1 4364 123 MIRNA DEREGULATION BY EPIGENETIC SILENCING DISRUPTS SUPPRESSION OF THE ONCOGENE PLAG1 IN CHRONIC LYMPHOCYTIC LEUKEMIA. MICRORNAS (MIRNA) PLAY A KEY ROLE IN CELLULAR REGULATION AND, IF DEREGULATED, IN THE DEVELOPMENT OF NEOPLASTIC DISORDERS INCLUDING CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). RNAS FROM PRIMARY CELLS OF 50 TREATMENT-NAIVE CLL PATIENTS AND PERIPHERAL B CELLS OF 14 HEALTHY DONORS WERE APPLIED TO MIRNA EXPRESSION PROFILING USING BEAD CHIP TECHNOLOGY. IN CLL CELLS, A SET OF 7 UP- AND 19 DOWN-REGULATED MIRNAS WAS IDENTIFIED. AMONG THE MIRNAS DOWN-REGULATED IN CLL CELLS, 6 OF 10 MIRNA PROMOTERS EXAMINED SHOWED GAIN OF METHYLATION COMPARED WITH NORMAL B-CELL CONTROLS. SUBSEQUENT TARGET PREDICTION OF DEREGULATED MIRNAS REVEALED A HIGHLY SIGNIFICANT BINDING PREDICTION AT THE 3' UNTRANSLATED REGION OF THE PLEOMORPHIC ADENOMA GENE 1 (PLAG1) ONCOGENE. LUCIFERASE REPORTER ASSAYS INCLUDING SITE-DIRECTED MUTAGENESIS OF BINDING SITES REVEALED A SIGNIFICANT REGULATION OF PLAG1 BY MIR-181A, MIR-181B, MIR-107, AND MIR-424. ALTHOUGH EXPRESSION OF PLAG1 MRNA WAS NOT AFFECTED, PLAG1 PROTEIN EXPRESSION WAS SHOWN TO BE SIGNIFICANTLY ELEVATED IN CLL CELLS COMPARED WITH THE LEVELS IN HEALTHY DONOR B CELLS. IN SUMMARY, WE COULD DEMONSTRATE DISRUPTION OF MIRNA-MEDIATED TRANSLATIONAL CONTROL, PARTLY DUE TO EPIGENETIC TRANSCRIPTIONAL SILENCING OF MIRNAS, WITH SUBSEQUENT OVEREXPRESSION OF THE ONCOGENIC TRANSCRIPTION FACTOR PLAG1 AS A PUTATIVE NOVEL MECHANISM OF CLL PATHOGENESIS. 2009 2 1227 46 CRITICAL ROLE OF MICRORNAS IN CHRONIC LYMPHOCYTIC LEUKEMIA: OVEREXPRESSION OF THE ONCOGENE PLAG1 BY DEREGULATED MIRNAS. MICRORNAS (MIRNAS) ARE SMALL, GENE ENCODED RNAS WHICH ARE ABLE TO INFLUENCE GENE EXPRESSION IN BINDING TO THE 3'UTR OF MRNAS. COMPARED TO HEALTHY TISSUES, THE GLOBAL EXPRESSION OF MIRNAS IN CANCEROUS TISSUE IS FREQUENTLY DOWN-REGULATED. LIKEWISE IN CHRONIC LYMPHOCYTIC LEUKEMIA (CLL), DOWN-REGULATION OF SEVERAL MIRNAS HAS BEEN REPORTED. ANALYSIS OF MIRNA PROMOTERS FOR EPIGENETIC MODIFICATIONS REVEALED A STRONGER METHYLATION OF DOWN-REGULATED MIRNAS IN CLL. TO DATE, SEVERAL TARGET GENES AFFECTED BY DEREGULATED MIRNAS HAVE BEEN IDENTIFIED THAT HAVE IMPACT ON CLL PATHOGENESIS. THE BEST-DESCRIBED CONSEQUENCE OF MIRNA DEREGULATION IS FOR MIRNA-15/16 CLUSTER