. CONCLUSIONS: THESE NOVEL FINDINGS UNCOVER KEY ELEMENTS OF DELTAFOSB'S MOLECULAR MECHANISMS IN TRANSCRIPTIONAL REGULATION AT BASELINE AND IN RESPONSE TO CHRONIC COCAINE EXPOSURE. FURTHER CHARACTERIZATION OF DELTAFOSB'S COLLABORATIVE TRANSCRIPTIONAL AND CHROMATIN PARTNERS SPECIFICALLY IN D1 AND D2 MEDIUM SPINY NEURONS WILL REVEAL A BROADER PICTURE OF THE FUNCTION OF DELTAFOSB AND THE MOLECULAR BASIS OF DRUG ADDICTION. 2023 6 3043 34 GENOME-WIDE ANALYSIS IDENTIFIES NR4A1 AS A KEY MEDIATOR OF T CELL DYSFUNCTION. T CELLS BECOME DYSFUNCTIONAL WHEN THEY ENCOUNTER SELF ANTIGENS OR ARE EXPOSED TO CHRONIC INFECTION OR TO THE TUMOUR MICROENVIRONMENT(1). THE FUNCTION OF T CELLS IS TIGHTLY REGULATED BY A COMBINATIONAL CO-STIMULATORY SIGNAL, AND DOMINANCE OF NEGATIVE CO-STIMULATION RESULTS IN T CELL DYSFUNCTION(2). HOWEVER, THE MOLECULAR MECHANISMS THAT UNDERLIE THIS DYSFUNCTION REMAIN UNCLEAR. HERE, USING AN IN VITRO T CELL TOLERANCE INDUCTION SYSTEM IN MICE, WE CHARACTERIZE GENOME-WIDE EPIGENETIC AND GENE EXPRESSION FEATURES IN TOLERANT T CELLS, AND SHOW THAT THEY ARE DISTINCT FROM EFFECTOR AND REGULATORY T CELLS. NOTABLY, THE TRANSCRIPTION FACTOR NR4A1 IS STABLY EXPRESSED AT HIGH LEVELS IN TOLERANT T CELLS. OVEREXPRESSION OF NR4A1 INHIBITS EFFECTOR T CELL DIFFERENTIATION, WHEREAS DELETION OF NR4A1 OVERCOMES T CELL TOLERANCE AND EXAGGERATES EFFECTOR FUNCTION, AS WELL AS ENHANCING IMMUNITY AGAINST TUMOUR AND CHRONIC VIRUS. MECHANISTICALLY, NR4A1 IS PREFERENTIALLY RECRUITED TO BINDING SITES OF THE TRANSCRIPTION FACTOR AP-1, WHERE IT REPRESSES EFFECTOR-GENE EXPRESSION BY INHIBITING AP-1 FUNCTION. NR4A1 BINDING ALSO PROMOTES ACETYLATION OF HISTONE 3 AT LYSINE 27 (H3K27AC), LEADING TO ACTIVATION OF TOLERANCE-RELATED GENES. THIS STUDY THUS IDENTIFIES NR4A1 AS A KEY GENERAL REGULATOR IN THE INDUCTION OF T CELL DYSFUNCTION, AND A POTENTIAL TARGET FOR TUMOUR IMMUNOTHERAPY. 2019 7 883 39 CHRONIC COCAINE-REGULATED EPIGENOMIC CHANGES IN MOUSE NUCLEUS ACCUMBENS. BACKGROUND: INCREASING EVIDENCE SUPPORTS A ROLE FOR ALTERED GENE EXPRESSION IN MEDIATING THE LASTING EFFECTS OF COCAINE ON THE BRAIN, AND RECENT WORK HAS DEMONSTRATED THE INVOLVEMENT OF CHROMATIN MODIFICATIONS IN THESE ALTERATIONS. HOWEVER, ALL SUCH STUDIES TO DATE HAVE BEEN RESTRICTED BY THEIR RELIANCE ON MICROARRAY TECHNOLOGIES THAT HAVE INTRINSIC LIMITATIONS. RESULTS: WE USE NEXT GENERATION SEQUENCING METHODS, RNA-SEQ AND CHIP-SEQ FOR RNA POLYMERASE II AND SEVERAL HISTONE METHYLATION MARKS, TO OBTAIN A MORE COMPLETE VIEW OF COCAINE-INDUCED CHANGES IN GENE EXPRESSION AND ASSOCIATED ADAPTATIONS IN NUMEROUS MODES OF CHROMATIN REGULATION IN THE MOUSE NUCLEUS ACCUMBENS, A KEY BRAIN REWARD REGION. WE DEMONSTRATE AN UNEXPECTEDLY LARGE NUMBER OF PRE-MRNA SPLICING ALTERATIONS IN RESPONSE TO REPEATED COCAINE TREATMENT. IN ADDITION, WE IDENTIFY COMBINATIONS OF CHROMATIN CHANGES, OR SIGNATURES, THAT CORRELATE WITH COCAINE-DEPENDENT REGULATION OF GENE EXPRESSION, INCLUDING THOSE INVOLVING PRE-MRNA ALTERNATIVE SPLICING. THROUGH BIOINFORMATIC PREDICTION AND BIOLOGICAL VALIDATION, WE IDENTIFY ONE PARTICULAR SPLICING FACTOR, A2BP1(RBFOX1/FOX-1), WHICH