1 3176 196 H3.3 BARCODING OF NUCLEUS ACCUMBENS TRANSCRIPTIONAL ACTIVITY IDENTIFIES NOVEL MOLECULAR CASCADES ASSOCIATED WITH COCAINE SELF-ADMINISTRATION IN MICE. ALTHOUGH NUMEROUS EPIGENETIC MODIFICATIONS HAVE BEEN ASSOCIATED WITH ADDICTION, LITTLE WORK HAS EXPLORED THE TURNOVER OF HISTONE VARIANTS. UNIQUELY, THE H3.3 VARIANT INCORPORATES STABLY AND PREFERENTIALLY INTO CHROMATIN INDEPENDENTLY OF DNA REPLICATION AT ACTIVE SITES OF TRANSCRIPTION AND TRANSCRIPTION FACTOR BINDING. THUS, GENOMIC REGIONS ASSOCIATED WITH H3.3-CONTAINING NUCLEOSOMES ARE PARTICULARLY LIKELY TO BE INVOLVED IN PLASTICITY, SUCH AS FOLLOWING REPEATED COCAINE EXPOSURE. A RECENTLY DEVELOPED MOUSE LINE EXPRESSING A NEURON-SPECIFIC HEMAGGLUTININ (HA)-TAGGED H3.3 PROTEIN WAS USED TO TRACK TRANSCRIPTIONALLY ACTIVE SITES CUMULATIVELY ACROSS 19 D OF COCAINE SELF-ADMINISTRATION. RNA-SEQ AND H3.3-HA CHIP-SEQ ANALYSES WERE PERFORMED ON NACC TISSUE COLLECTED FOLLOWING COCAINE OR FOOD SELF-ADMINISTRATION IN MALE MICE. RNA SEQUENCING REVEALED FIVE GENES UPREGULATED IN COCAINE RELATIVE TO FOOD SELF-ADMINISTERING MICE: FOSB, NPAS4, VGF, NPTX2, AND PMEPA1, WHICH REFLECT KNOWN AND NOVEL COCAINE PLASTICITY-ASSOCIATED GENES. SUBSEQUENT CHIP-SEQ ANALYSIS CONFIRMED INCREASED H3.3 AGGREGATION AT FOUR OF THESE FIVE LOCI, THUS VALIDATING H3.3 INSERTION AS A MARKER OF ENHANCED COCAINE-INDUCED TRANSCRIPTION. FURTHER MOTIF RECOGNITION ANALYSIS OF THE CHIP-SEQ DATA SHOWED THAT COCAINE-ASSOCIATED DIFFERENTIAL H3.3 ACCUMULATION CORRELATED WITH THE PRESENCE OF SEVERAL TRANSCRIPTION FACTOR BINDING MOTIFS, INCLUDING RBPJ1, EGR1, AND SOX4, SUGGESTING THAT THESE ARE POTENTIALLY IMPORTANT REGULATORS OF MOLECULAR CASCADES ASSOCIATED WITH COCAINE-INDUCED NEURONAL PLASTICITY. ADDITIONAL ONTOLOGICAL ANALYSIS REVEALED DIFFERENTIAL H3.3 ACCUMULATION MAINLY NEAR GENES INVOLVED IN NEURONAL DIFFERENTIATION AND DENDRITE FORMATION. THESE RESULTS ESTABLISH THE H3.3-HA TRANSGENIC MOUSE LINE AS A COMPELLING MOLECULAR BARCODING TOOL TO IDENTIFY THE CUMULATIVE EFFECTS OF LONG-TERM ENVIRONMENTAL PERTURBATIONS, SUCH AS EXPOSURE TO DRUGS OF ABUSE.SIGNIFICANCE STATEMENT HISTONE H3.3 IS A CORE HISTONE VARIANT THAT IS STABLY INCORPORATED AT ACTIVE SITES OF TRANSCRIPTION. WE USED A TAGGED VERSION OF H3.3 EXPRESSED EXCLUSIVELY IN NEURONS TO DELINEATE ACTIVE TRANSCRIPTION SITES FOLLOWING EXTENDED COCAINE SELF-ADMINISTRATION IN MICE. THIS APPROACH REVEALED THE CUMULATIVE LIST OF GENES EXPRESSED IN RESPONSE TO COCAINE TAKING OVER THE COURSE OF SEVERAL WEEKS. WE COMBINED THIS TECHNIQUE WITH RNA SEQUENCING OF TISSUE COLLECTED FROM THE SAME ANIMALS 24 H AFTER THE LAST COCAINE EXPOSURE. COMPARING THESE DATASETS PROVIDED A FULL PICTURE OF GENES THAT RESPOND TO CHRONIC COCAINE EXPOSURE IN NACC NEURONS. THESE STUDIES REVEALED NOVEL TRANSCRIPTION FACTORS THAT ARE LIKELY INVOLVED IN COCAINE-INDUCED PLASTICITY AND ADDICTION-LIKE BEHAVIORS. 2019 2 883 66 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 3 2442 39 EPIGENETIC STABILITY IN THE ADULT MOUSE CORTEX UNDER CONDITIONS OF PHARMACOLOGICALLY INDUCED HISTONE ACETYLATION. HISTONE ACETYLATION IS CONSIDERED A MAJOR EPIGENETIC PROCESS THAT AFFECTS BRAIN DEVELOPMENT AND SYNAPTIC PLASTICITY, AS WELL AS LEARNING AND MEMORY. THE TRANSCRIPTIONAL EFFECTORS AND MORPHOLOGICAL CHANGES RESPONSIBLE FOR PLASTICITY AS A RESULT OF LONG-TERM MODIFICATIONS TO HISTONE ACETYLATION ARE NOT FULLY UNDERSTOOD. TO THIS END, WE PHARMACOLOGICALLY INHIBITED HISTONE DEACETYLATION USING TRICHOSTATIN A IN ADULT (6-MONTH-OLD) MICE AND FOUND SIGNIFICANT INCREASES IN THE LEVELS OF THE ACETYLATED HISTONE MARKS H3LYS9, H3LYS14 AND H4LYS12. HIGH-RESOLUTION TRANSCRIPTOME ANALYSIS OF DIVERSE BRAIN REGIONS UNCOVERED FEW DIFFERENCES IN GENE EXPRESSION BETWEEN TREATED AND CONTROL ANIMALS, NONE OF WHICH WERE PLASTICITY RELATED. INSTEAD, AFTER INCREASED HISTONE ACETYLATION, WE DETECTED A LARGE NUMBER OF NOVEL TRANSCRIPTIONALLY ACTIVE REGIONS, WHICH CORRESPOND TO LONG NON-CODING RNAS (LNCRNAS). WE ALSO SURPRISINGLY FOUND NO SIGNIFICANT CHANGES IN DENDRITIC SPINE PLASTICITY IN LAYERS 1 AND 2/3 OF THE VISUAL CORTEX USING LONG-TERM IN VIVO TWO-PHOTON IMAGING. OUR RESULTS INDICATE THAT CHRONIC PHARMACOLOGICALLY INDUCED HISTONE ACETYLATION CAN BE DECOUPLED FROM GENE EXPRESSION AND INSTEAD, MAY POTENTIALLY EXERT A POST-TRANSCRIPTIONAL EFFECT THROUGH THE DIFFERENTIAL PRODUCTION OF LNCRNAS. 