DELETION, WHICH IS FREQUENTLY DOWN-REGULATED IN A SUBGROUP OF PATIENTS WITH CLL CARRYING 13Q14 DELETION. SO FAR, MODELS FOR MIRNA DEREGULATION HAVE ADDRESSED JUST SINGLE MIRNAS. FOR ASSESSMENT OF COMPLETE MIRNA DEREGULATION, FURTHER EVALUATION OF THE RESULTS FROM MICROARRAY STUDIES IS NEEDED. PREVIOUSLY WE IDENTIFIED THE ONCOGENE PLAG1, WHOSE EXPRESSION IS AFFECTED BY VARIOUS MIRNAS DEREGULATED IN CLL. THE INVOLVEMENT OF MIRNAS IN PLAG1 EXPRESSION WAS SHOWN TO BE RELEVANT IN PLEOMORPHIC ADENOMAS OF THE SALIVARY GLAND, TOO. AS PLAG1 IS HIGHLY OVEREXPRESSED, AND ITS TARGET GENES APPEAR TO BE DEREGULATED IN CLL, E.G. BCL-2, PLAG1 IS A PUTATIVE NEW RELEVANT ONCOGENE INVOLVED IN THE PATHOGENESIS OF CLL. 2010 3 129 29 A UNIQUE VIRULENCE GENE OCCUPIES A PRINCIPAL POSITION IN IMMUNE EVASION BY THE MALARIA PARASITE PLASMODIUM FALCIPARUM. MUTUALLY EXCLUSIVE GENE EXPRESSION, WHEREBY ONLY ONE MEMBER OF A MULTI-GENE FAMILY IS SELECTED FOR ACTIVATION, IS USED BY THE MALARIA PARASITE PLASMODIUM FALCIPARUM TO ESCAPE THE HUMAN IMMUNE SYSTEM AND PERPETUATE LONG-TERM, CHRONIC INFECTIONS. A FAMILY OF GENES CALLED VAR ENCODES THE CHIEF ANTIGENIC AND VIRULENCE DETERMINANT OF P. FALCIPARUM MALARIA. VAR GENES ARE TRANSCRIBED IN A MUTUALLY EXCLUSIVE MANNER, WITH SWITCHING BETWEEN ACTIVE GENES RESULTING IN ANTIGENIC VARIATION. WHILE RECENT WORK HAS SHED CONSIDERABLE LIGHT ON THE EPIGENETIC BASIS FOR VAR GENE ACTIVATION AND SILENCING, HOW SWITCHING IS CONTROLLED REMAINS A MYSTERY. IN PARTICULAR, SWITCHING SEEMS NOT TO BE RANDOM, BUT INSTEAD APPEARS TO BE COORDINATED TO RESULT IN TIMELY ACTIVATION OF INDIVIDUAL GENES LEADING TO SEQUENTIAL WAVES OF ANTIGENICALLY DISTINCT PARASITE POPULATIONS. THE MOLECULAR BASIS FOR THIS APPARENT COORDINATION IS UNKNOWN. HERE WE SHOW THAT VAR2CSA, AN UNUSUAL AND HIGHLY CONSERVED VAR GENE, OCCUPIES A UNIQUE POSITION WITHIN THE VAR GENE SWITCHING HIERARCHY. INDUCTION OF SWITCHING THROUGH THE DESTABILIZATION OF VAR SPECIFIC CHROMATIN USING BOTH GENETIC AND CHEMICAL METHODS REPEATEDLY LED TO THE RAPID AND EXCLUSIVE ACTIVATION OF VAR2CSA. ADDITIONAL EXPERIMENTS DEMONSTRATED THAT THESE REPRESENT "TRUE" SWITCHING EVENTS AND NOT SIMPLY DE-SILENCING OF THE VAR2CSA PROMOTER, AND THAT ACTIVATION IS LIMITED TO THE UNIQUE LOCUS ON CHROMOSOME 12. COMBINED WITH TRANSLATIONAL