IS ENRICHED AT GENES THAT DISPLAY CERTAIN CHROMATIN SIGNATURES AND CONTRIBUTES TO DRUG-INDUCED BEHAVIORAL ABNORMALITIES. TOGETHER, THIS DELINEATION OF THE COCAINE-INDUCED EPIGENOME IN THE NUCLEUS ACCUMBENS REVEALS SEVERAL NOVEL MODES OF REGULATION BY WHICH COCAINE ALTERS THE BRAIN. CONCLUSIONS: WE ESTABLISH COMBINATORIAL CHROMATIN AND TRANSCRIPTIONAL PROFILES IN MOUSE NUCLEUS ACCUMBENS AFTER REPEATED COCAINE TREATMENT. THESE RESULTS SERVE AS AN IMPORTANT RESOURCE FOR THE FIELD AND PROVIDE A TEMPLATE FOR THE ANALYSIS OF OTHER SYSTEMS TO REVEAL NEW TRANSCRIPTIONAL AND EPIGENETIC MECHANISMS OF NEURONAL REGULATION. 2014 8 4497 38 MORPHINE LEADS TO GLOBAL GENOME CHANGES IN H3K27ME3 LEVELS VIA A POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) SELF-REGULATORY MECHANISM IN MESCS. BACKGROUND: ENVIRONMENTALLY INDUCED EPIGENETIC CHANGES CAN LEAD TO HEALTH PROBLEMS OR DISEASE, BUT THE MECHANISMS INVOLVED REMAIN UNCLEAR. MORPHINE CAN PASS THROUGH THE PLACENTAL BARRIER LEADING TO ABNORMAL EMBRYO DEVELOPMENT. HOWEVER, THE MECHANISM BY WHICH MORPHINE CAUSES THESE EFFECTS AND HOW THEY SOMETIMES PERSIST INTO ADULTHOOD IS NOT WELL KNOWN. TO UNRAVEL THE MORPHINE-INDUCED CHROMATIN ALTERATIONS INVOLVED IN ABERRANT EMBRYO DEVELOPMENT, WE EXPLORED THE ROLE OF THE H3K27ME3/PRC2 REPRESSIVE COMPLEX IN GENE EXPRESSION AND ITS TRANSMISSION ACROSS CELLULAR GENERATIONS IN RESPONSE TO MORPHINE. RESULTS: USING MOUSE EMBRYONIC STEM CELLS AS A MODEL SYSTEM, WE FOUND THAT CHRONIC MORPHINE TREATMENT INDUCES A GLOBAL DOWNREGULATION OF THE HISTONE MODIFICATION H3K27ME3. CONVERSELY, CHIP-SEQ SHOWED A REMARKABLE INCREASE IN H3K27ME3 LEVELS AT SPECIFIC GENOMIC SITES, PARTICULARLY PROMOTERS, DISRUPTING SELECTIVE TARGET GENES RELATED TO EMBRYO DEVELOPMENT, CELL CYCLE AND METABOLISM. THROUGH A SELF-REGULATORY MECHANISM, MORPHINE DOWNREGULATED THE TRANSCRIPTION OF PRC2 COMPONENTS RESPONSIBLE FOR H3K27ME3 BY ENRICHING HIGH H3K27ME3 LEVELS AT THE PROMOTER REGION. DOWNREGULATION OF PRC2 COMPONENTS PERSISTED FOR AT LEAST 48 H (4 CELL CYCLES) FOLLOWING MORPHINE REMOVAL, THOUGH PROMOTER H3K27ME3 LEVELS RETURNED TO CONTROL LEVELS. CONCLUSIONS: MORPHINE INDUCES TARGETING OF THE PRC2 COMPLEX TO SELECTED PROMOTERS, INCLUDING THOSE OF PRC2 COMPONENTS, LEADING TO CHARACTERISTIC CHANGES IN GENE EXPRESSION AND A GLOBAL REDUCTION IN H3K27ME3. FOLLOWING MORPHINE REMOVAL, ENHANCED PROMOTER H3K27ME3 LEVELS REVERT TO NORMAL SOONER THAN GLOBAL H3K27ME3 OR PRC2 COMPONENT TRANSCRIPT LEVELS. WE SUGGEST THAT H3K27ME3 IS INVOLVED IN INITIATING MORPHINE-INDUCED CHANGES IN GENE EXPRESSION, BUT NOT IN THEIR MAINTENANCE. MODEL OF POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) AND H3K27ME3 ALTERATIONS INDUCED BY CHRONIC MORPHINE EXPOSURE. MORPHINE INDUCES H3K27ME3 ENRICHMENT AT PROMOTERS OF GENES ENCODING CORE MEMBERS OF THE PRC2 COMPLEX AND IS ASSOCIATED WITH THEIR TRANSCRIPTIONAL DOWNREGULATION. 