2016 4 4236 37 METHYLATION OF THE TYROSINE HYDROXYLASE GENE IS DYSREGULATED BY COCAINE DEPENDENCE IN THE HUMAN STRIATUM. COCAINE DEPENDENCE IS A CHRONIC, RELAPSING DISORDER CAUSED BY LASTING CHANGES IN THE BRAIN. ANIMAL STUDIES HAVE IDENTIFIED COCAINE-RELATED ALTERATIONS IN STRIATAL DNA METHYLATION; HOWEVER, IT IS UNCLEAR HOW METHYLATION IS RELATED TO COCAINE DEPENDENCE IN HUMANS. WE GENERATED METHYLOMIC PROFILES OF THE NUCLEUS ACCUMBENS USING HUMAN POSTMORTEM BRAINS FROM A COHORT OF INDIVIDUALS WITH COCAINE DEPENDENCE AND HEALTHY CONTROLS (N = 25 PER GROUP). WE FOUND HYPERMETHYLATION IN A CLUSTER OF CPGS WITHIN THE GENE BODY OF TYROSINE HYDROXYLASE (TH), CONTAINING A PUTATIVE BINDING SITE FOR THE EARLY GROWTH RESPONSE 1 (EGR1) TRANSCRIPTION FACTOR, WHICH IS HYPERMETHYLATED IN THE CAUDATE NUCLEUS OF COCAINE-DEPENDENT INDIVIDUALS. WE REPLICATED THIS FINDING AND FOUND IT TO BE SPECIFIC TO STRIATAL NEURONAL NUCLEI. FURTHERMORE, THIS LOCUS DEMONSTRATES ENHANCER ACTIVITY WHICH IS ATTENUATED BY METHYLATION AND ENHANCED BY EGR1 OVEREXPRESSION. THESE RESULTS SUGGEST THAT COCAINE DEPENDENCE ALTERS THE EPIGENETIC REGULATION OF DOPAMINERGIC SIGNALING GENES. 2021 5 1089 40 COCAINE-RELATED DNA METHYLATION IN CAUDATE NEURONS ALTERS 3D CHROMATIN STRUCTURE OF THE IRXA GENE CLUSTER. EPIGENETIC MECHANISMS, LIKE THOSE INVOLVING DNA METHYLATION, ARE THOUGHT TO MEDIATE THE RELATIONSHIP BETWEEN CHRONIC COCAINE DEPENDENCE AND MOLECULAR CHANGES IN ADDICTION-RELATED NEUROCIRCUITRY, BUT HAVE BEEN UNDERSTUDIED IN HUMAN BRAIN. WE INITIALLY USED REDUCED REPRESENTATION BISULFITE SEQUENCING (RRBS) TO GENERATE A METHYLOME-WIDE PROFILE OF COCAINE DEPENDENCE IN HUMAN POST-MORTEM CAUDATE TISSUE. WE FOCUSED ON THE IROQUOIS HOMEOBOX A (IRXA) GENE CLUSTER, WHERE HYPOMETHYLATION IN EXON 3 OF IRX2 IN NEURONAL NUCLEI WAS ASSOCIATED WITH COCAINE DEPENDENCE. WE REPLICATED THIS FINDING IN AN INDEPENDENT COHORT AND FOUND SIMILAR RESULTS IN THE DORSAL STRIATUM FROM COCAINE SELF-ADMINISTERING MICE. USING EPIGENOME EDITING AND 3C ASSAYS, WE DEMONSTRATED A CAUSAL RELATIONSHIP BETWEEN METHYLATION WITHIN THE IRX2 GENE BODY, CTCF PROTEIN BINDING, THREE-DIMENSIONAL (3D) CHROMATIN INTERACTION, AND GENE EXPRESSION. TOGETHER, THESE FINDINGS SUGGEST THAT COCAINE-RELATED HYPOMETHYLATION OF IRX2 CONTRIBUTES TO THE DEVELOPMENT AND MAINTENANCE OF COCAINE DEPENDENCE THROUGH ALTERATIONS IN 3D CHROMATIN STRUCTURE IN THE CAUDATE NUCLEUS. 2021 6 5177 50 PREFRONTAL CORTEX EXPRESSION OF CHROMATIN MODIFIER GENES IN MALE WSP AND WSR MICE CHANGES ACROSS ETHANOL DEPENDENCE, WITHDRAWAL, AND ABSTINENCE. ALCOHOL-USE DISORDER (AUD) IS A RELAPSING DISORDER ASSOCIATED WITH EXCESSIVE ETHANOL CONSUMPTION. RECENT STUDIES SUPPORT THE INVOLVEMENT OF EPIGENETIC MECHANISMS IN THE DEVELOPMENT OF AUD. STUDIES CARRIED OUT SO FAR HAVE FOCUSED ON A FEW SPECIFIC EPIGENETIC MODIFICATIONS. THE GOAL OF THIS PROJECT WAS TO INVESTIGATE GENE EXPRESSION CHANGES OF EPIGENETIC REGULATORS THAT MEDIATE A BROAD ARRAY OF CHROMATIN MODIFICATIONS AFTER CHRONIC ALCOHOL EXPOSURE, CHRONIC ALCOHOL EXPOSURE FOLLOWED BY 8 H WITHDRAWAL, AND CHRONIC ALCOHOL EXPOSURE FOLLOWED BY 21 DAYS OF ABSTINENCE IN WITHDRAWAL-RESISTANT (WSR) AND WITHDRAWAL SEIZURE-PRONE (WSP) SELECTED MOUSE LINES. WE FOUND THAT CHRONIC VAPOR EXPOSURE TO HIGHLY INTOXICATING LEVELS OF ETHANOL ALTERS THE EXPRESSION OF SEVERAL CHROMATIN REMODELING GENES MEASURED BY QUANTITATIVE PCR ARRAY ANALYSES. THE IDENTIFIED EFFECTS WERE INDEPENDENT OF SELECTED LINES, WHICH, HOWEVER, DISPLAYED BASELINE DIFFERENCES IN EPIGENETIC GENE EXPRESSION. WE REPORTED DYSREGULATION IN THE EXPRESSION OF GENES INVOLVED IN HISTONE ACETYLATION, DEACETYLATION, LYSINE AND ARGININE METHYLATION AND UBIQUITINATIONHYLATION DURING CHRONIC ETHANOL EXPOSURE AND WITHDRAWAL, BUT NOT AFTER 21 DAYS OF ABSTINENCE. ETHANOL-INDUCED CHANGES ARE CONSISTENT WITH DECREASED HISTONE ACETYLATION AND WITH DECREASED DEPOSITION OF THE PERMISSIVE UBIQUITINATION MARK H2BK120UB, ASSOCIATED WITH REDUCED TRANSCRIPTION. ON THE OTHER HAND, ETHANOL-INDUCED CHANGES IN THE EXPRESSION OF GENES INVOLVED IN HISTONE LYSINE METHYLATION ARE CONSISTENT WITH INCREASED TRANSCRIPTION. THE NET RESULT OF THESE MODIFICATIONS ON GENE EXPRESSION IS LIKELY TO DEPEND ON THE COMBINATION OF THE SPECIFIC HISTONE TAIL MODIFICATIONS PRESENT AT A GIVEN TIME ON A GIVEN PROMOTER. SINCE ALCOHOL DOES NOT MODULATE GENE EXPRESSION UNIDIRECTIONALLY, IT IS NOT SURPRISING THAT ALCOHOL DOES NOT UNIDIRECTIONALLY ALTER CHROMATIN STRUCTURE TOWARD A CLOSED OR OPEN STATE, AS SUGGESTED BY THE RESULTS OF THIS STUDY. 