REPRESSION OF VAR2CSA TRANSCRIPTS, FREQUENT "DEFAULT" SWITCHING TO THIS LOCUS AND DETECTION OF VAR2CSA UNTRANSLATED TRANSCRIPTS IN NON-PREGNANT INDIVIDUALS, THESE DATA SUGGEST THAT VAR2CSA COULD PLAY A CENTRAL ROLE IN COORDINATING SWITCHING, FULFILLING A PREDICTION MADE BY MATHEMATICAL MODELS DERIVED FROM POPULATION SWITCHING PATTERNS. THESE STUDIES PROVIDE THE FIRST INSIGHTS INTO THE MECHANISMS BY WHICH VAR GENE SWITCHING IS COORDINATED AS WELL AS AN EXAMPLE OF HOW A PHARMACOLOGICAL AGENT CAN DISRUPT ANTIGENIC VARIATION IN PLASMODIUM FALCIPARUM. 2015 4 5981 33 TET2 PROMOTES PATHOGEN INFECTION-INDUCED MYELOPOIESIS THROUGH MRNA OXIDATION. VARIETIES OF RNA MODIFICATION FORM THE EPITRANSCRIPTOME FOR POST-TRANSCRIPTIONAL REGULATION. 5-METHYLCYTOSINE (5-MC) IS A SPARSE RNA MODIFICATION IN MESSENGER RNA (MRNA) UNDER PHYSIOLOGICAL CONDITIONS. THE FUNCTION OF RNA 5-HYDROXYMETHYLCYTOSINE (5-HMC) OXIDIZED BY TEN-ELEVEN TRANSLOCATION (TET) PROTEINS IN DROSOPHILA HAS BEEN REVEALED MORE RECENTLY. HOWEVER, THE TURNOVER AND FUNCTION OF 5-MC IN MAMMALIAN MRNA HAVE BEEN LARGELY UNKNOWN. TET2 SUPPRESSES MYELOID MALIGNANCIES MOSTLY IN AN ENZYMATIC ACTIVITY-DEPENDENT MANNER, AND IS IMPORTANT IN RESOLVING INFLAMMATORY RESPONSE IN AN ENZYMATIC ACTIVITY-INDEPENDENT WAY. MYELOPOIESIS IS A COMMON HOST IMMUNE RESPONSE IN ACUTE AND CHRONIC INFECTIONS; HOWEVER, ITS EPIGENETIC MECHANISM NEEDS TO BE IDENTIFIED. HERE WE DEMONSTRATE THAT TET2 PROMOTES INFECTION-INDUCED MYELOPOIESIS IN AN MRNA OXIDATION-DEPENDENT MANNER THROUGH ADAR1-MEDIATED REPRESSION OF SOCS3 EXPRESSION AT THE POST-TRANSCRIPTION LEVEL. TET2 PROMOTES BOTH ABDOMINAL SEPSIS-INDUCED EMERGENCY MYELOPOIESIS AND PARASITE-INDUCED MAST CELL EXPANSION THROUGH DECREASING MRNA LEVELS OF SOCS3, A KEY NEGATIVE REGULATOR OF THE JAK-STAT PATHWAY THAT IS CRITICAL FOR CYTOKINE-INDUCED MYELOPOIESIS. TET2 REPRESSES SOCS3 EXPRESSION THROUGH ADAR1, WHICH BINDS AND DESTABILIZES SOCS3 MRNA IN A RNA EDITING-INDEPENDENT MANNER. FOR THE UNDERLYING MECHANISM OF TET2 REGULATION AT THE MRNA LEVEL, TET2 MEDIATES OXIDATION OF 5-MC IN MRNA. TET2 DEFICIENCY LEADS TO THE TRANSCRIPTOME-WIDE APPEARANCE OF METHYLATED CYTOSINES, INCLUDING ONES IN THE 3' UNTRANSLATED REGION OF SOCS3, WHICH INFLUENCES DOUBLE-STRANDED RNA FORMATION FOR ADAR1 BINDING, PROBABLY