2020 9 4004 35 LOSS OF THE POLYCOMB MARK FROM BIVALENT PROMOTERS LEADS TO ACTIVATION OF CANCER-PROMOTING GENES IN COLORECTAL TUMORS. IN COLON TUMORS, THE TRANSCRIPTION OF MANY GENES BECOMES DEREGULATED BY POORLY DEFINED EPIGENETIC MECHANISMS THAT HAVE BEEN STUDIED MAINLY IN ESTABLISHED CELL LINES. IN THIS STUDY, WE USED FROZEN HUMAN COLON TISSUES TO ANALYZE PATTERNS OF HISTONE MODIFICATION AND DNA CYTOSINE METHYLATION IN CANCER AND MATCHED NORMAL MUCOSA SPECIMENS. DNA METHYLATION IS STRONGLY TARGETED TO BIVALENT H3K4ME3- AND H3K27ME3-ASSOCIATED PROMOTERS, WHICH LOSE BOTH HISTONE MARKS AND ACQUIRE DNA METHYLATION. HOWEVER, WE FOUND THAT LOSS OF THE POLYCOMB MARK H3K27ME3 FROM BIVALENT PROMOTERS WAS ACCOMPANIED OFTEN BY ACTIVATION OF GENES ASSOCIATED WITH CANCER PROGRESSION, INCLUDING NUMEROUS STEM CELL REGULATORS, ONCOGENES, AND PROLIFERATION-ASSOCIATED GENES. INDEED, WE FOUND MANY OF THESE SAME GENES WERE ALSO ACTIVATED IN PATIENTS WITH ULCERATIVE COLITIS WHERE CHRONIC INFLAMMATION PREDISPOSES THEM TO COLON CANCER. BASED ON OUR FINDINGS, WE PROPOSE THAT A LOSS OF POLYCOMB REPRESSION AT BIVALENT GENES COMBINED WITH AN ENSUING SELECTION FOR TUMOR-DRIVING EVENTS PLAYS A MAJOR ROLE IN CANCER PROGRESSION. 2014 10 3357 29 HISTONE H3 LYSINE 9 DI-METHYLATION AS AN EPIGENETIC SIGNATURE OF THE INTERFERON RESPONSE. EFFECTIVE ANTIVIRAL IMMUNITY DEPENDS ON THE ABILITY OF INFECTED CELLS OR CELLS TRIGGERED WITH VIRUS-DERIVED NUCLEIC ACIDS TO PRODUCE TYPE I INTERFERON (IFN), WHICH ACTIVATES TRANSCRIPTION OF NUMEROUS ANTIVIRAL GENES. HOWEVER, DISPROPORTIONATELY STRONG OR CHRONIC IFN EXPRESSION IS A COMMON CAUSE OF INFLAMMATORY AND AUTOIMMUNE DISEASES. WE DESCRIBE AN EPIGENETIC MECHANISM THAT DETERMINES CELL TYPE-SPECIFIC DIFFERENCES IN IFN AND IFN-STIMULATED GENE (ISG) EXPRESSION IN RESPONSE TO EXOGENOUS SIGNALS. WE IDENTIFY DI-METHYLATION OF HISTONE H3 AT LYSINE 9 (H3K9ME2) AS A SUPPRESSOR OF IFN AND IFN-INDUCIBLE ANTIVIRAL GENE EXPRESSION. WE SHOW THAT LEVELS OF H3K9ME2 AT IFN AND ISG CORRELATE INVERSELY WITH THE SCOPE AND AMPLITUDE OF IFN AND ISG EXPRESSION IN FIBROBLASTS AND DENDRITIC CELLS. ACCORDINGLY, GENETIC ABLATION OR PHARMACOLOGICAL INACTIVATION OF LYSINE METHYLTRANSFERASE G9A, WHICH IS ESSENTIAL FOR THE GENERATION OF H3K9ME2, RESULTED IN PHENOTYPIC CONVERSION OF FIBROBLASTS INTO HIGHLY POTENT IFN-PRODUCING CELLS AND RENDERED THESE CELLS RESISTANT TO PATHOGENIC RNA VIRUSES. IN SUMMARY, OUR STUDIES IMPLICATE H3K9ME2 AND ENZYMES CONTROLLING ITS ABUNDANCE AS KEY REGULATORS OF INNATE ANTIVIRAL IMMUNITY. 2012 11 3072 32 GENOME-WIDE DNA METHYLATION REPROGRAMMING IN RESPONSE TO INORGANIC ARSENIC LINKS INHIBITION OF CTCF BINDING, DNMT EXPRESSION AND CELLULAR TRANSFORMATION. CHRONIC LOW DOSE INORGANIC ARSENIC (IAS) EXPOSURE LEADS TO CHANGES IN GENE EXPRESSION AND EPITHELIAL-TO-MESENCHYMAL TRANSFORMATION. DURING THIS TRANSFORMATION, CELLS ADOPT A FIBROBLAST-LIKE PHENOTYPE ACCOMPANIED BY PROFOUND GENE EXPRESSION CHANGES. WHILE MANY MECHANISMS HAVE BEEN IMPLICATED IN THIS TRANSFORMATION, STUDIES THAT FOCUS ON THE ROLE OF EPIGENETIC ALTERATIONS IN THIS PROCESS ARE JUST EMERGING. DNA METHYLATION CONTROLS GENE EXPRESSION IN PHYSIOLOGIC AND PATHOLOGIC STATES. SEVERAL STUDIES SHOW ALTERATIONS IN DNA METHYLATION PATTERNS IN IAS-MEDIATED PATHOGENESIS, BUT THESE STUDIES FOCUSED ON