2017 7 3141 45 GLOBAL GENE EXPRESSION AND CHROMATIN ACCESSIBILITY OF THE PERIPHERAL NERVOUS SYSTEM IN ANIMAL MODELS OF PERSISTENT PAIN. BACKGROUND: EFFORTS TO UNDERSTAND GENETIC VARIABILITY INVOLVED IN AN INDIVIDUAL'S SUSCEPTIBILITY TO CHRONIC PAIN SUPPORT A ROLE FOR UPSTREAM REGULATION BY EPIGENETIC MECHANISMS. METHODS: TO EXAMINE THE TRANSCRIPTOMIC AND EPIGENETIC BASIS OF CHRONIC PAIN THAT RESIDES IN THE PERIPHERAL NERVOUS SYSTEM, WE USED RNA-SEQ AND ATAC-SEQ OF THE RAT DORSAL ROOT GANGLION (DRG) TO IDENTIFY NOVEL MOLECULAR PATHWAYS ASSOCIATED WITH PAIN HYPERSENSITIVITY IN TWO WELL-STUDIED PERSISTENT PAIN MODELS INDUCED BY CHRONIC CONSTRICTION INJURY (CCI) OF THE SCIATIC NERVE AND INTRA-PLANTAR INJECTION OF COMPLETE FREUND'S ADJUVANT (CFA) IN RATS. RESULTS: OUR RNA-SEQ STUDIES IDENTIFY A VARIETY OF BIOLOGICAL PROCESS RELATED TO SYNAPSE ORGANIZATION, MEMBRANE POTENTIAL, TRANSMEMBRANE TRANSPORT, AND ION BINDING. INTERESTINGLY, GENES THAT ENCODE TRANSCRIPTIONAL REGULATORS WERE DISPROPORTIONATELY DOWNREGULATED IN BOTH MODELS. OUR ATAC-SEQ DATA PROVIDE A COMPREHENSIVE MAP OF CHROMATIN ACCESSIBILITY CHANGES IN THE DRG. A TOTAL OF 1123 REGIONS SHOWED CHANGES IN CHROMATIN ACCESSIBILITY IN ONE OR BOTH MODELS WHEN COMPARED TO THE NAIVE AND 31 SHARED DIFFERENTIALLY ACCESSIBLE REGIONS (DAR)S. FUNCTIONAL ANNOTATION OF THE DARS IDENTIFIED DISPARATE MOLECULAR FUNCTIONS ENRICHED FOR EACH PAIN MODEL WHICH SUGGESTS THAT CHROMATIN STRUCTURE MAY BE ALTERED DIFFERENTLY FOLLOWING SCIATIC NERVE INJURY AND HIND PAW INFLAMMATION. MOTIF ANALYSIS IDENTIFIED 17 DNA SEQUENCES KNOWN TO BIND TRANSCRIPTION FACTORS IN THE CCI DARS AND 33 IN THE CFA DARS. TWO MOTIFS WERE SIGNIFICANTLY ENRICHED IN BOTH MODELS. CONCLUSIONS: OUR IMPROVED UNDERSTANDING OF THE CHANGES IN CHROMATIN ACCESSIBILITY THAT OCCUR IN CHRONIC PAIN STATES MAY IDENTIFY REGULATORY GENOMIC ELEMENTS THAT PLAY ESSENTIAL ROLES IN MODULATING GENE EXPRESSION IN THE DRG. 2021 8 226 41 ACUTE TRANSCRIPTOMIC AND EPIGENETIC ALTERATIONS AT T12 AFTER RAT T10 SPINAL CORD CONTUSIVE INJURY. SPINAL CORD INJURY IS A SEVERELY DEBILITATING CONDITION AFFECTING A SIGNIFICANT POPULATION IN THE USA. SPINAL CORD INJURY PATIENTS OFTEN HAVE INCREASED RISK OF DEVELOPING PERSISTENT NEUROPATHIC PAIN AND OTHER NEURODEGENERATIVE CONDITIONS BEYOND THE PRIMARY LESION CENTER LATER IN THEIR LIFE. THE MOLECULAR MECHANISM CONFERRING TO THE "LATENT" DAMAGES AT DISTAL TISSUES, HOWEVER, REMAINS ELUSIVE. HERE, WE STUDIED MOLECULAR CHANGES CONFERRING ABNORMAL FUNCTIONALITY AT DISTAL SPINAL CORD (T12) BEYOND THE LESION CENTER (T10) BY COMBINING NEXT-GENERATION SEQUENCING (RNA- AND BISULFITE SEQUENCING), SUPER-RESOLUTION MICROSCOPY, AND IMMUNOFLUORESCENCE STAINING AT 7 DAYS POST INJURY. WE OBSERVED SIGNIFICANT TRANSCRIPTOMIC CHANGES PRIMARILY ENRICHED IN NEUROINFLAMMATION AND SYNAPTOGENESIS ASSOCIATED PATHWAYS. TRANSCRIPTION FACTORS (TFS) THAT REGULATE NEUROGENESIS AND NEURON PLASTICITY, INCLUDING EGR1, KLF4, AND MYC, ARE SIGNIFICANTLY UPREGULATED. ALONG WITH GLOBAL CHANGES IN CHROMATIN ARRANGEMENTS AND DNA METHYLATION, INCLUDING 5-METHYLCYTOSINE (5MC) AND 5-HYDROXYMETHYLCYTOSINE (5HMC), BISULFITE SEQUENCING FURTHER REVEALS THE INVOLVEMENT OF DNA METHYLATION CHANGES IN REGULATING CYTOKINE, GROWTH FACTOR, AND ION CHANNEL EXPRESSION. COLLECTIVELY, OUR RESULTS PAVE THE WAY TOWARDS UNDERSTANDING TRANSCRIPTOMIC AND EPIGENOMIC MECHANISM IN CONFERRING LONG-TERM DISEASE RISKS AT DISTAL TISSUES AWAY FROM THE PRIMARY LESION CENTER AND SHED LIGHT ON POTENTIAL MOLECULAR TARGETS THAT GOVERN THE REGULATORY MECHANISM AT DISTAL SPINAL CORD TISSUES. 2023 9 1731 50 DYSREGULATION OF THE HISTONE DEMETHYLASE KDM6B IN ALCOHOL DEPENDENCE IS ASSOCIATED WITH EPIGENETIC REGULATION OF INFLAMMATORY SIGNALING PATHWAYS. EPIGENETIC ENZYMES OVERSEE LONG-TERM CHANGES IN GENE EXPRESSION BY INTEGRATING GENETIC AND ENVIRONMENTAL CUES. WHILE THERE ARE HUNDREDS OF ENZYMES THAT CONTROL HISTONE AND DNA MODIFICATIONS, THEIR POTENTIAL ROLES IN SUBSTANCE ABUSE AND ALCOHOL DEPENDENCE REMAIN UNDEREXPLORED. A FEW RECENT STUDIES HAVE SUGGESTED THAT EPIGENETIC PROCESSES COULD UNDERLIE TRANSCRIPTOMIC AND BEHAVIORAL HALLMARKS OF ALCOHOL ADDICTION. IN THE PRESENT STUDY, WE SOUGHT TO IDENTIFY EPIGENETIC ENZYMES IN THE BRAIN THAT ARE DYSREGULATED DURING PROTRACTED ABSTINENCE AS A CONSEQUENCE OF CHRONIC AND INTERMITTENT ALCOHOL EXPOSURE. THROUGH QUANTITATIVE MRNA EXPRESSION ANALYSIS OF OVER 100 EPIGENETIC ENZYMES, WE IDENTIFIED 11 THAT ARE SIGNIFICANTLY ALTERED IN ALCOHOL-DEPENDENT RATS COMPARED WITH CONTROLS. FOLLOW-UP STUDIES OF ONE OF THESE ENZYMES, THE HISTONE DEMETHYLASE KDM6B, SHOWED THAT THIS ENZYME EXHIBITS REGION-SPECIFIC DYSREGULATION IN THE PREFRONTAL CORTEX AND NUCLEUS ACCUMBENS OF ALCOHOL-DEPENDENT RATS. KDM6B WAS ALSO UPREGULATED IN THE HUMAN ALCOHOLIC BRAIN. UPREGULATION OF KDM6B PROTEIN IN ALCOHOL-DEPENDENT RATS WAS ACCOMPANIED BY A DECREASE OF TRIMETHYLATION LEVELS AT HISTONE H3, LYSINE 27 (H3K27ME3), CONSISTENT WITH THE KNOWN DEMETHYLASE SPECIFICITY OF KDM6B. SUBSEQUENT EPIGENETIC (CHROMATIN IMMUNOPRECIPITATION [CHIP]-SEQUENCING) ANALYSIS SHOWED THAT ALCOHOL-INDUCED CHANGES IN H3K27ME3 WERE SIGNIFICANTLY ENRICHED AT GENES IN THE IL-6 SIGNALING PATHWAY, CONSISTENT WITH THE WELL-CHARACTERIZED ROLE OF KDM6B IN MODULATION OF INFLAMMATORY RESPONSES. KNOCKDOWN OF KDM6B IN CULTURED MICROGLIAL CELLS DIMINISHED IL-6 INDUCTION IN RESPONSE TO AN INFLAMMATORY STIMULUS. OUR FINDINGS IMPLICATE A NOVEL KDM6B-MEDIATED EPIGENETIC SIGNALING PATHWAY INTEGRATED WITH INFLAMMATORY SIGNALING PATHWAYS THAT ARE KNOWN TO UNDERLIE THE DEVELOPMENT OF ALCOHOL ADDICTION. 