THROUGH CYTOSINE METHYLATION-SPECIFIC READERS, SUCH AS RNA HELICASES. OUR STUDY REVEALS A PREVIOUSLY UNKNOWN REGULATORY ROLE OF TET2 AT THE EPITRANSCRIPTOMIC LEVEL, PROMOTING MYELOPOIESIS DURING INFECTION IN THE MAMMALIAN SYSTEM BY DECREASING 5-MCS IN MRNAS. MOREOVER, THE INHIBITORY FUNCTION OF CYTOSINE METHYLATION ON DOUBLE-STRANDED RNA FORMATION AND ADAR1 BINDING IN MRNA REVEALS ITS NEW PHYSIOLOGICAL ROLE IN THE MAMMALIAN SYSTEM. 2018 5 5955 34 TELBIVUDINE TREATMENT CORRECTS HBV-INDUCED EPIGENETIC ALTERATIONS IN LIVER CELLS OF PATIENTS WITH CHRONIC HEPATITIS B. HEPATITIS B VIRUS (HBV) ALTERS THE EXPRESSION OF HOST CELLULAR GENES TO SUPPORT ITS REPLICATION AND SURVIVAL AND TO PROMOTE THE LIVER CELL INJURY. HOWEVER, THE UNDERLYING MECHANISM REMAINED INCOMPLETELY UNDERSTOOD. IN THIS STUDY, WE INVESTIGATED HBV-INDUCED EPIGENETIC CHANGES IN HEPG2 CELLS BY PROFILING THE LANDSCAPES OF THE ACTIVE HISTONE MODIFICATION MARK H3K4ME3 AND REPRESSIVE MARK H3K27ME3 USING CHROMATIN IMMUNOPRECIPITATION-SEQUENCING. HBV CAUSED THE ALTERED HISTONE MODIFICATIONS AT THOUSANDS OF GENOMIC LOCI, WHICH ARE CRITICALLY INVOLVED IN HBV ENTRY, INFLAMMATION, FIBROSIS AND CARCINOGENESIS OF HOST CELLS. INTERESTINGLY, TREATMENT OF THE HBV-TRANSFORMED HEPG2 CELLS WITH THE ANTI-HBV DRUG TELBIVUDINE SUBSTANTIALLY RESTORED THE H3K4ME3 LEVEL TO THAT OF UNTRANSFORMED HEPG2 CELLS. MORE IMPORTANTLY, OUR ANALYSIS OF LIVER SAMPLES FROM CONTROL AND CHRONIC HEPATITIS B PATIENTS REVEALED THAT TREATMENT OF THE PATIENTS WITH TELBIVUDINE NOT ONLY CORRECTED THE TARGET GENE EXPRESSION BUT ALSO THE EPIGENETIC MODIFICATION OF CRITICAL GENES. IN ADDITION, THE EXPRESSION OF THE HISTONE METHYLTRANSFERASES SMYD3 AND EZH2 THAT REGULATE HISTONE H3-SPECIFIC METHYLATION SHOWED NO DIFFERENCE IN HEPG2 CELL WITH OR WITHOUT HBV EXISTENCE. THUS, OUR DATA SUGGEST THAT ABNORMAL HISTONE MODIFICATIONS MIGHT CRITICALLY INVOLVED IN HBV-MEDIATED LIVER PATHOGENESIS AND TELBIVUDINE THERAPY MIGHT BENEFIT PATIENTS WITH HBV-RELATED CHRONIC INFECTION, LIVER CIRRHOSIS AND EVEN HEPATIC CARCINOMA. SUMMARY: TELBIVUDINE SUBSTANTIALLY RESTORES IN VITRO AND IN VIVO HBV-CAUSED ABNORMAL EXPRESSIONS AND HISTONE H3K4ME3 AND H3K27ME3 MODIFICATIONS AT THOUSANDS OF GENOMIC LOCI THAT ARE INVOLVED IN THE PATHOGENESIS OF LIVER CELLS, REVEALING A NOVEL MECHANISM FOR HBV-MEDIATED LIVER DAMAGE. 