SINGLE GENES. WE PRESENT A COMPREHENSIVE GENOME-WIDE DNA METHYLATION ANALYSIS USING METHYL-SEQUENCING TO MEASURE CHANGES BETWEEN NORMAL AND IAS-TRANSFORMED CELLS. ADDITIONALLY, THESE DIFFERENTIAL METHYLATION CHANGES CORRELATED POSITIVELY WITH CHANGES IN GENE EXPRESSION AND ALTERNATIVE SPLICING. INTERESTINGLY, MOST OF THESE DIFFERENTIALLY METHYLATED GENES FUNCTION IN CELL ADHESION AND COMMUNICATION PATHWAYS. TO GAIN INSIGHT INTO HOW GENOMIC DNA METHYLATION PATTERNS ARE REGULATED DURING IAS-MEDIATED CARCINOGENESIS, WE SHOW THAT IAS PROBABLY TARGETS CTCF BINDING AT THE PROMOTER OF DNA METHYLTRANSFERASES, REGULATING THEIR EXPRESSION. THESE FINDINGS REVEAL HOW CTCF BINDING REGULATES DNA METHYLTRANSFERASE TO REPROGRAM THE METHYLOME IN RESPONSE TO AN ENVIRONMENTAL TOXIN. 2017 12 3375 23 HISTONE POSTTRANSLATIONAL MODIFICATIONS PREDICT SPECIFIC ALTERNATIVE EXON SUBTYPES IN MAMMALIAN BRAIN. A COMPELLING BODY OF LITERATURE, BASED ON NEXT GENERATION CHROMATIN IMMUNOPRECIPITATION AND RNA SEQUENCING OF REWARD BRAIN REGIONS INDICATES THAT THE REGULATION OF THE EPIGENETIC LANDSCAPE LIKELY UNDERLIES CHRONIC DRUG ABUSE AND ADDICTION. IT IS NOW CRITICAL TO DEVELOP HIGHLY INNOVATIVE COMPUTATIONAL STRATEGIES TO REVEAL THE RELEVANT REGULATORY TRANSCRIPTIONAL MECHANISMS THAT MAY UNDERLIE NEUROPSYCHIATRIC DISEASE. WE HAVE ANALYZED CHROMATIN REGULATION OF ALTERNATIVE SPLICING, WHICH IS IMPLICATED IN COCAINE EXPOSURE IN MICE. RECENT LITERATURE HAS DESCRIBED CHROMATIN-REGULATED ALTERNATIVE SPLICING, SUGGESTING A NOVEL FUNCTION FOR DRUG-INDUCED NEUROEPIGENETIC REMODELING. HOWEVER, THE EXTENT OF THE GENOME-WIDE ASSOCIATION BETWEEN PARTICULAR HISTONE MODIFICATIONS AND ALTERNATIVE SPLICING REMAINS UNEXPLORED. TO ADDRESS THIS, WE HAVE DEVELOPED NOVEL COMPUTATIONAL APPROACHES TO MODEL THE ASSOCIATION BETWEEN ALTERNATIVE SPLICING AND HISTONE POSTTRANSLATIONAL MODIFICATIONS IN THE NUCLEUS ACCUMBENS (NAC), A BRAIN REWARD REGION. USING CLASSICAL STATISTICAL METHODS AND MACHINE LEARNING TO COMBINE CHIP-SEQ AND RNA-SEQ DATA, WE FOUND THAT SPECIFIC HISTONE MODIFICATIONS ARE STRONGLY ASSOCIATED WITH VARIOUS ASPECTS OF DIFFERENTIAL SPLICING. H3K36ME3 AND H3K4ME1 HAVE THE STRONGEST ASSOCIATION WITH SPLICING INDICATING THEY PLAY A SIGNIFICANT ROLE IN ALTERNATIVE SPLICING IN BRAIN REWARD TISSUE. 2017 13 784 27 CELL-SPECIFIC EXON METHYLATION AND CTCF BINDING IN NEURONS REGULATE CALCIUM ION CHANNEL SPLICING AND FUNCTION. CELL-SPECIFIC ALTERNATIVE SPLICING MODULATES MYRIAD CELL FUNCTIONS AND IS DISRUPTED IN DISEASE. THE MECHANISMS GOVERNING ALTERNATIVE SPLICING ARE KNOWN FOR RELATIVELY FEW GENES AND TYPICALLY FOCUS ON RNA SPLICING FACTORS. IN SENSORY NEURONS, CELL-SPECIFIC ALTERNATIVE SPLICING OF THE PRESYNAPTIC CA(V) CHANNEL CACNA1B GENE MODULATES OPIOID SENSITIVITY. HOW THIS SPLICING IS REGULATED IS UNKNOWN. WE FIND THAT CELL AND EXON-SPECIFIC DNA HYPOMETHYLATION PERMITS CTCF BINDING, THE MASTER REGULATOR OF MAMMALIAN CHROMATIN STRUCTURE, WHICH, IN TURN, CONTROLS SPLICING IN A DRG-DERIVED CELL LINE. IN VIVO, HYPOMETHYLATION OF AN ALTERNATIVE EXON SPECIFICALLY IN NOCICEPTORS, LIKELY PERMITS CTCF BINDING AND