2021 10 1186 45 COORDINATED DYNAMIC GENE EXPRESSION CHANGES IN THE CENTRAL NUCLEUS OF THE AMYGDALA DURING ALCOHOL WITHDRAWAL. BACKGROUND: CHRONIC ALCOHOL USE CAUSES WIDESPREAD CHANGES IN THE CELLULAR BIOLOGY OF THE AMYGDALA'S CENTRAL NUCLEUS (CEA), A GABAERGIC CENTER THAT INTEGRATES AUTONOMIC PHYSIOLOGY WITH THE EMOTIONAL ASPECTS OF MOTIVATION AND LEARNING. WHILE ALCOHOL-INDUCED NEUROCHEMICAL CHANGES PLAY A ROLE IN DEPENDENCE AND DRINKING BEHAVIOR, LITTLE IS KNOWN ABOUT THE CEA'S DYNAMIC CHANGES DURING WITHDRAWAL, A PERIOD OF EMOTIONAL AND PHYSIOLOGIC DISTURBANCE. METHODS: WE USED A QRT-PCR PLATFORM TO MEASURE 139 TRANSCRIPTS IN 92 RAT CEA SAMPLES FROM CONTROL (N = 33), CHRONICALLY ALCOHOL EXPOSED (N = 26), AND WITHDRAWN RATS (T = 4, 8, 18, 32, AND 48 HOURS; N = 5, 10, 7, 6, 5). THIS FOCUSED TRANSCRIPT SET ALLOWED US TO IDENTIFY SIGNIFICANT DYNAMIC EXPRESSION PATTERNS DURING THE FIRST 48 HOURS OF WITHDRAWAL AND PROPOSE POTENTIAL REGULATORY MECHANISMS. RESULTS: CHRONIC ALCOHOL EXPOSURE CAUSES A LIMITED NUMBER OF SMALL MAGNITUDE EXPRESSION CHANGES. IN CONTRAST, WITHDRAWAL RESULTS IN A GREATER NUMBER OF LARGE CHANGES WITHIN 4 HOURS OF REMOVAL OF THE ALCOHOL DIET. SIXTY-FIVE OF THE 139 MEASURED TRANSCRIPTS (47%) SHOWED DIFFERENTIAL REGULATION DURING WITHDRAWAL. OVER THE 48-HOUR PERIOD, DYNAMIC CHANGES IN THE EXPRESSION OF GAMMA-AMINOBUTYRIC ACID TYPE A (GABA(A) ), IONOTROPIC GLUTAMATE AND NEUROPEPTIDE SYSTEM-RELATED G-PROTEIN-COUPLED RECEPTOR SUBUNITS, AND THE RAS/RAF SIGNALING PATHWAY WERE SEEN AS WELL AS DOWNSTREAM TRANSCRIPTION FACTORS (TFS) AND EPIGENETIC REGULATORS. FOUR TEMPORALLY CORRELATED GENE CLUSTERS WERE IDENTIFIED WITH SHARED FUNCTIONAL ROLES INCLUDING NMDA RECEPTORS, MAPKKK AND CHEMOKINE SIGNALING CASCADES, AND MEDIATORS OF LONG-TERM POTENTIATION, AMONG OTHERS. CLUSTER PROMOTER REGIONS SHARED OVERREPRESENTED BINDING SITES FOR MULTIPLE TFS INCLUDING CEBP, USF-1, SMAD3, AP-2, AND C-ETS, SUGGESTING A POTENTIAL REGULATORY ROLE. CONCLUSIONS: DURING ALCOHOL WITHDRAWAL, THE CEA EXPERIENCES RAPID CHANGES IN MRNA EXPRESSION OF THESE FUNCTIONALLY RELATED TRANSCRIPTS THAT WERE NOT PREDICTED BY MEASUREMENT DURING CHRONIC EXPOSURE. THIS STUDY PROVIDES NEW INSIGHT INTO DYNAMIC EXPRESSION CHANGES DURING ALCOHOL WITHDRAWAL AND SUGGESTS NOVEL REGULATORY RELATIONSHIPS THAT POTENTIALLY IMPACT THE ASPECTS OF EMOTIONAL MODULATION. 2013 11 6804 52 [EPIGENETIC REGULATION IN DEPRESSION]. RECENT RESEARCH HAS RAISED THE NOTION THAT EPIGENETIC MECHANISMS (E.G., DNA METHYLATION AND HISTONE MODIFICATIONS), WHICH EXERT LASTING CONTROL OVER GENE EXPRESSION WITHOUT ALTERING THE GENETIC CODE, COULD MEDIATE STABLE CHANGES IN BRAIN FUNCTION. HOWEVER, THE ROLE OF ENVIRONMENTAL FACTORS ALONG WITH GENETIC FACTORS IN THE EPIGENETIC REGULATION OF THE PATHOGENESIS OF DEPRESSION IS LARGELY UNKNOWN. TWO GENETICALLY DISTINCT MICE STRAINS, BALB/C (BALB) AND C57BL/6 (B6), EXHIBIT DIFFERENT BEHAVIORAL RESPONSES TO CHRONIC STRESS. WITH CHRONIC STRESS, BALB MICE SHOWED DEPRESSIVE-LIKE BEHAVIORS, BUT NOT B6 MICE, AND GLIAL CELL-DERIVED NEUROTROPHIC FACTOR (GDNF) EXPRESSION LEVEL WAS DECREASED IN THE VENTRAL STRIATUM OF BALB MICE BUT INCREASED IN B6 MICE. IN BALB MICE, DEPRESSIVE-LIKE BEHAVIORS AND DECREASED GDNF EXPRESSION WERE RECOVERED BY CHRONIC ANTIDEPRESSANT TREATMENT. THEREFORE, WE USED THESE TWO MICE STRAINS TO INVESTIGATE HOW THE EPIGENETIC STATUS OF THE GDNF GENE IN THE VENTRAL STRIATUM MODULATES STRESS VULNERABILITY. BOTH MICE STRAINS SHOWED INCREASED DNA METHYLATION LEVELS AND MECP2 RECRUITMENT IN THE GDNF PROMOTER REGION. HOWEVER, HISTONE H3 ACETYLATION LEVEL WAS DECREASED IN BALB MICE, BUT INCREASED IN B6 MICE. FURTHERMORE, BALB MICE SHOWED INCREASED HISTONE DEACETYLASE2 (HDAC2) EXPRESSION LEVEL AND RE-CHIP ASSAY REVEALED HDAC2-MECP2 COMPLEX IN BALB MICE. OUR RESULTS INDICATE THE CRUCIAL ROLE OF HISTONE MODIFICATION BY HDAC2 AND MECP2 COMPLEX FOR THE CONTROL OF GDNF EXPRESSION AND SUBSEQUENT BEHAVIORAL RESPONSES TO CHRONIC STRESS, IN OTHER WORDS, THE SUSCEPTIBILITY TO STRESS. IN ADDITION, WE INVESTIGATED THE EFFECT OF ANTIDEPRESSANTS ON THE EPIGENETIC REGULATION OF GDNF EXPRESSION. WE FOUND A REDUCED LEVEL OF HDAC4 RECRUITMENT AT THE GDNF PROMOTER REGION WITH ANTIDEPRESSANTS. THUS, OUR DATA SUGGEST THAT ANTIDEPRESSANTS INCREASE TRANSCRIPTIONAL ACTIVITY OF THE GDNF GENE THROUGH THE MODULATION OF HISTONE ACETYLATION BY HDAC4. FINALLY, WE EXAMINED THE EXPRESSIONS OF GDNF AND EPIGENETIC-RELATED MOLECULES MRNAS WITH MAJOR DEPRESSIVE AND BIPOLAR DISORDER PATIENTS BY USING QUANTITATIVE REAL-TIME PCR. WE FOUND THE ABERRANT EXPRESSION OF GDNF AND EPIGENETIC-RELATED GENES INCLUDING HDAC2 AND HDAC4 IN MOOD DISORDER PATIENTS. THUS, OUR DATA PROVIDE NOVEL INSIGHTS SUGGESTING THAT EPIGENETIC MECHANISMS OF GDNF EXPRESSION ARE INVOLVED IN THE PATHOGENESIS OR PATHOPHYSIOLOGY OF DEPRESSION. 