2014 6 1219 32 CRISPR/CAS9 GENOME EDITING REVEALS THAT THE INTRON IS NOT ESSENTIAL FOR VAR2CSA GENE ACTIVATION OR SILENCING IN PLASMODIUM FALCIPARUM. PLASMODIUM FALCIPARUM RELIES ON MONOALLELIC EXPRESSION OF 1 OF 60 VAR VIRULENCE GENES FOR ANTIGENIC VARIATION AND HOST IMMUNE EVASION. EACH VAR GENE CONTAINS A CONSERVED INTRON WHICH HAS BEEN IMPLICATED IN PREVIOUS STUDIES IN BOTH ACTIVATION AND REPRESSION OF TRANSCRIPTION VIA SEVERAL EPIGENETIC MECHANISMS, INCLUDING INTERACTION WITH THE VAR PROMOTER, PRODUCTION OF LONG NONCODING RNAS (LNCRNAS), AND LOCALIZATION TO REPRESSIVE PERINUCLEAR SITES. HOWEVER, FUNCTIONAL STUDIES HAVE RELIED PRIMARILY ON ARTIFICIAL EXPRESSION CONSTRUCTS. USING THE RECENTLY DEVELOPED P. FALCIPARUM CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS (CRISPR)/CAS9 SYSTEM, WE DIRECTLY DELETED THE VAR2CSA P. FALCIPARUM 3D7_1200600 (PF3D7_1200600) ENDOGENOUS INTRON, RESULTING IN AN INTRONLESS VAR GENE IN A NATURAL, MARKER-FREE CHROMOSOMAL CONTEXT. DELETION OF THE VAR2CSA INTRON RESULTED IN AN UPREGULATION OF TRANSCRIPTION OF THE VAR2CSA GENE IN RING-STAGE PARASITES AND SUBSEQUENT EXPRESSION OF THE PFEMP1 PROTEIN IN LATE-STAGE PARASITES. INTRON DELETION DID NOT AFFECT THE NORMAL TEMPORAL REGULATION AND SUBSEQUENT TRANSCRIPTIONAL SILENCING OF THE VAR GENE IN TROPHOZOITES BUT DID RESULT IN INCREASED RATES OF VAR GENE SWITCHING IN SOME MUTANT CLONES. TRANSCRIPTIONAL REPRESSION OF THE INTRONLESS VAR2CSA GENE COULD BE ACHIEVED VIA LONG-TERM CULTURE OR PANNING WITH THE CD36 RECEPTOR, AFTER WHICH REACTIVATION WAS POSSIBLE WITH CHONDROITIN SULFATE A (CSA) PANNING. THESE DATA SUGGEST THAT THE VAR2CSA INTRON IS NOT REQUIRED FOR SILENCING OR ACTIVATION IN RING-STAGE PARASITES BUT POINT TO A SUBTLE ROLE IN REGULATION OF SWITCHING WITHIN THE VAR GENE FAMILY.IMPORTANCEPLASMODIUM FALCIPARUM IS THE MOST VIRULENT SPECIES OF MALARIA PARASITE, CAUSING HIGH RATES OF MORBIDITY AND MORTALITY IN THOSE INFECTED. CHRONIC INFECTION DEPENDS ON AN IMMUNE EVASION MECHANISM TERMED ANTIGENIC VARIATION, WHICH IN TURN RELIES ON MONOALLELIC EXPRESSION OF 1 OF ~60 VAR GENES. UNDERSTANDING ANTIGENIC VARIATION AND THE TRANSCRIPTIONAL REGULATION OF MONOALLELIC EXPRESSION IS IMPORTANT FOR DEVELOPING DRUGS AND/OR VACCINES. THE VAR GENE FAMILY ENCODES