EXPRESSION OF CA(V)2.2 CHANNEL ISOFORMS WITH INCREASED OPIOID SENSITIVITY IN MICE. FOLLOWING NERVE INJURY, EXON METHYLATION IS INCREASED, AND SPLICING IS DISRUPTED. OUR STUDIES DEFINE THE MOLECULAR MECHANISMS OF CELL-SPECIFIC ALTERNATIVE SPLICING OF A FUNCTIONALLY VALIDATED EXON IN NORMAL AND DISEASE STATES - AND REVEAL A POTENTIAL TARGET FOR THE TREATMENT OF CHRONIC PAIN. 2020 14 926 28 CHRONIC INFLAMMATION PATHWAY NF-KAPPAB COOPERATES WITH EPIGENETIC REPROGRAMMING TO DRIVE THE MALIGNANT PROGRESSION OF GLIOBLASTOMA. WITHOUT AN EFFECTIVE STRATEGY FOR TARGETED THERAPY, GLIOBLASTOMA IS STILL INCURABLE WITH A MEDIAN SURVIVAL OF ONLY 15 MONTHS. BOTH CHRONIC INFLAMMATION AND EPIGENETIC REPROGRAMMING ARE HALLMARKS OF CANCER. HOWEVER, THE MECHANISMS AND CONSEQUENCES OF THEIR COOPERATION IN GLIOBLASTOMA REMAIN UNKNOWN. HERE, WE DISCOVER THAT CHRONIC INFLAMMATION GOVERNS H3K27ME3 REPROGRAMMING IN GLIOBLASTOMA THROUGH THE CANONICAL NF-KAPPAB PATHWAY TO TARGET EZH2. BEING A CRUCIAL MEDIATOR OF CHRONIC INFLAMMATION, THE CANONICAL NF-KAPPAB SIGNALLING SPECIFICALLY DIRECTS THE EXPRESSION AND REDISTRIBUTION OF H3K27ME3 BUT NOT H3K4ME3, H3K9ME3 AND H3K36ME3. USING RNA-SEQ SCREENING TO FOCUS ON GENES ENCODING METHYLTRANSFERASES AND DEMETHYLASES OF HISTONE, WE IDENTIFY EZH2 AS A KEY METHYLTRANSFERASE TO CONTROL INFLAMMATION-TRIGGERED EPIGENETIC REPROGRAMMING IN GLIOMAGENESIS. MECHANISTICALLY, NF-KAPPAB SELECTIVELY DRIVES THE EXPRESSION OF EZH2 BY ACTIVATING ITS TRANSCRIPTION, CONSEQUENTLY RESULTING IN A GLOBAL CHANGE IN H3K27ME3 EXPRESSION AND DISTRIBUTION. FURTHERMORE, WE FIND THAT CO-ACTIVATION OF NF-KAPPAB AND EZH2 CONFERS THE POOREST CLINICAL OUTCOME, AND THAT THE RISK FOR GLIOBLASTOMA CAN BE ACCURATELY MOLECULARLY STRATIFIED BY NF-KAPPAB AND EZH2. IT IS NOTABLE THAT NF-KAPPAB CAN POTENTIALLY COOPERATE WITH EZH2 IN MORE THAN ONE WAY, AND MOST IMPORTANTLY, WE DEMONSTRATE A SYNERGISTIC EFFECT OF CANCER CELLS INDUCED BY COMBINATORY INHIBITION OF NF-KAPPAB AND EZH2, WHICH BOTH ARE FREQUENTLY OVER-ACTIVATED IN GLIOBLASTOMA. IN SUMMARY, WE UNCOVER A FUNCTIONAL COOPERATION BETWEEN CHRONIC INFLAMMATION AND EPIGENETIC REPROGRAMMING IN GLIOBLASTOMA, COMBINED TARGETING OF WHICH BY INHIBITORS GUARANTEED IN SAFETY AND AVAILABILITY FURNISHES A POTENT STRATEGY FOR EFFECTIVE TREATMENT OF THIS FATAL DISEASE. 2022 15 2380 36 EPIGENETIC REGULATION OF WNT SIGNALING IN CHRONIC LYMPHOCYTIC LEUKEMIA. CERTAIN WNT AND WNT NETWORK TARGET GENES ARE EXPRESSED AT HIGHER OR LOWER LEVELS IN CHRONIC LYMPHOCYTIC LEUKEMIA COMPARED WITH NORMAL B-CELLS. THIS INCLUDES UPREGULATION OF NUCLEAR COMPLEX GENES, AS WELL AS GENES FOR CYTOPLASMIC PROTEINS AND WNT LIGANDS AND THEIR COGNATE RECEPTORS. IN ADDITION, EPIGENETIC SILENCING OF SEVERAL NEGATIVE REGULATORS OF THE WNT PATHWAY HAVE BEEN IDENTIFIED. THE BALANCE BETWEEN EPIGENETIC DOWNREGULATION OF NEGATIVE EFFECTOR GENES AND INCREASED EXPRESSION OF POSITIVE EFFECTOR GENES DEMONSTRATE THAT THE EPIGENETIC DOWNREGULATION OF WNT ANTAGONISTS IS ONE MECHANISM, PERHAPS THE MAIN MECHANISM, THAT IS PERMISSIVE TO ACTIVE WNT SIGNALING IN CHRONIC LYMPHOCYTIC