1 1133 165 COMPREHENSIVE EPIGENOMIC PROFILING OF HUMAN ALVEOLAR EPITHELIAL DIFFERENTIATION IDENTIFIES KEY EPIGENETIC STATES AND TRANSCRIPTION FACTOR CO-REGULATORY NETWORKS FOR MAINTENANCE OF DISTAL LUNG IDENTITY. BACKGROUND: DISRUPTION OF ALVEOLAR EPITHELIAL CELL (AEC) DIFFERENTIATION IS IMPLICATED IN DISTAL LUNG DISEASES SUCH AS CHRONIC OBSTRUCTIVE PULMONARY DISEASE, IDIOPATHIC PULMONARY FIBROSIS, AND LUNG ADENOCARCINOMA THAT IMPACT MORBIDITY AND MORTALITY WORLDWIDE. ELUCIDATING UNDERLYING DISEASE PATHOGENESIS REQUIRES A MECHANISTIC MOLECULAR UNDERSTANDING OF AEC DIFFERENTIATION. PREVIOUS STUDIES HAVE FOCUSED ON CHANGES OF INDIVIDUAL TRANSCRIPTION FACTORS, AND TO DATE NO STUDY HAS COMPREHENSIVELY CHARACTERIZED THE DYNAMIC, GLOBAL EPIGENOMIC ALTERATIONS THAT FACILITATE THIS CRITICAL DIFFERENTIATION PROCESS IN HUMANS. RESULTS: WE COMPREHENSIVELY PROFILED THE EPIGENOMIC STATES OF HUMAN AECS DURING TYPE 2 TO TYPE 1-LIKE CELL DIFFERENTIATION, INCLUDING THE METHYLOME AND CHROMATIN FUNCTIONAL DOMAINS, AND INTEGRATED THIS WITH TRANSCRIPTOME-WIDE RNA EXPRESSION DATA. ENHANCER REGIONS WERE DRASTICALLY ALTERED DURING AEC DIFFERENTIATION. TRANSCRIPTION FACTOR BINDING ANALYSIS WITHIN ENHANCER REGIONS REVEALED DIVERSE INTERACTIVE NETWORKS WITH ENRICHMENT FOR MANY TRANSCRIPTION FACTORS, INCLUDING NKX2-1 AND FOXA FAMILY MEMBERS, AS WELL AS TRANSCRIPTION FACTORS WITH LESS WELL CHARACTERIZED ROLES IN AEC DIFFERENTIATION, SUCH AS MEMBERS OF THE MEF2, TEAD, AND AP1 FAMILIES. ADDITIONALLY, ASSOCIATIONS AMONG TRANSCRIPTION FACTORS CHANGED DURING DIFFERENTIATION, IMPLICATING A COMPLEX NETWORK OF HETEROTRIMERIC COMPLEX SWITCHING IN DRIVING DIFFERENTIATION. INTEGRATION OF AEC ENHANCER STATES WITH THE CATALOG OF ENHANCER ELEMENTS IN THE ROADMAP EPIGENOMICS MAPPING CONSORTIUM AND ENCYCLOPEDIA OF DNA ELEMENTS (ENCODE) REVEALED THAT AECS HAVE SIMILAR EPIGENOMIC STRUCTURES TO OTHER PROFILED EPITHELIAL CELL TYPES, INCLUDING HUMAN MAMMARY EPITHELIAL CELLS (HMECS), WITH NKX2-1 SERVING AS A DISTINGUISHING FEATURE OF DISTAL LUNG DIFFERENTIATION. CONCLUSIONS: ENHANCER REGIONS ARE HOTSPOTS OF EPIGENOMIC ALTERATION THAT REGULATE AEC DIFFERENTIATION. FURTHERMORE, THE DIFFERENTIATION PROCESS IS REGULATED BY DYNAMIC NETWORKS OF TRANSCRIPTION FACTORS ACTING IN CONCERT, RATHER THAN INDIVIDUALLY. THESE FINDINGS PROVIDE A ROADMAP FOR UNDERSTANDING THE RELATIONSHIP BETWEEN DISRUPTION OF THE EPIGENETIC STATE DURING AEC DIFFERENTIATION AND DEVELOPMENT OF LUNG DISEASES THAT MAY BE THERAPEUTICALLY AMENABLE. 2021 2 4603 33 NEGATIVE ALLOSTERIC MODULATION OF MGLUR5 PARTIALLY CORRECTS PATHOPHYSIOLOGY IN A MOUSE MODEL OF RETT SYNDROME. RETT SYNDROME (RTT) IS CAUSED BY MUTATIONS IN THE GENE ENCODING METHYL-CPG BINDING PROTEIN 2 (MECP2), AN EPIGENETIC REGULATOR OF MRNA TRANSCRIPTION. HERE, WE REPORT A TEST OF THE HYPOTHESIS OF SHARED PATHOPHYSIOLOGY OF RTT AND FRAGILE X, ANOTHER MONOGENIC CAUSE OF AUTISM AND INTELLECTUAL DISABILITY. IN FRAGILE X, THE LOSS OF THE MRNA TRANSLATIONAL REPRESSOR FMRP LEADS TO EXAGGERATED PROTEIN SYNTHESIS DOWNSTREAM OF METABOTROPIC GLUTAMATE RECEPTOR 5 (MGLUR5). WE FOUND THAT MGLUR5- AND PROTEIN-SYNTHESIS-DEPENDENT SYNAPTIC PLASTICITY WERE SIMILARLY ALTERED IN AREA CA1 OF MECP2 KO MICE. CA1 PYRAMIDAL CELL-TYPE-SPECIFIC, GENOME-WIDE PROFILING OF RIBOSOME-BOUND MRNAS WAS PERFORMED IN WILD-TYPE AND MECP2 KO HIPPOCAMPAL CA1 NEURONS TO REVEAL THE MECP2-REGULATED "TRANSLATOME." WE FOUND