2012 12 3328 55 HISTONE DEACETYLASE 5 MODULATES THE EFFECTS OF SOCIAL ADVERSITY IN EARLY LIFE ON COCAINE-INDUCED BEHAVIOR. PSYCHOSTIMULANTS INDUCE STABLE CHANGES IN NEURAL PLASTICITY AND BEHAVIOR IN A TRANSCRIPTION-DEPENDENT MANNER. FURTHER, STABLE CELLULAR CHANGES REQUIRE TRANSCRIPTION THAT IS REGULATED BY EPIGENETIC MECHANISMS THAT ALTER CHROMATIN STRUCTURE, SUCH AS HISTONE ACETYLATION. THIS MECHANISM IS TYPICALLY CATALYZED BY ENZYMES WITH HISTONE ACETYLTRANSFERASE OR HISTONE DEACETYLASE (HDAC) ACTIVITY. CLASS IIA HDACS ARE NOTABLE FOR THEIR HIGH EXPRESSION IN IMPORTANT REGIONS OF THE BRAIN REWARD CIRCUITRY AND THEIR NEURAL ACTIVITY-DEPENDENT SHUTTLING IN AND OUT OF THE CELL NUCLEUS. IN PARTICULAR, HDAC5 HAS AN IMPORTANT MODULATORY FUNCTION IN COCAINE-INDUCED BEHAVIORS AND SOCIAL DEFEAT STRESS-INDUCED EFFECTS. ALTHOUGH A MUTATION IN HDAC5 HAS BEEN SHOWN TO CAUSE HYPERSENSITIVE RESPONSES TO CHRONIC COCAINE USE WHETHER THIS RESPONSE WORSENS DURING CHRONIC EARLY LIFE STRESS HAS NOT BEEN EXAMINED YET. IN THIS STUDY, WE EXPOSED MOUSE PUPS TO TWO DIFFERENT EARLY LIFE STRESS PARADIGMS (SOCIAL ISOLATION, ESI, AND SOCIAL THREAT, EST) TO DETERMINE WHETHER THE HETEROZYGOUS NULL MUTATION IN HDAC5 (HDAC5+/-) MODERATED THE EFFECTS OF EXPOSURE TO STRESS IN EARLY LIFE ON ADULT COCAINE-INDUCED CONDITIONED PLACE PREFERENCE (CPP). NOTABLY, HDAC5+/- MICE THAT HAD BEEN EXPOSED TO ESI WERE MORE SUSCEPTIBLE TO DEVELOPING COCAINE-INDUCED CPP AND MORE RESISTANT TO EXTINGUISHING THIS BEHAVIOR. THE SAME EFFECT WAS NOT OBSERVED FOR HDAC5+/- MICE EXPERIENCING EST, SUGGESTING THAT ONLY ESI INDUCES BEHAVIORAL CHANGES BY ACTING PRECISELY THROUGH HDAC5-RELATED BIOLOGICAL PATHWAYS. FINALLY, AN ANALYSIS OF C-FOS EXPRESSION PERFORMED TO DISCOVER THE NEUROBIOLOGICAL SUBSTRATES THAT MEDIATED THIS PHENOTYPE, IDENTIFIED THE DORSOLATERAL STRIATUM AS AN IMPORTANT STRUCTURE THAT MEDIATES THE INTERACTION BETWEEN HDAC5 MUTATION AND ESI. OUR DATA DEMONSTRATE THAT DECREASED HDAC5 FUNCTION IS ABLE TO EXACERBATE THE LONG-TERM BEHAVIORAL EFFECTS OF ADVERSE REARING ENVIRONMENT IN MOUSE. 2017 13 2325 52 EPIGENETIC REGULATION OF HIPPOCAMPAL FOSB EXPRESSION CONTROLS BEHAVIORAL RESPONSES TO COCAINE. DRUG ADDICTION RESULTS IN PART FROM MALADAPTIVE LEARNING, INCLUDING THE FORMATION OF STRONG ASSOCIATIONS BETWEEN THE DRUG AND THE CIRCUMSTANCES OF CONSUMPTION. HOWEVER, DRUG-INDUCED CHANGES IN GENE EXPRESSION UNDERLYING THE SALIENCY OF THESE ASSOCIATIONS REMAIN UNDERSTUDIED. CONSOLIDATION OF EXPLICIT MEMORIES OCCURS WITHIN THE HIPPOCAMPUS, AND WE HAVE SHOWN THAT SPATIAL LEARNING INDUCES EXPRESSION OF THE TRANSCRIPTION FACTOR DELTAFOSB IN HIPPOCAMPUS AND THAT THIS INDUCTION IS CRITICAL FOR LEARNING. DRUGS OF ABUSE ALSO UPREGULATE DELTAFOSB IN HIPPOCAMPUS, BUT THE MECHANISM OF ITS INDUCTION BY COCAINE AND ITS ROLE IN HIPPOCAMPUS-DEPENDENT COCAINE RESPONSES IS UNKNOWN. WE INVESTIGATED DIFFERENCES IN MOUSE DORSAL AND VENTRAL HIPPOCAMPAL DELTAFOSB EXPRESSION IN RESPONSE TO CHRONIC COCAINE, BECAUSE THESE REGIONS APPEAR TO REGULATE DISTINCT COCAINE-RELATED BEHAVIORS. WE FOUND THAT COCAINE-MEDIATED INDUCTION OF DELTAFOSB WAS SUBREGION-SPECIFIC, AND THAT DELTAFOSB TRANSCRIPTIONAL ACTIVITY IN BOTH THE DORSAL AND VENTRAL HIPPOCAMPUS IS NECESSARY FOR COCAINE CONDITIONED PLACE PREFERENCE. FURTHER, WE CHARACTERIZE CHANGES IN HISTONE MODIFICATIONS AT THE FOSB PROMOTER IN HIPPOCAMPUS IN RESPONSE TO CHRONIC COCAINE AND FOUND THAT LOCUS-SPECIFIC EPIGENETIC MODIFICATION IS ESSENTIAL FOR FOSB INDUCTION AND MULTIPLE HIPPOCAMPUS-DEPENDENT BEHAVIORS, INCLUDING COCAINE PLACE PREFERENCE. COLLECTIVELY, THESE FINDINGS SUGGEST THAT EXPOSURE TO COCAINE INDUCES HISTONE MODIFICATION AT THE HIPPOCAMPAL FOSB GENE PROMOTER TO CAUSE DELTAFOSB INDUCTION CRITICAL FOR COCAINE-RELATED LEARNING.SIGNIFICANCE STATEMENT ALTHOUGH COCAINE ADDICTION IS DRIVEN IN PART BY THE FORMATION OF INDELIBLE ASSOCIATIONS BETWEEN THE DRUG AND THE ENVIRONMENT, PARAPHERNALIA, AND CIRCUMSTANCES OF USE, AND ALTHOUGH THIS TYPE OF ASSOCIATIVE LEARNING IS DEPENDENT UPON CHANGES IN GENE EXPRESSION IN A BRAIN REGION CALLED THE HIPPOCAMPUS, THE MECHANISMS BY WHICH COCAINE ALTERS HIPPOCAMPAL GENE EXPRESSION TO DRIVE FORMATION OF THESE ASSOCIATIONS IS POORLY UNDERSTOOD. HERE, WE DEMONSTRATE THAT CHRONIC COCAINE ENGAGES LOCUS-SPECIFIC CHANGES IN THE EPIGENETIC PROFILE OF THE FOSB GENE IN THE HIPPOCAMPUS, AND THAT THESE ALTERATIONS ARE REQUIRED FOR COCAINE-DEPENDENT GENE EXPRESSION AND COCAINE-ENVIRONMENT ASSOCIATIONS. THIS WORK PROVIDES NOVEL INSIGHT INTO ADDICTION ETIOLOGY AND POTENTIAL INROADS FOR THERAPEUTIC INTERVENTION IN COCAINE ADDICTION. 