LEUKEMIA. MOREOVER, CONSTITUTIVE ACTIVATION OF THE WNT NETWORK AND TARGET GENES IS LIKELY TO IMPACT ON ADDITIONAL INTERACTING SIGNALING PATHWAYS. BASED ON PUBLISHED STUDIES, WE PROPOSE A MODEL OF WNT SIGNALING THAT INVOLVES MAINLY PERMISSIVE EXPRESSION, AND SOMETIMES OVEREXPRESSION, OF POSITIVE EFFECTORS AND DOWNREGULATION OF NEGATIVE REGULATORS IN THE NETWORK. IN THIS MODEL, DNA METHYLATION, HISTONE MODIFICATIONS AND ALTERED EXPRESSION OF MICRORNA MOLECULES INTERACT TO ALLOW CONTINUOUS WNT SIGNALING. 2010 16 857 37 CHROMATIN ARCHITECTURE REVEALS CELL TYPE-SPECIFIC TARGET GENES FOR KIDNEY DISEASE RISK VARIANTS. BACKGROUND: CELL TYPE-SPECIFIC TRANSCRIPTIONAL PROGRAMMING RESULTS FROM THE COMBINATORIAL INTERPLAY BETWEEN THE REPERTOIRE OF ACTIVE REGULATORY ELEMENTS. DISEASE-ASSOCIATED VARIANTS DISRUPT SUCH PROGRAMMING, LEADING TO ALTERED EXPRESSION OF DOWNSTREAM REGULATED GENES AND THE ONSET OF PATHOLOGICAL STATES. HOWEVER, DUE TO THE NON-LINEAR REGULATORY PROPERTIES OF NON-CODING ELEMENTS SUCH AS ENHANCERS, WHICH CAN ACTIVATE TRANSCRIPTION AT LONG DISTANCES AND IN A NON-DIRECTIONAL WAY, THE IDENTIFICATION OF CAUSAL VARIANTS AND THEIR TARGET GENES REMAINS CHALLENGING. HERE, WE PROVIDE A MULTI-OMICS ANALYSIS TO IDENTIFY REGULATORY ELEMENTS ASSOCIATED WITH FUNCTIONAL KIDNEY DISEASE VARIANTS, AND DOWNSTREAM REGULATED GENES. RESULTS: IN ORDER TO UNDERSTAND THE GENETIC RISK OF KIDNEY DISEASES, WE GENERATED A COMPREHENSIVE DATASET OF THE CHROMATIN LANDSCAPE OF HUMAN KIDNEY TUBULE CELLS, INCLUDING TRANSCRIPTION-CENTERED 3D CHROMATIN ORGANIZATION, HISTONE MODIFICATIONS DISTRIBUTION AND TRANSCRIPTOME WITH HICHIP, CHIP-SEQ AND RNA-SEQ. WE IDENTIFIED GENOME-WIDE FUNCTIONAL ELEMENTS AND THOUSANDS OF INTERACTIONS BETWEEN THE DISTAL ELEMENTS AND TARGET GENES. THE RESULTS REVEALED THAT RISK VARIANTS FOR RENAL TUMOR AND CHRONIC KIDNEY DISEASE WERE ENRICHED IN KIDNEY TUBULE CELLS. WE FURTHER PINPOINTED THE TARGET GENES FOR THE VARIANTS AND VALIDATED TWO TARGET GENES BY CRISPR/CAS9 GENOME EDITING TECHNIQUES IN ZEBRAFISH, DEMONSTRATING THAT SLC34A1 AND MTX1 WERE INDISPENSABLE GENES TO MAINTAIN KIDNEY FUNCTION. CONCLUSIONS: OUR RESULTS PROVIDE A VALUABLE MULTI-OMICS RESOURCE ON THE CHROMATIN LANDSCAPE OF HUMAN KIDNEY TUBULE CELLS AND ESTABLISH A BIOINFORMATIC PIPELINE IN DISSECTING FUNCTIONS OF KIDNEY DISEASE-ASSOCIATED VARIANTS BASED ON CELL TYPE-SPECIFIC EPIGENOME. 2021 17 925 31 CHRONIC INFLAMMATION INDUCES A NOVEL EPIGENETIC PROGRAM THAT IS CONSERVED IN INTESTINAL ADENOMAS AND IN COLORECTAL CANCER. CHRONIC INFLAMMATION REPRESENTS A MAJOR RISK FACTOR FOR TUMOR FORMATION, BUT THE UNDERLYING MECHANISMS HAVE REMAINED LARGELY UNKNOWN. EPIGENETIC MECHANISMS CAN RECORD THE EFFECTS OF ENVIRONMENTAL CHALLENGES ON THE GENOME LEVEL AND COULD THEREFORE PLAY AN IMPORTANT ROLE IN THE PATHOGENESIS OF INFLAMMATION-ASSOCIATED TUMORS. USING SINGLE-BASE METHYLATION MAPS AND TRANSCRIPTOME ANALYSES OF A COLITIS-INDUCED MOUSE COLON CANCER MODEL, WE IDENTIFIED A NOVEL EPIGENETIC PROGRAM THAT IS CHARACTERIZED BY HYPERMETHYLATION OF DNA METHYLATION VALLEYS THAT ARE CHARACTERIZED BY LOW CPG DENSITY AND ACTIVE CHROMATIN