SIGNIFICANT OVERLAP BETWEEN RIBOSOME-BOUND TRANSCRIPTS OVEREXPRESSED IN THE MECP2 KO AND FMRP MRNA TARGETS. THESE TENDED TO ENCODE LONG GENES THAT WERE FUNCTIONALLY RELATED TO EITHER CYTOSKELETON ORGANIZATION OR THE DEVELOPMENT OF NEURONAL CONNECTIVITY. IN THE FMR1 KO MOUSE, CHRONIC TREATMENT WITH MGLUR5-NEGATIVE ALLOSTERIC MODULATORS (NAMS) HAS BEEN SHOWN TO AMELIORATE MANY MUTANT PHENOTYPES BY CORRECTING EXCESSIVE PROTEIN SYNTHESIS. IN MECP2 KO MICE, WE FOUND THAT MGLUR5 NAM TREATMENT SIGNIFICANTLY REDUCED THE LEVEL OF OVEREXPRESSED RIBOSOME-ASSOCIATED TRANSCRIPTS, PARTICULARLY THOSE THAT WERE ALSO FMRP TARGETS. SOME RETT PHENOTYPES WERE ALSO AMELIORATED BY TREATMENT, MOST NOTABLY HIPPOCAMPAL CELL SIZE AND LIFESPAN. TOGETHER, THESE RESULTS SUGGEST A POTENTIAL MECHANISTIC LINK BETWEEN MECP2-MEDIATED TRANSCRIPTION REGULATION AND MGLUR5/FMRP-MEDIATED PROTEIN TRANSLATION REGULATION THROUGH COREGULATION OF A SUBSET OF GENES RELEVANT TO SYNAPTIC FUNCTIONS. SIGNIFICANCE STATEMENT: ALTERED REGULATION OF SYNAPTIC PROTEIN SYNTHESIS HAS BEEN HYPOTHESIZED TO CONTRIBUTE TO THE PATHOPHYSIOLOGY THAT UNDERLIES MULTIPLE FORMS OF INTELLECTUAL DISABILITY AND AUTISM SPECTRUM DISORDER. HERE, WE SHOW IN A MOUSE MODEL OF RETT SYNDROME (MECP2 KO) THAT METABOTROPIC GLUTAMATE RECEPTOR 5 (MGLUR5)- AND PROTEIN-SYNTHESIS-DEPENDENT SYNAPTIC PLASTICITY ARE ABNORMAL IN THE HIPPOCAMPUS. WE FOUND THAT A SUBSET OF RIBOSOME-BOUND MRNAS WAS ABERRANTLY UPREGULATED IN HIPPOCAMPAL CA1 NEURONS OF MECP2 KO MICE, THAT THESE SIGNIFICANTLY OVERLAPPED WITH FMRP DIRECT TARGETS AND/OR SFARI HUMAN AUTISM GENES, AND THAT CHRONIC TREATMENT OF MECP2 KO MICE WITH AN MGLUR5-NEGATIVE ALLOSTERIC MODULATOR TUNES DOWN UPREGULATED RIBOSOME-BOUND MRNAS AND PARTIALLY IMPROVES MUTANT MICE PHENOTYPES. 2016 3 1336 28 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 1240 33 CURRENT ADVANCES OF EPIGENETICS IN PERIODONTOLOGY FROM ENCODE PROJECT: A REVIEW AND FUTURE PERSPECTIVES. BACKGROUND: THE ENCYCLOPEDIA OF DNA ELEMENTS (ENCODE) PROJECT HAS ADVANCED OUR KNOWLEDGE OF THE FUNCTIONAL ELEMENTS IN THE GENOME AND EPIGENOME. THE AIM OF THIS ARTICLE WAS TO PROVIDE THE COMPREHENSION ABOUT CURRENT RESEARCH TRENDS FROM ENCODE PROJECT AND ESTABLISH THE LINK BETWEEN EPIGENETICS AND PERIODONTAL DISEASES BASED ON EPIGENOME STUDIES AND SEEK THE FUTURE DIRECTION. MAIN BODY: GLOBAL EPIGENOME RESEARCH PROJECTS HAVE EMPHASIZED THE IMPORTANCE OF EPIGENETIC RESEARCH FOR UNDERSTANDING HUMAN HEALTH AND DISEASE, AND CURRENT INTERNATIONAL CONSORTIA SHOW AN IMPROVED INTEREST IN THE IMPORTANCE OF ORAL HEALTH WITH SYSTEMIC HEALTH. THE EPIGENETIC STUDIES IN DENTAL FIELD HAVE BEEN MAINLY CONDUCTED IN PERIODONTOLOGY AND HAVE FOCUSED ON DNA METHYLATION ANALYSIS. ADVANCES IN SEQUENCING TECHNOLOGY HAVE BROADENED THE TARGET FOR EPIGENETIC STUDIES FROM SPECIFIC GENES TO GENOME-WIDE ANALYSES. CONCLUSIONS: IN LINE WITH GLOBAL RESEARCH TRENDS, FURTHER EXTENDED AND ADVANCED EPIGENETIC STUDIES WOULD PROVIDE CRUCIAL INFORMATION FOR THE REALIZATION OF COMPREHENSIVE DENTAL MEDICINE AND EXPAND THE SCOPE OF ONGOING LARGE-SCALE RESEARCH PROJECTS. 