2019 14 6411 53 THE SITE SPECIFIC DEMETHYLATION IN THE 5'-REGULATORY AREA OF NMDA RECEPTOR 2B SUBUNIT GENE ASSOCIATED WITH CIE-INDUCED UP-REGULATION OF TRANSCRIPTION. BACKGROUND: THE NMDA RECEPTOR REPRESENTS A PARTICULARLY IMPORTANT SITE OF ETHANOL ACTION IN THE CNS. WE RECENTLY REPORTED THAT NMDA RECEPTOR 2B (NR2B) GENE EXPRESSION WAS PERSISTENTLY UP-REGULATED FOLLOWING CHRONIC INTERMITTENT ETHANOL (CIE) TREATMENT. INCREASING EVIDENCE THAT EPIGENETIC MECHANISMS ARE INVOLVED IN DYNAMIC AND LONG-LASTING REGULATION OF GENE EXPRESSION IN MULTIPLE NEUROADAPTIVE PROCESSES PROMPTED US TO INVESTIGATE THE ROLE OF DNA METHYLATION IN MEDIATING CIE-INDUCED UP-REGULATION OF NR2B GENE TRANSCRIPTION. TO DISSECT THE CHANGES OF DNA METHYLATION IN THE NR2B GENE, WE HAVE SCREENED A LARGE NUMBER OF CPG SITES WITHIN ITS 5'-REGULATORY AREA FOLLOWING CIE TREATMENT. METHODS: PRIMARY CORTICAL CULTURED NEURONS WERE SUBJECTED TO ETHANOL TREATMENT IN A CIE PARADIGM. BISULFITE CONVERSION FOLLOWED BY PYROSEQUENCING WAS USED FOR QUANTITATIVE MEASUREMENT AND ANALYSIS OF CPG METHYLATION STATUS WITHIN THE 5'-REGULATORY AREA OF THE NR2B GENE; CHROMATIN IMMUNOPRECIPITATION (CHIP) ASSAY WAS USED TO EXAMINE DNA LEVELS ASSOCIATED WITH METHYLATION AND TRANSCRIPTION FACTOR BINDING. ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA) AND IN VITRO DNA METHYLATION ASSAYS WERE PERFORMED TO DETERMINE THE DIRECT IMPACT OF DNA METHYLATION ON THE INTERACTION BETWEEN DNA AND TRANSCRIPTION FACTOR AND PROMOTER ACTIVITY. RESULTS: ANALYSIS OF INDIVIDUAL CPG METHYLATION SITES WITHIN THE NR2B 5'REGULATORY AREA REVEALED THREE REGIONS WITH CLUSTERS OF SITE-SPECIFIC CPG DEMETHYLATION FOLLOWING CIE TREATMENT AND WITHDRAWAL. THIS WAS CONFIRMED BY CHIP SHOWING SIMILAR DECREASES OF METHYLATED DNA IN THE SAME REGIONS. THE CIE-INDUCED DEMETHYLATION IS CHARACTERIZED BY BEING LOCATED NEAR CERTAIN TRANSCRIPTION FACTOR BINDING SEQUENCES, AP-1 AND CRE, AND OCCURRED DURING TREATMENT AS WELL AS AFTER ETHANOL WITHDRAWAL. FURTHERMORE, THE INCREASE IN VITRO OF METHYLATED DNA DECREASED TRANSCRIPTION FACTOR BINDING ACTIVITY AND PROMOTER ACTIVITY. AN ADDITIONAL CHIP ASSAY INDICATED THAT THE CIE-INDUCED DNA DEMETHYLATION IS ACCOMPANIED BY INCREASED OCCUPATION BY TRANSCRIPTION FACTORS. CONCLUSIONS: THESE RESULTS SUGGEST AN IMPORTANT ROLE OF DNA DEMETHYLATION IN MEDIATING CIE-INDUCED NR2B GENE UP-REGULATION, THUS IMPLICATING A NOVEL MOLECULAR SITE OF ALCOHOL ACTION. 2010 15 1086 45 COCAINE ADMINISTRATION AND ITS WITHDRAWAL ENHANCE THE EXPRESSION OF GENES ENCODING HISTONE-MODIFYING ENZYMES AND HISTONE ACETYLATION IN THE RAT PREFRONTAL CORTEX. CHRONIC EXPOSURE TO COCAINE, CRAVING, AND RELAPSE ARE ATTRIBUTED TO LONG-LASTING CHANGES IN GENE EXPRESSION ARISING THROUGH EPIGENETIC AND TRANSCRIPTIONAL MECHANISMS. ALTHOUGH SEVERAL BRAIN REGIONS ARE INVOLVED IN THESE PROCESSES, THE PREFRONTAL CORTEX SEEMS TO PLAY A CRUCIAL ROLE NOT ONLY IN MOTIVATION AND DECISION-MAKING BUT ALSO IN EXTINCTION AND SEEKING BEHAVIOR. IN THIS STUDY, WE APPLIED COCAINE SELF-ADMINISTRATION AND EXTINCTION TRAINING PROCEDURES IN RATS WITH A YOKED TRIAD TO DETERMINE DIFFERENTIALLY EXPRESSED GENES IN PREFRONTAL CORTEX. MICROARRAY ANALYSIS SHOWED SIGNIFICANT UPREGULATION OF SEVERAL GENES ENCODING HISTONE MODIFICATION ENZYMES DURING EARLY EXTINCTION TRAINING. SUBSEQUENT REAL-TIME PCR TESTING OF THESE GENES FOLLOWING COCAINE SELF-ADMINISTRATION OR EARLY (THIRD DAY) AND LATE (TENTH DAY) EXTINCTION REVEALED ELEVATED LEVELS OF THEIR TRANSCRIPTS. INTERESTINGLY, WE FOUND THE ENRICHMENT OF BRD1 MESSENGER RNA IN RATS SELF-ADMINISTERING COCAINE THAT LASTED UNTIL EXTINCTION TRAINING DURING COCAINE WITHDRAWAL WITH CONCOMITANT INCREASED ACETYLATION OF H3K9 AND H4K8. HOWEVER, DESPITE ELEVATED LEVELS OF METHYL- AND DEMETHYLTRANSFERASE-ENCODED TRANSCRIPTS, NO CHANGES IN GLOBAL DI- AND TRI-METHYLATION OF HISTONE H3 AT LYSINE 4, 9, 27, AND 79 WERE OBSERVED. SURPRISINGLY, AT THE END OF EXTINCTION TRAINING (10 DAYS OF COCAINE WITHDRAWAL), MOST OF THE ANALYZED GENES IN THE RATS ACTIVELY AND PASSIVELY ADMINISTERING COCAINE RETURNED TO THE CONTROL LEVEL. TOGETHER, THE ALTERATIONS IDENTIFIED IN THE RAT PREFRONTAL CORTEX MAY SUGGEST ENHANCED CHROMATIN REMODELING AND TRANSCRIPTIONAL ACTIVITY INDUCED BY EARLY COCAINE ABSTINENCE; HOWEVER, TO KNOW WHETHER THEY ARE BENEFICIAL OR NOT FOR THE EXTINCTION OF DRUG-SEEKING BEHAVIOR, FURTHER IN VIVO EVALUATION IS REQUIRED. 