MARKS. THIS PROGRAM IS CONSERVED AND FUNCTIONAL IN MOUSE INTESTINAL ADENOMAS AND RESULTS IN SILENCING OF ACTIVE INTESTINAL GENES THAT ARE INVOLVED IN GASTROINTESTINAL HOMEOSTASIS AND INJURY RESPONSE. FURTHER ANALYSES REVEAL THAT THE PROGRAM REPRESENTS A PROMINENT FEATURE OF HUMAN COLORECTAL CANCER AND CAN BE USED TO CORRECTLY CLASSIFY COLORECTAL CANCER SAMPLES WITH HIGH ACCURACY. TOGETHER, OUR RESULTS SHOW THAT INFLAMMATORY SIGNALS ESTABLISH A NOVEL EPIGENETIC PROGRAM THAT SILENCES A SPECIFIC SET OF GENES THAT CONTRIBUTE TO INFLAMMATION-INDUCED CELLULAR TRANSFORMATION. 2015 18 329 31 ALPHA-OXOGLUTARATE INHIBITS THE PROLIFERATION OF IMMORTALIZED NORMAL BLADDER EPITHELIAL CELLS VIA AN EPIGENETIC SWITCH INVOLVING ARID1A. INTERSTITIAL CYSTITIS (IC) IS A CHRONIC URINARY TRACT DISEASE THAT IS CHARACTERIZED BY UNPLEASANT SENSATIONS, SUCH AS PERSISTENT PELVIC PAIN, IN THE ABSENCE OF INFECTION OR OTHER IDENTIFIABLE CAUSES. WE PREVIOUSLY PERFORMED COMPREHENSIVE METABOLOMICS PROFILING OF URINE SAMPLES FROM IC PATIENTS USING NUCLEAR MAGNETIC RESONANCE AND GAS-CHROMATOGRAPHY/MASS SPECTROMETRY AND FOUND THAT URINARY ALPHA-OXOGLUTARATE (ALPHA-OG), WAS SIGNIFICANTLY ELEVATED. ALPHA-OG, A TRICARBOXYLIC ACID (TCA) CYCLE INTERMEDIATE, REPORTEDLY FUNCTIONS TO SUPPRESS THE PROLIFERATION OF IMMORTALIZED NORMAL HUMAN BLADDER EPITHELIAL CELLS. HERE, WE IDENTIFIED AT-RICH INTERACTIVE DOMAIN 1 A (ARID1A), A KEY CHROMATIN REMODELER, AS BEING HYPOMETHYLATED AND UPREGULATED BY ALPHA-OG TREATMENT. THIS WAS DONE THROUGH EPIC DNA METHYLATION PROFILING AND SUBSEQUENT BIOCHEMICAL APPROACHES, INCLUDING QUANTITATIVE RT-PCR AND WESTERN BLOT ANALYSES. FURTHERMORE, WE FOUND THAT ALPHA-OG ALMOST COMPLETELY SUPPRESSES TEN-ELEVEN TRANSLOCATION (TET) ACTIVITY, BUT DOES NOT AFFECT DNA METHYLTRANSFERASE (DNMT) ACTIVITY. ALTOGETHER, OUR STUDIES REVEAL THE POTENTIAL ROLE OF ALPHA-OG IN EPIGENETIC REMODELING THROUGH ITS EFFECTS ON ARID1A AND TET EXPRESSION IN THE BLADDER. THIS MAY PROVIDE A NEW POSSIBLE THERAPEUTIC STRATEGY IN TREATING IC. 2018 19 3362 37 HISTONE LYSINE DEMETHYLASE KDM5B MAINTAINS CHRONIC MYELOID LEUKEMIA VIA MULTIPLE EPIGENETIC ACTIONS. THE HISTONE LYSINE DEMETHYLASE KDM5 FAMILY IS IMPLICATED IN NORMAL DEVELOPMENT AND STEM CELL MAINTENANCE BY EPIGENETIC MODULATION OF HISTONE METHYLATION STATUS. DEREGULATION OF THE KDM5 FAMILY HAS BEEN REPORTED IN VARIOUS TYPES OF CANCERS, INCLUDING HEMATOLOGICAL MALIGNANCIES. HOWEVER, THEIR TRANSCRIPTIONAL REGULATORY ROLES IN THE CONTEXT OF LEUKEMIA REMAIN UNCLEAR. HERE, WE FIND THAT KDM5B IS STRONGLY EXPRESSED IN NORMAL CD34(+) HEMATOPOIETIC STEM/PROGENITOR CELLS AND CHRONIC MYELOID LEUKEMIA (CML) CELLS. KNOCKDOWN OF KDM5B IN K562 CML CELLS REDUCED LEUKEMIA COLONY-FORMING POTENTIAL. TRANSCRIPTOME PROFILING OF KDM5B KNOCKDOWN K562 CELLS REVEALED THE DEREGULATION OF GENES INVOLVED IN MYELOID DIFFERENTIATION AND TOLL-LIKE RECEPTOR SIGNALING. THROUGH THE INTEGRATION OF TRANSCRIPTOME AND CHIP-SEQ PROFILING DATA, WE SHOW THAT KDM5B IS ENRICHED AT THE BINDING SITES OF THE GATA AND AP-1 TRANSCRIPTION FACTOR FAMILIES, SUGGESTING THEIR COLLABORATIONS IN THE