2021 5 3141 49 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 6 3254 21 HEPATITIS B VIRUS X PROTEIN AND HEPATOCARCINOGENESIS. CHRONIC HEPATITIS B VIRUS (HBV) INFECTION IS ONE OF THE MOST ASSOCIATED FACTORS IN HEPATOCARCINOGENESIS. HBV IS ABLE TO INTEGRATE INTO THE HOST GENOME AND ENCODE THE MULTI-FUNCTIONAL HEPATITIS B VIRUS X PROTEIN (HBX). ALTHOUGH THE MECHANISM BETWEEN HBX AND CARCINOGENESIS IS STILL ELUSIVE, RECENT STUDIES HAVE SHOWN THAT HBX WAS ABLE TO INFLUENCE VARIOUS SIGNALING PATHWAYS, AS WELL AS EPIGENETIC AND GENETIC PROCESSES. THIS REVIEW WILL EXAMINE AND SUMMARIZE RECENT LITERATURE ABOUT HBX'S ROLE IN THESE VARIOUS PROCESSES. 2016 7 3257 41 HEPATITIS B X ANTIGEN (HBX) IS AN IMPORTANT THERAPEUTIC TARGET IN THE PATHOGENESIS OF HEPATOCELLULAR CARCINOMA. HEPATITIS B VIRUS (HBV) IS A HUMAN PATHOGEN THAT HAS INFECTED AN ESTIMATED TWO BILLION PEOPLE WORLDWIDE. DESPITE THE AVAILABILITY OF HIGHLY EFFICACIOUS VACCINES, UNIVERSAL SCREENING OF THE BLOOD SUPPLY FOR VIRUS, AND POTENT DIRECT ACTING ANTI-VIRAL DRUGS, THERE ARE MORE THAN 250 MILLION CARRIERS OF HBV WHO ARE AT RISK FOR THE SEQUENTIAL DEVELOPMENT OF HEPATITIS, FIBROSIS, CIRRHOSIS AND HEPATOCELLULAR CARCINOMA (HCC). MORE THAN 800,000 DEATHS PER YEAR ARE ATTRIBUTED TO CHRONIC HEPATITIS B. MANY DIFFERENT THERAPEUTIC APPROACHES HAVE BEEN DEVELOPED TO BLOCK VIRUS REPLICATION, AND ALTHOUGH EFFECTIVE, NONE ARE CURATIVE. THESE TREATMENTS HAVE LITTLE OR NO IMPACT UPON THE PORTIONS OF INTEGRATED HBV DNA, WHICH OFTEN ENCODE THE VIRUS REGULATORY PROTEIN, HBX. ALTHOUGH GIVEN LITTLE ATTENTION, HBX IS AN IMPORTANT THERAPEUTIC TARGET BECAUSE IT CONTRIBUTES IMPORTANTLY TO (A) HBV REPLICATION, (B) IN PROTECTING INFECTED CELLS FROM IMMUNE MEDIATED DESTRUCTION DURING CHRONIC INFECTION, AND (C) IN THE DEVELOPMENT OF HCC. THUS, THE DEVELOPMENT OF THERAPIES TARGETING HBX, COMBINED WITH OTHER ESTABLISHED THERAPIES, WILL PROVIDE A FUNCTIONAL CURE THAT WILL TARGET VIRUS REPLICATION AND FURTHER REDUCE OR ELIMINATE BOTH THE MORBIDITY AND MORTALITY ASSOCIATED WITH CHRONIC LIVER DISEASE AND HCC. SIMULTANEOUS TARGETING OF ALL THESE CHARACTERISTICS UNDERSCORES THE IMPORTANCE OF DEVELOPING THERAPIES AGAINST HBX. 2021 8 1129 40 COMPREHENSIVE ANALYSIS OF MRNA-LNCRNA CO-EXPRESSION PROFILES IN MOUSE BRAIN DURING INFECTION WITH TOXOPLASMA GONDII. TOXOPLASMA GONDII IS AN OBLIGATE INTRACELLULAR PROTOZOAN PARASITE WHICH SERIOUSLY THREATENS THE HEALTH OF DOMESTIC ANIMALS AND HUMANS. LONG NON-CODING RNAS (LNCRNAS) ARE NON-PROTEIN-CODING TRANSCRIPTS GREATER THAN 200 NUCLEOTIDES, WHICH ARE WIDELY INVOLVED IN TRANSCRIPTIONAL AND EPIGENETIC REGULATIONS. HOWEVER, LITTLE IS KNOWN ABOUT THE ROLES OF HOST LNCRNAS IN THE RESPONSE TO T. GONDII INFECTIONS. IN THIS STUDY, USING ILLUMINA SEQUENCING TECHNOLOGY, WE ANALYZED THE EXPRESSION PROFILES OF MRNAS AND LNCRNAS IN BALB/C MOUSE BRAIN FOLLOWING INFECTION BY T. GONDII PRU STRAIN (TYPE II GENOTYPE) CYSTS. THE IDENTIFIED DIFFERENTIALLY EXPRESSED (DE) RNAS WERE SUBJECTED TO BIOINFORMATICS ANALYSIS. A TOTAL OF 2,090 ANNOTATED LNCRNAS ALONG WITH 3,577 NOVEL LNCRNAS WERE IDENTIFIED. IN THE ACUTELY INFECTED MOUSE BRAIN, A TOTAL OF 330 MRNAS AND 19 LNCRNAS WERE DYS-REGULATED, WHEREAS 136 DE MRNAS AND 9 DE LNCRNAS WERE IDENTIFIED IN CHRONICALLY INFECTED MOUSE BRAIN. GO ANALYSIS REVEALED THAT THESE DE MRNAS IDENTIFIED AT ACUTE INFECTION STAGE WERE INVOLVED IN IMMUNE RESPONSE, WHEREAS DE MRNAS FOUND AT CHRONIC INFECTION STAGE WERE MOSTLY ENRICHED IN RESPONSE TO PROTOZOAN. KEGG ANALYSIS SHOWED THAT DE MRNAS WERE SIGNIFICANTLY ENRICHED IN DISEASE RELATED PATHWAYS. IN ADDITION, THE PUTATIVE MRNA-LNCRNA CO-EXPRESSION NETWORK WAS CONSTRUCTED, AND SEVERAL HUB REGULATORY RNAS WERE IDENTIFIED BASED ON THE TRANSCRIPTOME DATA. THIS STUDY FIRSTLY CHARACTERIZED THE CO-EXPRESSION PROFILE OF MRNAS AND LNCRNAS IN MOUSE BRAIN INFECTED WITH T. GONDII AND PROVIDED A FRAMEWORK FOR FURTHER STUDIES OF THE ROLES OF LNCRNAS IN HOST NEUROPATHOLOGY DURING TOXOPLASMOSIS PROGRESSION. 