2017 16 1789 31 EFFECT OF CHRONIC HEROIN AND COCAINE ADMINISTRATION ON GLOBAL DNA METHYLATION IN BRAIN AND LIVER. DRUG ABUSE IS ASSOCIATED WITH EPIGENETIC CHANGES, SUCH AS HISTONE MODIFICATIONS AND DNA METHYLATION. THE PURPOSE OF THE PRESENT STUDY WAS TO EXAMINE THE EFFECT OF CHRONIC COCAINE AND HEROIN ADMINISTRATION ON GLOBAL DNA METHYLATION IN BRAIN AND LIVER. MALE, 8 WEEK OLD, C57BL/6J MICE RECEIVED HEROIN IN A CHRONIC 'INTERMITTENT' ESCALATING DOSE PARADIGM, OR COCAINE IN A CHRONIC ESCALATING DOSE 'BINGE' PARADIGM, WHICH MIMIC THE HUMAN PATTERN OF OPIOID OR COCAINE ABUSE RESPECTIVELY. FOLLOWING SACRIFICE, LIVERS AND BRAINS WERE REMOVED AND DNA WAS EXTRACTED FROM THEM. THE EXTRACTED DNA WAS HYDROLYZED AND 2'-DEOXYCYTIDINE AND 5-METHYL-2'-DEOXYCYTIDINE WERE DETERMINED BY HPLC-UV. THE % 5-METHYL-2'-DEOXYCYTIDINE CONTENT OF DNA WAS SIGNIFICANTLY HIGHER IN THE BRAIN COMPARED TO THE LIVER. THERE WERE NO DIFFERENCES BETWEEN THE CONTROL ANIMALS AND THE COCAINE OR HEROIN TREATED ANIMALS IN NEITHER OF THE TISSUES EXAMINED, WHICH IS SURPRISING SINCE COCAINE ADMINISTRATION INDUCED GROSS MORPHOLOGICAL CHANGES IN THE LIVER. MOREOVER, THERE WAS NO DIFFERENCE IN THE % 5-METHYL-2'-DEOXYCYTIDINE CONTENT OF DNA BETWEEN THE COCAINE AND THE HEROIN TREATED ANIMALS. THE GLOBAL DNA METHYLATION STATUS IN THE BRAIN AND LIVER OF MICE CHRONICALLY TREATED WITH COCAINE OR HEROIN REMAINS UNAFFECTED, BUT THIS FINDING CANNOT EXCLUDE THE EXISTENCE OF ANATOMICAL REGION OR GENE-SPECIFIC METHYLATION DIFFERENCES. THIS IS THE FIRST TIME THAT GLOBAL DNA METHYLATION IN THE LIVER AND WHOLE BRAIN HAS BEEN STUDIED FOLLOWING CHRONIC COCAINE OR HEROIN TREATMENT. 2013 17 2328 37 EPIGENETIC REGULATION OF IMMEDIATE-EARLY GENE NR4A2/NURR1 IN THE MEDIAL HABENULA DURING REINSTATEMENT OF COCAINE-ASSOCIATED BEHAVIOR. PROPENSITY TO RELAPSE FOLLOWING LONG PERIODS OF ABSTINENCE IS A KEY FEATURE OF SUBSTANCE USE DISORDER. DRUGS OF ABUSE, SUCH AS COCAINE, CAUSE LONG-TERM CHANGES IN THE NEURAL CIRCUITRY REGULATING REWARD, MOTIVATION, AND MEMORY PROCESSES THROUGH DYSREGULATION OF VARIOUS MOLECULAR MECHANISMS, INCLUDING EPIGENETIC REGULATION OF ACTIVITY-DEPENDENT GENE EXPRESSION. UNDERLYING DRUG-INDUCED CHANGES TO NEURAL CIRCUIT FUNCTION ARE THE MOLECULAR MECHANISMS REGULATING ACTIVITY-DEPENDENT GENE EXPRESSION. OF NOTE, HISTONE ACETYLTRANSFERASES AND HISTONE DEACETYLASES (HDACS), POWERFUL EPIGENETIC REGULATORS OF GENE EXPRESSION, ARE DYSREGULATED FOLLOWING BOTH ACUTE AND CHRONIC COCAINE EXPOSURE AND ARE LINKED TO COCAINE-INDUCED CHANGES IN NEURAL CIRCUIT FUNCTION. TO BETTER UNDERSTAND THE EFFECT OF DRUG-INDUCED CHANGES ON EPIGENETIC FUNCTION AND BEHAVIOR, WE INVESTIGATED HDAC3-MEDIATED REGULATION OF NR4A2/NURR1 IN THE MEDIAL HABENULA, AN UNDERSTUDIED PATHWAY IN COCAINE-ASSOCIATED BEHAVIORS. NR4A2, A TRANSCRIPTION FACTOR CRITICAL IN COCAINE-ASSOCIATED BEHAVIORS AND NECESSARY FOR MHB DEVELOPMENT, IS ENRICHED IN THE CHOLINERGIC CELL-POPULATION OF THE MHB; YET, THE ROLE OF NR4A2 WITHIN THE MHB IN THE ADULT BRAIN REMAINS ELUSIVE. HERE, WE EVALUATED WHETHER EPIGENETIC REGULATION OF NR4A2 IN THE MHB HAS A ROLE IN REINSTATEMENT OF COCAINE-ASSOCIATED BEHAVIORS. WE FOUND THAT HDAC3 DISENGAGES FROM NR4A2 IN THE MHB IN RESPONSE TO COCAINE-PRIMED REINSTATEMENT. WHEREAS ENHANCING HDAC3 FUNCTION IN THE MHB HAD NO EFFECT ON REINSTATEMENT, WE FOUND, USING A DOMINANT-NEGATIVE SPLICE VARIANT (NURR2C), THAT LOSS OF NR4A2 FUNCTION IN THE MHB BLOCKED REINSTATEMENT BEHAVIORS. THESE RESULTS SHOW FOR THE FIRST TIME THAT REGULATION OF NR4A2 FUNCTION IN THE MHB IS CRITICAL IN RELAPSE-LIKE BEHAVIORS. 2019 18 2119 35 EPIGENETIC HISTONE MODIFICATION REGULATES DEVELOPMENTAL LEAD EXPOSURE INDUCED HYPERACTIVITY IN RATS. LEAD (PB) EXPOSURE WAS COMMONLY CONSIDERED AS A HIGH ENVIRONMENTAL RISK FACTOR FOR THE DEVELOPMENT OF ATTENTION-DEFICIT/HYPERACTIVITY DISORDER (ADHD). HOWEVER, THE MOLECULAR BASIS OF THIS PATHOLOGICAL PROCESS STILL REMAINS ELUSIVE. IN LIGHT OF THE ROLE OF EPIGENETICS IN MODULATING THE NEUROLOGICAL DISEASE AND THE CAUSATIVE ENVIRONMENT, THE ALTERATIONS OF HISTONE MODIFICATIONS IN THE HIPPOCAMPUS OF RATS EXPOSED BY VARIOUS DOSES OF LEAD, ALONG WITH CONCOMITANT BEHAVIORAL DEFICITS, WERE INVESTIGATED IN THIS STUDY. ACCORDING TO THE FREE AND FORCED OPEN FIELD TEST, THERE SHOWED THAT IN A DOSAGE-DEPENDENT MANNER, LEAD