REGULATION OF TRANSCRIPTION. EVEN THOUGH THE BINDING OF KDM5B SUBSTANTIALLY OVERLAPPED WITH H3K4ME1 OR H3K4ME3 MARK AT GENE PROMOTERS, ONLY A SMALL SUBSET OF THE KDM5B TARGETS SHOWED DIFFERENTIAL EXPRESSION IN ASSOCIATION WITH THE HISTONE DEMETHYLATION ACTIVITY. BY CHARACTERIZING THE INTERACTING PROTEINS IN K562 CELLS, WE DISCOVERED THAT KDM5B RECRUITS PROTEIN COMPLEXES INVOLVED IN THE MRNA PROCESSING MACHINERY, IMPLYING AN ALTERNATIVE EPIGENETIC ACTION MEDIATED BY KDM5B IN GENE REGULATION. OUR STUDY HIGHLIGHTS THE ONCOGENIC FUNCTIONS OF KDM5B IN CML CELLS AND SUGGESTS THAT KDM5B IS VITAL TO THE TRANSCRIPTIONAL REGULATION VIA MULTIPLE EPIGENETIC MECHANISMS. 2020 20 6074 43 THE DYNAMIC CHROMATIN ARCHITECTURE OF THE REGENERATING LIVER. BACKGROUND & AIMS: THE ADULT LIVER IS THE MAIN DETOXIFICATION ORGAN AND ROUTINELY IS EXPOSED TO ENVIRONMENTAL INSULTS BUT RETAINS THE ABILITY TO RESTORE ITS MASS AND FUNCTION UPON TISSUE DAMAGE. HOWEVER, EXTENSIVE INJURY CAN LEAD TO LIVER FAILURE, AND CHRONIC INJURY CAUSES FIBROSIS, CIRRHOSIS, AND HEPATOCELLULAR CARCINOMA. CURRENTLY, THE TRANSCRIPTIONAL REGULATION OF ORGAN REPAIR IN THE ADULT LIVER IS INCOMPLETELY UNDERSTOOD. METHODS: WE ISOLATED NUCLEI FROM QUIESCENT AS WELL AS REPOPULATING HEPATOCYTES IN A MOUSE MODEL OF HEREDITARY TYROSINEMIA, WHICH RECAPITULATES THE INJURY AND REPOPULATION SEEN IN TOXIC LIVER INJURY IN HUMAN BEINGS. WE THEN PERFORMED THE ASSAY FOR TRANSPOSASE ACCESSIBLE CHROMATIN WITH HIGH-THROUGHPUT SEQUENCING SPECIFICALLY IN REPOPULATING HEPATOCYTES TO IDENTIFY DIFFERENTIALLY ACCESSIBLE CHROMATIN REGIONS AND NUCLEOSOME POSITIONING. IN ADDITION, WE USED MOTIF ANALYSIS TO PREDICT DIFFERENTIAL TRANSCRIPTION FACTOR OCCUPANCY AND VALIDATED THE IN SILICO RESULTS WITH CHROMATIN IMMUNOPRECIPITATION FOLLOWED BY SEQUENCING FOR HEPATOCYTE NUCLEAR FACTOR 4ALPHA (HNF4ALPHA) AND CCCTC-BINDING FACTOR (CTCF). RESULTS: CHROMATIN ACCESSIBILITY IN REPOPULATING HEPATOCYTES WAS INCREASED IN THE REGULATORY REGIONS OF GENES PROMOTING PROLIFERATION AND DECREASED IN THE REGULATORY REGIONS OF GENES INVOLVED IN METABOLISM. THE EPIGENETIC CHANGES AT PROMOTERS AND LIVER ENHANCERS CORRESPOND WITH THE REGULATION OF GENE EXPRESSION, WITH ENHANCERS OF MANY LIVER FUNCTION GENES SHOWING A LESS ACCESSIBLE STATE DURING THE REGENERATIVE PROCESS. MOREOVER, INCREASED CTCF OCCUPANCY AT PROMOTERS AND DECREASED HNF4ALPHA BINDING AT ENHANCERS IMPLICATE THESE FACTORS AS KEY DRIVERS OF THE TRANSCRIPTOMIC CHANGES IN REPLICATING HEPATOCYTES THAT ENABLE LIVER REPOPULATION. CONCLUSIONS: OUR ANALYSIS OF HEPATOCYTE-SPECIFIC EPIGENOMIC CHANGES DURING LIVER REPOPULATION IDENTIFIED CTCF AND HNF4ALPHA AS KEY REGULATORS OF HEPATOCYTE PROLIFERATION AND REGULATION OF METABOLIC PROGRAMS. THUS, LIVER REPOPULATION IN THE SETTING OF TOXIC INJURY MAKES USE OF BOTH GENERAL TRANSCRIPTION FACTORS (CTCF) FOR PROMOTER ACTIVATION, AND REDUCED BINDING BY A HEPATOCYTE-ENRICHED FACTOR (HNF4ALPHA) TO TEMPORARILY LIMIT ENHANCER ACTIVITY. ALL SEQUENCING DATA IN THIS STUDY WERE DEPOSITED TO THE GENE EXPRESSION OMNIBUS DATABASE AND CAN BE DOWNLOADED WITH ACCESSION NUMBER GSE109466. 2020