2023 9 4373 41 MIRNAS: IMPORTANT TARGETS FOR ORAL CANCER PAIN RESEARCH. PAIN IS A SYMPTOM SHARED BY AN INCREDIBLE NUMBER OF DISEASES. IT IS ALSO ONE OF THE PRIMARY CONDITIONS THAT PROMPT INDIVIDUALS TO SEEK MEDICAL TREATMENT. HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) CORRESPONDS TO A HETEROGENEOUS DISEASE THAT MAY ARISE FROM MANY DISTINCT STRUCTURES OF A LARGE, HIGHLY COMPLEX, AND INTRICATE REGION. HNSCC AFFECTS A GREAT NUMBER OF PATIENTS WORLDWIDE AND IS DIRECTLY ASSOCIATED WITH CHRONIC PAIN, WHICH IS ESPECIALLY PROMINENT DURING THE ADVANCED STAGES OF ORAL SQUAMOUS CELL CARCINOMA (OSCC), AN ANATOMICAL AND CLINICAL SUBTYPE THAT CORRESPONDS TO THE GREAT MAJORITY ORAL CANCERS. ALTHOUGH THE CELLULAR AND MOLECULAR BASES OF ORAL CANCER PAIN HAVE NOT BEEN FULLY ESTABLISHED YET, THE RESULTS OF RECENT STUDIES SUGGEST THAT DIFFERENT EPIGENETIC MECHANISMS MAY CONTRIBUTE TO THIS PROCESS. FOR INSTANCE, THERE IS STRONG SCIENTIFIC EVIDENCE THAT MICRORNAS (MIRNAS), SMALL RNA MOLECULES THAT DO NOT ENCODE PROTEINS, MIGHT ACT BY REGULATING THE MECHANISMS UNDERLYING CANCER-RELATED PAIN. AMONG THE MIRNAS THAT COULD POSSIBLY INTERFERE IN PAIN-SIGNALING PATHWAYS, MIR-125B, MIR-181, AND MIR-339 EMERGE AS SOME OF THE MOST PROMISING CANDIDATES. IN FACT, SUCH MOLECULES APPARENTLY CONTRIBUTE TO INFLAMMATORY PAIN. MOREOVER, THESE MOLECULES POSSIBLY INFLUENCE THE ACTIVITY OF ENDOGENOUS PAIN CONTROL SYSTEMS (E.G., OPIOIDERGIC AND SEROTONERGIC SYSTEMS), WHICH COULD ULTIMATELY RESULT IN PERIPHERAL AND CENTRAL SENSITIZATION, CENTRAL NERVOUS SYSTEM (CNS) PHENOMENA INNATELY ASSOCIATED WITH CHRONIC PAIN. THIS REVIEW PAPER FOCUSES ON THE CURRENT SCIENTIFIC KNOWLEDGE REGARDING THE INVOLVEMENT OF MIRNAS IN CANCER PAIN, WITH SPECIAL ATTENTION DEDICATED TO OSCC-RELATED PAIN. 2017 10 4348 43 MIR-146A DYSREGULATES ENERGY METABOLISM DURING NEUROINFLAMMATION. ALZHEIMER'S DISEASE (AD) AND OTHER NEURODEGENERATIVE DISEASES ARE CHARACTERIZED BY CHRONIC NEUROINFLAMMATION AND A REDUCTION IN BRAIN ENERGY METABOLISM. AN IMPORTANT ROLE HAS EMERGED FOR SMALL, NON-CODING RNA MOLECULES KNOWN AS MICRORNAS (MIRNAS) IN THE PATHOPHYSIOLOGY OF MANY NEURODEGENERATIVE DISORDERS. AS EPIGENETIC REGULATORS, MIRNAS POSSESS THE CAPACITY TO REGULATE AND FINE TUNE PROTEIN PRODUCTION BY INHIBITING TRANSLATION. SEVERAL MIRNAS, WHICH INCLUDE MIR-146A, ARE ELEVATED IN THE BRAIN, CSF, AND PLASMA OF AD PATIENTS. MIR-146A PARTICIPATES IN PATHWAYS THAT REGULATE IMMUNE ACTIVATION AND HAS SEVERAL MRNA TARGETS WHICH ENCODE FOR PROTEINS INVOLVED IN CELLULAR ENERGY METABOLISM. AN ADDITIONAL ROLE FOR EXTRACELLULAR VESICLES (EVS) HAS ALSO EMERGED IN THE PROGRESSION AD, AS EVS CAN TRANSFER FUNCTIONALLY ACTIVE PROTEINS AND RNAS FROM DISEASED TO HEALTHY CELLS. IN THE CURRENT STUDY, WE EXPOSED VARIOUS CELL TYPES PRESENT WITHIN THE CNS TO IMMUNOMODULATORY MOLECULES AND OBSERVED SIGNIFICANT UPREGULATION OF MIR-146A EXPRESSION, BOTH WITHIN CELLS AND WITHIN THEIR SECRETED EVS. FURTHER, WE ASSESSED THE EFFECTS OF MIR-146A OVEREXPRESSION ON BIOENERGETIC FUNCTION IN PRIMARY RAT GLIAL CELLS AND FOUND SIGNIFICANT REDUCTIONS IN OXIDATIVE PHOSPHORYLATION AND GLYCOLYSIS. LASTLY, WE CORRELATED