EXPOSURE COULD RESULT IN THE INCREASED LOCOMOTOR ACTIVITY OF RATS, THAT IS, HYPERACTIVITY: A SUBTYPE OF ADHD. WESTERN BLOTTING ASSAYS REVEALED THAT THE LEVELS OF HISTONE ACETYLATION INCREASED SIGNIFICANTLY IN THE HIPPOCAMPUS BY CHRONIC LEAD EXPOSURE, WHILE NO DRAMATIC CHANGES WERE DETECTED IN TERMS OF EXPRESSION YIELDS OF ADHD-RELATED DOPAMINERGIC PROTEINS, INDICATING THAT HISTONE ACETYLATION PLAYS ESSENTIAL ROLES IN THIS TOXICANT-INVOLVED PATHOGENESIS. IN ADDITION, THE INCREASED LEVEL OF HISTONE ACETYLATION MIGHT BE ATTRIBUTED TO THE ENZYMATIC ACTIVITY OF P300, A TYPICAL HISTONE ACETYLTRANSFERASE, AS THE TRANSCRIPTIONAL LEVEL OF P300 WAS SIGNIFICANTLY INCREASED UPON HIGHER-DOSE PB EXPOSURE. IN SUMMARY, THIS STUDY FIRST DISCOVERED THE EPIGENETIC MECHANISM BRIDGING THE ENVIRONMENTAL INFLUENCE (PB) AND THE DISEASE ITSELF (ADHD) IN THE HISTONE MODIFICATION LEVEL, PAVING THE WAY FOR THE COMPREHENSIVE UNDERSTANDING OF ADHD'S ETIOLOGY AND IN FURTHER STEPS, ESTABLISHING THE THERAPY STRATEGY OF THIS WIDESPREAD NEUROLOGICAL DISORDER. 2014 19 4742 40 NOVEL HISTONE MODIFICATIONS IN MICROGLIA DERIVED FROM A MOUSE MODEL OF CHRONIC PAIN. AS THE RESIDENT IMMUNE CELLS IN THE CENTRAL NERVOUS SYSTEM, MICROGLIA PLAY AN IMPORTANT ROLE IN THE MAINTENANCE OF ITS HOMEOSTASIS. DYSREGULATION OF MICROGLIA HAS BEEN ASSOCIATED WITH THE DEVELOPMENT AND MAINTENANCE OF CHRONIC PAIN. HOWEVER, THE RELEVANT MOLECULAR PATHWAYS REMAIN POORLY DEFINED. IN THIS STUDY, WE USED A MASS SPECTROMETRY-BASED PROTEOMIC APPROACH TO SCREEN POTENTIAL CHANGES OF HISTONE PROTEIN MODIFICATIONS IN MICROGLIA ISOLATED FROM THE BRAIN OF CONTROL AND CISPLATIN-INDUCED NEUROPATHIC PAIN ADULT C57BL/6J MALE MICE. WE IDENTIFIED SEVERAL NOVEL MICROGLIAL HISTONE MODIFICATIONS ASSOCIATED WITH PAIN, INCLUDING STATISTICALLY SIGNIFICANTLY DECREASED HISTONE H3.1 LYSINE 27 MONO-METHYLATION (H3.1K27ME1, 54.8% OF CONTROL) AND H3 LYSINE 56 TRI-METHYLATION (7.5% OF CONTROL), AS WELL AS A TREND SUGGESTING INCREASED H3 TYROSINE 41 NITRATION. WE FURTHER INVESTIGATED THE FUNCTIONAL ROLE OF H3.1K27ME1 AND FOUND THAT TREATMENT OF CULTURED MICROGLIAL CELLS FOR 4 CONSECUTIVE DAYS WITH 1-10 MUM OF NCDM-64, A POTENT AND SELECTIVE INHIBITOR OF LYSINE DEMETHYLASE 7A, AN ENZYME RESPONSIBLE FOR THE DEMETHYLATION OF H3K27ME1, DOSE-DEPENDENTLY ELEVATED ITS LEVELS WITH A GREATER THAN A TWO-FOLD INCREASE OBSERVED AT 10 MUM COMPARED TO VEHICLE-TREATED CONTROL CELLS. MOREOVER, PRETREATMENT OF MICE WITH NCDM-64 (10 OR 25 MG/KG/DAY, I.P.) PRIOR TO CISPLATIN TREATMENT PREVENTED THE DEVELOPMENT OF NEUROPATHIC PAIN IN MICE. THE IDENTIFICATION OF SPECIFIC CHROMATIN MARKS IN MICROGLIA ASSOCIATED WITH CHRONIC PAIN MAY YIELD CRITICAL INSIGHT INTO THE CONTRIBUTION OF MICROGLIA TO THE DEVELOPMENT AND MAINTENANCE OF PAIN, AND OPENS NEW AVENUES FOR THE DEVELOPMENT OF NOVEL NONOPIOID THERAPEUTICS FOR THE EFFECTIVE MANAGEMENT OF CHRONIC PAIN. 2022 20 1117 36 COMPARATIVE AND EXPERIMENTAL STUDIES ON THE GENES ALTERED BY CHRONIC HYPOXIA IN HUMAN BRAIN MICROENDOTHELIAL CELLS. BACKGROUND : HYPOXIA INDUCIBLE FACTOR 1 ALPHA (HIF1A) IS A MASTER REGULATOR OF ACUTE HYPOXIA; HOWEVER, WITH CHRONIC HYPOXIA, HIF1A LEVELS RETURN TO THE NORMOXIC LEVELS. IMPORTANTLY, THE GENES THAT ARE INVOLVED IN THE CELL SURVIVAL AND VIABILITY UNDER CHRONIC HYPOXIA ARE NOT KNOWN. THEREFORE, WE TESTED THE HYPOTHESIS THAT CHRONIC HYPOXIA LEADS TO THE UPREGULATION OF A CORE GROUP OF GENES WITH ASSOCIATED CHANGES IN THE PROMOTER DNA METHYLATION THAT MEDIATES THE CELL SURVIVAL UNDER HYPOXIA. RESULTS : WE EXAMINED THE EFFECT OF CHRONIC HYPOXIA (3 DAYS; 0.5% OXYGEN) ON HUMAN BRAIN MICRO ENDOTHELIAL CELLS (HBMEC) VIABILITY AND APOPTOSIS. HYPOXIA CAUSED A SIGNIFICANT REDUCTION IN CELL VIABILITY AND AN INCREASE IN APOPTOSIS. NEXT, WE EXAMINED CHRONIC HYPOXIA ASSOCIATED CHANGES IN TRANSCRIPTOME AND GENOME-WIDE PROMOTER METHYLATION. THE DATA OBTAINED WAS COMPARED WITH 16 OTHER MICROARRAY STUDIES ON CHRONIC HYPOXIA. NINE GENES WERE ALTERED IN RESPONSE TO CHRONIC HYPOXIA IN ALL 17 STUDIES. INTERESTINGLY, HIF1A WAS NOT ALTERED WITH CHRONIC HYPOXIA IN ANY OF THE STUDIES. FURTHERMORE, WE COMPARED OUR DATA TO THREE OTHER STUDIES THAT IDENTIFIED HIF-RESPONSIVE GENES BY VARIOUS APPROACHES. ONLY TWO GENES WERE FOUND TO BE HIF DEPENDENT. WE SILENCED EACH OF THESE 9 GENES USING CRISPR/CAS9 SYSTEM. DOWNREGULATION OF EGLN3 SIGNIFICANTLY INCREASED THE CELL DEATH UNDER CHRONIC HYPOXIA, WHEREAS DOWNREGULATION OF ERO1L, ENO2, ADRENOMEDULLIN, AND SPAG4 REDUCED THE CELL DEATH UNDER HYPOXIA. CONCLUSIONS : WE PROVIDE A CORE GROUP OF GENES THAT REGULATES CELLULAR ACCLIMATIZATION UNDER CHRONIC HYPOXIC STRESS, AND MOST OF THEM ARE HIF INDEPENDENT. 2017