MIR-146A EXPRESSION LEVELS WITHIN VARIOUS REGIONS OF THE AD BRAIN TO DISEASE STAGING AND FOUND SIGNIFICANT, POSITIVE CORRELATIONS. THESE NOVEL RESULTS DEMONSTRATE THAT THE MODULATION OF MIR-146A IN RESPONSE TO NEUROINFLAMMATORY STIMULI MAY MEDIATE THE LOSS OF MITOCHONDRIAL INTEGRITY AND FUNCTION IN CELLS, THEREBY CONTRIBUTING TO THE PROGRESSION OF BETA-AMYLOID AND TAU PATHOLOGY IN THE AD BRAIN. MULTIPLE INFLAMMATORY STIMULI CAN UPREGULATE MIRNA-146A EXPRESSION WITHIN NEURONS, MIXED GLIAL CELLS, AND BRAIN ENDOTHELIAL CELLS, WHICH IS EITHER RETAINED WITHIN THESE CELLS OR RELEASED FROM THEM AS EXTRACELLULAR VESICLE CARGO. THE UPREGULATION OF MIR-146A DISRUPTS CELLULAR BIOENERGETICS IN MIXED GLIAL CELLS. THIS MECHANISM MAY PLAY A CRITICAL ROLE IN THE NEUROINFLAMMATORY RESPONSE OBSERVED DURING ALZHEIMER'S DISEASE. 2022 11 4055 31 MAPPING OF HISTONE MODIFICATIONS IN EPISOMAL HBV CCCDNA UNCOVERS AN UNUSUAL CHROMATIN ORGANIZATION AMENABLE TO EPIGENETIC MANIPULATION. CHRONIC HEPATITIS B VIRUS (HBV) INFECTION AFFECTS 240 MILLION PEOPLE WORLDWIDE AND IS A MAJOR RISK FACTOR FOR LIVER FAILURE AND HEPATOCELLULAR CARCINOMA. CURRENT ANTIVIRAL THERAPY INHIBITS CYTOPLASMIC HBV GENOMIC REPLICATION, BUT IS NOT CURATIVE BECAUSE IT DOES NOT DIRECTLY AFFECT NUCLEAR HBV CLOSED CIRCULAR DNA (CCCDNA), THE GENOMIC FORM THAT TEMPLATES VIRAL TRANSCRIPTION AND SUSTAINS VIRAL PERSISTENCE. NOVEL APPROACHES THAT DIRECTLY TARGET CCCDNA REGULATION WOULD THEREFORE BE HIGHLY DESIRABLE. CCCDNA IS ASSEMBLED WITH CELLULAR HISTONE PROTEINS INTO CHROMATIN, BUT LITTLE IS KNOWN ABOUT THE REGULATION OF HBV CHROMATIN BY HISTONE POSTTRANSLATIONAL MODIFICATIONS (PTMS). HERE, USING A NEW CCCDNA CHIP-SEQ APPROACH, WE REPORT, TO OUR KNOWLEDGE, THE FIRST GENOME-WIDE MAPS OF PTMS IN CCCDNA-CONTAINING CHROMATIN FROM DE NOVO INFECTED HEPG2 CELLS, PRIMARY HUMAN HEPATOCYTES, AND FROM HBV-INFECTED LIVER TISSUE. WE FIND HIGH LEVELS OF PTMS ASSOCIATED WITH ACTIVE TRANSCRIPTION ENRICHED AT SPECIFIC SITES WITHIN THE HBV GENOME AND, SURPRISINGLY, VERY LOW LEVELS OF PTMS LINKED TO TRANSCRIPTIONAL REPRESSION EVEN AT SILENT HBV PROMOTERS. WE SHOW THAT TRANSCRIPTION AND ACTIVE PTMS IN HBV CHROMATIN ARE REDUCED BY THE ACTIVATION OF AN INNATE IMMUNITY PATHWAY, AND THAT THIS EFFECT CAN BE RECAPITULATED WITH A SMALL MOLECULE EPIGENETIC MODIFYING AGENT, OPENING THE POSSIBILITY THAT CHROMATIN-BASED REGULATION OF CCCDNA TRANSCRIPTION COULD BE A NEW THERAPEUTIC APPROACH TO CHRONIC HBV INFECTION. 2015 12 2053 32 EPIGENETIC CONNECTIONS OF THE TRPA1 ION CHANNEL IN PAIN TRANSMISSION AND NEUROGENIC INFLAMMATION - A THERAPEUTIC PERSPECTIVE IN MIGRAINE? PERSISTENT REPROGRAMMING OF EPIGENETIC PATTERN LEADS TO CHANGES IN GENE EXPRESSION OBSERVED IN MANY NEUROLOGICAL DISORDERS. TRANSIENT RECEPTOR POTENTIAL CATION CHANNEL SUBFAMILY A MEMBER 1 (TRPA1), A MEMBER OF THE TRP CHANNELS SUPERFAMILY, IS ACTIVATED BY MANY MIGRAINE TRIGGERS AND EXPRESSED IN TRIGEMINAL NEURONS AND BRAIN REGIONS THAT ARE IMPORTANT IN MIGRAINE PATHOGENESIS. TRP CHANNELS CHANGE NOXIOUS STIMULI INTO PAIN SIGNALS WITH THE INVOLVEMENT OF EPIGENETIC REGULATION. THE EXPRESSION OF THE TRPA1 ENCODING GENE, TRPA1, IS MODULATED IN PAIN-RELATED SYNDROMES BY EPIGENETIC ALTERATIONS, INCLUDING DNA METHYLATION, HISTONE MODIFICATIONS, AND EFFECTS OF NON-CODING RNAS: MICRO RNAS (MIRNAS), LONG NON-CODING RNAS, AND CIRCULAR RNAS. TRPA1 MAY CHANGE EPIGENETIC PROFILE OF MANY PAIN-RELATED GENES AS IT MAY MODIFY ENZYMES RESPONSIBLE FOR EPIGENETIC MODIFICATIONS AND EXPRESSION OF NON-CODING RNAS. TRPA1 MAY INDUCE THE RELEASE OF CALCITONIN GENE RELATED PEPTIDE (CGRP), FROM TRIGEMINAL NEURONS AND DURAL TISSUE. THEREFORE, EPIGENETIC REGULATION OF TRPA1 MAY PLAY A ROLE IN EFFICACY AND SAFETY OF ANTI-MIGRAINE THERAPIES TARGETING TRP CHANNELS AND CGRP. TRPA1 IS ALSO INVOLVED IN NEUROGENIC INFLAMMATION, IMPORTANT IN MIGRAINE PATHOGENESIS. THE FUNDAMENTAL ROLE OF TRPA1 IN INFLAMMATORY PAIN TRANSMISSION MAY BE EPIGENETICALLY REGULATED. IN CONCLUSION, EPIGENETIC CONNECTIONS OF TRPA1 MAY PLAY A ROLE IN EFFICACY AND SAFETY OF ANTI-MIGRAINE THERAPY TARGETING TRP CHANNELS OR CGRP AND THEY SHOULD BE FURTHER EXPLORED FOR EFFICIENT AND SAFE ANTIMIGRAINE TREATMENT. THIS NARRATIVE/PERSPECTIVE REVIEW PRESENTS INFORMATION ON THE STRUCTURE AND FUNCTIONS OF TRPA1 AS WELL AS ROLE OF ITS EPIGENETIC CONNECTIONS IN PAIN TRANSMISSION AND POTENTIAL IN MIGRAINE THERAPY. 2023 13 6468 41 TISSUE-SPECIFIC ENRICHMENT OF LYMPHOMA RISK LOCI IN REGULATORY ELEMENTS. THOUGH NUMEROUS POLYMORPHISMS HAVE BEEN ASSOCIATED WITH RISK OF DEVELOPING LYMPHOMA, HOW THESE VARIANTS FUNCTION TO PROMOTE TUMORIGENESIS IS POORLY UNDERSTOOD. HERE, WE REPORT THAT LYMPHOMA RISK SNPS, ESPECIALLY IN THE NON-HODGKIN'S LYMPHOMA SUBTYPE CHRONIC LYMPHOCYTIC LEUKEMIA, ARE SIGNIFICANTLY ENRICHED FOR CO-LOCALIZATION WITH EPIGENETIC MARKS OF ACTIVE GENE REGULATION. THESE ENRICHMENTS WERE SEEN IN A LYMPHOID-SPECIFIC MANNER FOR NUMEROUS ENCODE DATASETS, INCLUDING DNASE-HYPERSENSITIVITY AS WELL AS MULTIPLE SEGMENTATION-DEFINED ENHANCER REGIONS. FURTHERMORE, WE IDENTIFY PUTATIVELY FUNCTIONAL SNPS THAT ARE BOTH IN REGULATORY ELEMENTS IN LYMPHOCYTES AND ARE ASSOCIATED WITH GENE EXPRESSION CHANGES IN BLOOD. WE DEVELOPED AN ALGORITHM, UES, THAT USES A MONTE CARLO SIMULATION APPROACH TO CALCULATE THE ENRICHMENT OF PREVIOUSLY IDENTIFIED RISK SNPS IN VARIOUS FUNCTIONAL ELEMENTS. THIS MULTISCALE APPROACH INTEGRATING MULTIPLE DATASETS HELPS DISENTANGLE THE UNDERLYING BIOLOGY OF LYMPHOMA, AND MORE BROADLY, IS GENERALLY APPLICABLE TO GWAS RESULTS FROM OTHER DISEASES AS WELL. 2015 14 5936 26 TARGETING HEPATITIS B VIRUS COVALENTLY CLOSED CIRCULAR DNA AND HEPATITIS B VIRUS X PROTEIN: RECENT ADVANCES AND NEW APPROACHES. CHRONIC HEPATITIS B VIRUS (HBV) INFECTION REMAINS A WORLDWIDE CONCERN AND PUBLIC HEALTH PROBLEM. TWO KEY ASPECTS OF THE HBV LIFE CYCLE ARE ESSENTIAL FOR VIRAL REPLICATION AND THUS THE DEVELOPMENT OF CHRONIC INFECTIONS: THE ESTABLISHMENT OF THE VIRAL MINICHROMOSOME, COVALENTLY CLOSED CIRCULAR (CCC) DNA, WITHIN THE NUCLEUS OF INFECTED HEPATOCYTES AND THE EXPRESSION OF THE REGULATORY HEPATITIS B VIRUS X PROTEIN (HBX). INTERESTINGLY, NUCLEAR HBX REDIRECTS HOST EPIGENETIC MACHINERY TO ACTIVATE CCCDNA TRANSCRIPTION. IN THIS PERSPECTIVE, WE PROVIDE AN OVERVIEW OF RECENT ADVANCES IN UNDERSTANDING THE REGULATION OF CCCDNA AND THE MECHANISTIC AND FUNCTIONAL ROLES OF HBX. WE ALSO DESCRIBE THE PROGRESS TOWARD TARGETING BOTH CCCDNA AND HBX FOR THERAPEUTIC PURPOSES. FINALLY, WE OUTLINE STANDING QUESTIONS IN THE FIELD AND PROPOSE COMPLEMENTARY CHEMICAL BIOLOGY APPROACHES TO ADDRESS THEM. 2019 15 2565 29 EPIGENETICS INVOLVEMENT IN OXALIPLATIN-INDUCED POTASSIUM CHANNEL TRANSCRIPTIONAL DOWNREGULATION AND HYPERSENSITIVITY. PERIPHERAL NEUROPATHY IS THE MOST FREQUENT DOSE-LIMITING ADVERSE EFFECT OF OXALIPLATIN. ACUTE PAIN SYMPTOMS THAT ARE INDUCED OR EXACERBATED BY COLD OCCUR IN ALMOST ALL PATIENTS IMMEDIATELY FOLLOWING THE FIRST INFUSIONS. EVIDENCE HAS SHOWN THAT OXALIPLATIN CAUSES ION CHANNEL EXPRESSION MODULATIONS IN DORSAL ROOT GANGLIA NEURONS, WHICH ARE THOUGHT TO CONTRIBUTE TO PERIPHERAL HYPERSENSITIVITY. MOST DYSREGULATED GENES ENCODE ION CHANNELS INVOLVED IN COLD AND MECHANICAL PERCEPTION, NOTEWORTHY MEMBERS OF A SUB-GROUP OF POTASSIUM CHANNELS OF THE K2P FAMILY, TREK AND TRAAK. DOWNREGULATION OF THESE K2P CHANNELS HAS BEEN IDENTIFIED AS AN IMPORTANT TUNER OF ACUTE OXALIPLATIN-INDUCED HYPERSENSITIVITY. WE INVESTIGATED THE MOLECULAR MECHANISMS UNDERLYING THIS PERIPHERAL DYSREGULATION IN A MURINE MODEL OF NEUROPATHIC PAIN TRIGGERED BY A SINGLE OXALIPLATIN ADMINISTRATION. WE FOUND THAT OXALIPLATIN-MEDIATED TREK-TRAAK DOWNREGULATION, AS WELL AS DOWNREGULATION OF OTHER K(+) CHANNELS OF THE K2P AND KV FAMILIES, INVOLVES A TRANSCRIPTION FACTOR KNOWN AS THE NEURON-RESTRICTIVE SILENCER FACTOR (NRSF) AND ITS EPIGENETIC CO-REPRESSORS HISTONE DEACETYLASES (HDACS). NRSF KNOCKDOWN WAS ABLE TO PREVENT MOST OF THESE K(+) CHANNEL MRNA DOWNREGULATION IN MICE DORSAL ROOT GANGLION NEURONS AS WELL AS OXALIPLATIN-INDUCED ACUTE COLD AND MECHANICAL HYPERSENSITIVITY. INTERESTINGLY, PHARMACOLOGICAL INHIBITION OF CLASS I HDAC REPRODUCES THE ANTINOCICEPTIVE EFFECTS OF NRSF KNOCKDOWN AND LEADS TO AN INCREASED K(+) CHANNEL EXPRESSION IN OXALIPLATIN-TREATED MICE. 2021 16 3754 38 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 17 60 32 A GENOME-WIDE SCREEN REVEALS MICRORNAS IN PERIPHERAL SENSORY NEURONS DRIVING PAINFUL DIABETIC NEUROPATHY. DIABETES IS A LEADING CAUSE OF PERIPHERAL NEUROPATHY (DIABETIC PERIPHERAL NEUROPATHY, DPN), AND UNCONTROLLED LONG-LASTING HYPERGLYCEMIA LEADS TO SEVERE COMPLICATIONS. A MAJOR PROPORTION OF DIABETICS DEVELOP EXCRUCIATING PAIN WITH A VARIABLE COURSE. MECHANISMS LEADING TO PAINFUL DPN ARE NOT COMPLETELY UNDERSTOOD AND TREATMENT OPTIONS LIMITED. WE HYPOTHESIZED THAT EPIGENETIC MODULATION AT THE LEVEL OF MICRORNA (MIRNA) EXPRESSION TRIGGERED BY METABOLIC IMBALANCE AND NERVE DAMAGE REGULATES THE COURSE OF PAIN DEVELOPMENT. WE USED CLINICALLY RELEVANT PRECLINICAL MODELS, GENOME-WIDE SCREENING, IN SILICO ANALYSES, CELLULAR ASSAYS, MIRNA FLUORESCENT IN SITU HYBRIDIZATION, IN VIVO MOLECULAR MANIPULATIONS, AND BEHAVIORAL ANALYSES IN THE CURRENT STUDY. WE IDENTIFIED MIRNAS AND THEIR TARGETS THAT CRITICALLY IMPACT ON NOCICEPTIVE HYPERSENSITIVITY IN PAINFUL DPN. OUR ANALYSES IDENTIFY MIR-33 AND MIR-380 EXPRESSED IN NOCICEPTIVE NEURONS AS CRITICAL DENOMINATORS OF DIABETIC PAIN AND MIR-124-1 AS A MEDIATOR OF PHYSIOLOGICAL NOCICEPTION. OUR COMPREHENSIVE ANALYSES ON THE PUTATIVE MRNA TARGETS FOR MIR-33 OR MIR-124-1 IDENTIFIED A SET OF MRNAS THAT ARE REGULATED AFTER MIR-33 OR MIR-124-1 OVEREXPRESSION IN DORSAL ROOT GANGLIA IN VIVO. OUR RESULTS SHED LIGHT ON THE REGULATION OF DPN PATHOPHYSIOLOGY AND IMPLICATE SPECIFIC MIRNAS AS NOVEL THERAPEUTIC TARGETS FOR TREATING PAINFUL DPN. 2021 18 4713 32 NON-CODING RNA AND N6-METHYLADENOSINE MODIFICATION PLAY CRUCIAL ROLES IN NEUROPATHIC PAIN. AFTER PERIPHERAL NERVE INJURY, PAIN SIGNALS ARE TRANSMITTED FROM PRIMARY SENSORY NEURONS IN THE DORSAL ROOT GANGLION (DRG) TO THE CENTRAL NERVOUS SYSTEM. EPIGENETIC MODIFICATION AFFECTS NEUROPATHIC PAIN THROUGH ALTERATIONS IN THE GENE EXPRESSION IN PAIN-RELATED AREAS AND GLIAL CELL ACTIVATION. RECENT STUDIES HAVE SHOWN THAT NON-CODING RNA AND N6-METHYLADENOSINE (M6A) METHYLATION MODIFICATION PLAY PIVOTAL REGULATORY ROLES IN THE OCCURRENCE AND MAINTENANCE OF NEUROPATHIC PAIN. DYSREGULATION OF THE RNA M6A LEVEL VIA DYNAMIC CHANGES IN METHYLTRANSFERASE AND DEMETHYLASE AFTER CENTRAL OR PERIPHERAL NERVE INJURY COMMONLY REGULATES PAIN-ASSOCIATED GENES, CONTRIBUTING TO THE INDUCTION AND MAINTENANCE OF NEUROPATHIC PAIN. THE DYNAMIC PROCESS HAS SIGNIFICANT IMPLICATIONS FOR THE DEVELOPMENT AND MAINTENANCE OF NEUROPATHIC PAIN. HOWEVER, THE UNDERLYING MECHANISMS BY WHICH NON-CODING RNA AND M6A RNA MODIFICATION REGULATE NEUROPATHIC PAIN ARE NOT WELL-CHARACTERIZED. THIS ARTICLE ELUCIDATES THE MULTIPLE MECHANISMS OF NON-CODING RNA AND M6A METHYLATION IN THE CONTEXT OF NEUROPATHIC PAIN, AND SUMMARIZES ITS POTENTIAL FUNCTIONS AS WELL AS RECENT ADVANCES. 2022 19 1198 47 CORTICOSTERONE-MEDIATED REGULATION AND FUNCTIONS OF MIR-218-5P IN RAT BRAIN. CHRONIC STRESS IS ONE OF THE KEY PRECIPITATING FACTORS IN MAJOR DEPRESSIVE DISORDER (MDD). STRESS ASSOCIATED STUDIES HAVE UNDERSCORED THE MECHANISTIC ROLE OF EPIGENETIC MASTER PLAYERS LIKE MICRORNAS (MIRNAS) IN DEPRESSION PATHOPHYSIOLOGY AT BOTH PRECLINICAL AND CLINICAL LEVELS. PREVIOUSLY, WE HAD REPORTED CHANGES IN MIR-218-5P EXPRESSION IN RESPONSE TO CORTICOSTERONE (CORT) INDUCED CHRONIC STRESS. MIR-218-5P WAS ONE OF THE MOST SIGNIFICANTLY INDUCED MIRNAS IN THE PREFRONTAL CORTEX (PFC) OF RATS UNDER CHRONIC STRESS. IN THE PRESENT REPORT, WE HAVE INVESTIGATED HOW CHRONIC CORT EXPOSURE MECHANISTICALLY AFFECTED MIR-218-5P EXPRESSION IN THE RAT BRAIN AND HOW MIR-218 COULD TRIGGER MOLECULAR CHANGES ON ITS DOWNSTREAM REGULATORY PATHWAYS. ELEVATED EXPRESSION OF MIR-218-5P WAS FOUND IN THE PFC OF CORT-TREATED RATS. A GLUCOCORTICOID RECEPTOR (GR) TARGETED CHROMATIN-IMMUNOPRECIPITATION (CHIP) ASSAY REVEALED HIGH GR OCCUPANCY ON THE PROMOTER REGION OF SLIT3 GENE HOSTING MIR-218-2 IN ITS 3RD INTRON. RNA-SEQUENCING DATA BASED ON RNA INDUCED SILENCING COMPLEX IMMUNOPRECIPITATION (RISC-IP) WITH AGO2 IN SH-SY5Y CELLS DETECTED SIX CONSISTENT TARGET GENES OF MIR-218-5P (APOL4, DTWD1, BNIP1, METTL22, SNAPC1, AND HDAC6). THE EXPRESSION OF ALL FIVE GENES, EXCEPT APOL4, WAS SUCCESSFULLY VALIDATED WITH QPCR IN CORT-TREATED RAT PFC. FURTHER, HDAC6-BASED CHIP-SEQ EXPERIMENT HELPED IN MAPPING MAJOR GENOMIC LOCI ENRICHED FOR INTERGENIC REGIONS IN THE PFC OF CORT-TREATED RAT. A PROXIMITY-BASED GENE ONTOLOGY (GO) ANALYSIS REVEALED A MAJORITY OF THE INTERGENIC SITES TO BE PART OF KEY GENES IMPLICATED IN CENTRAL NERVOUS SYSTEM FUNCTIONS, NOTABLY SYNAPSE ORGANIZATION, NEURON PROJECTION MORPHOGENESIS, AND AXONOGENESIS. OUR RESULTS SUGGEST THAT THE UPREGULATION OF MIR-218-5P IN PFC OF CORT-TREATED RATS POSSIBLY RESULTED FROM GR BIDING IN THE PROMOTER REGION OF SLIT3 GENE. INTERESTINGLY, HDAC6 WAS ONE OF THE CONSISTENT TARGET GENES POTENTIALLY FOUND TO REGULATE CNS RELATED GENES BY CHROMATIN MODIFICATION. COLLECTIVELY, THESE FINDINGS ESTABLISH THE ROLE OF MIR-218-5P IN CHRONIC STRESS AND THE EPIGENETIC FUNCTION IT PLAYS TO INDUCE CHROMATIN-BASED TRANSCRIPTIONAL CHANGES OF SEVERAL CNS GENES IN TRIGGERING STRESS-INDUCED DISORDERS, INCLUDING DEPRESSION. THIS ALSO OPENS UP THE SCOPE TO UNDERSTAND THE ROLE OF MIR-218-5P AS A POTENTIAL TARGET FOR NONCODING RNA THERAPEUTICS IN CLINICAL DEPRESSION. 2022 20 784 30 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