THE ANTIGENIC SURFACE PROTEINS THAT DECORATE INFECTED ERYTHROCYTES. UNTIL RECENTLY, STUDYING THE UNDERLYING GENETIC ELEMENTS THAT REGULATE MONOALLELIC EXPRESSION IN P. FALCIPARUM WAS DIFFICULT, AND MOST STUDIES RELIED ON ARTIFICIAL SYSTEMS SUCH AS EPISOMAL REPORTER GENES. OUR STUDY WAS THE FIRST TO USE CRISPR/CAS9 GENOME EDITING FOR THE FUNCTIONAL STUDY OF AN IMPORTANT, CONSERVED GENETIC ELEMENT OF VAR GENES-THE INTRON-IN AN ENDOGENOUS, EPISOME-FREE MANNER. OUR FINDINGS SHED LIGHT ON THE ROLE OF THE VAR GENE INTRON IN TRANSCRIPTIONAL REGULATION OF MONOALLELIC EXPRESSION. 2017 7 5529 23 RNA N(6) -METHYLADENOSINE MODIFICATIONS AND POTENTIAL TARGETED THERAPEUTIC STRATEGIES IN KIDNEY DISEASE. EPIGENETIC MODIFICATIONS HAVE RECEIVED INCREASING ATTENTION AND HAVE BEEN SHOWN TO BE EXTENSIVELY INVOLVED IN KIDNEY DEVELOPMENT AND DISEASE PROGRESSION. AMONG THEM, THE MOST COMMON RNA MODIFICATION, N(6) -METHYLADENOSINE (M(6) A), HAS BEEN SHOWN TO DYNAMICALLY AND REVERSIBLY EXERT ITS FUNCTIONS IN MULTIPLE WAYS, INCLUDING SPLICING, EXPORT, DECAY AND TRANSLATION INITIATION EFFICIENCY TO REGULATE MRNA FATE. MOREOVER, M(6) A HAS ALSO BEEN REPORTED TO EXERT BIOLOGICAL EFFECTS BY DESTABILIZING BASE PAIRING TO MODULATE VARIOUS FUNCTIONS OF RNAS. MOST IMPORTANTLY, AN INCREASING NUMBER OF KIDNEY DISEASES, SUCH AS RENAL CELL CARCINOMA, ACUTE KIDNEY INJURY AND CHRONIC KIDNEY DISEASE, HAVE BEEN FOUND TO BE ASSOCIATED WITH ABERRANT M(6) A PATTERNS. IN THIS REVIEW, WE COMPREHENSIVELY REVIEW THE CRITICAL ROLES OF M(6) A IN KIDNEY DISEASES AND DISCUSS THE POSSIBILITIES AND RELEVANCE OF M(6) A-TARGETED EPIGENETIC THERAPY, WITH AN INTEGRATED COMPREHENSIVE DESCRIPTION OF THE DETAILED ALTERATIONS IN SPECIFIC LOCI THAT CONTRIBUTE TO CELLULAR PROCESSES THAT ARE ASSOCIATED WITH KIDNEY DISEASES. 2023 8 6229 24 THE LNCRNAS IN HBV-RELATED HCCS: TARGETING CHROMATIN DYNAMICS AND BEYOND. HEPATOCELLULAR CARCINOMA (HCC) REPRESENTS THE FOURTH LEADING AND FASTEST RISING CAUSE OF CANCER DEATH (841,000 NEW CASES AND 782,000 DEATHS ANNUALLY), AND HEPATITIS B (HBV), WITH 250 MILLION PEOPLE CHRONICALLY INFECTED AT RISK OF DEVELOPING HCC, ACCOUNTS FOR >50% OF THE CASES WORLDWIDE. LONG NON-CODING RNAS (LNCRNAS), UNTRANSLATED TRANSCRIPTS LONGER THAN 200 NUCLEOTIDES, ARE IMPLICATED IN GENE REGULATION AT THE TRANSCRIPTIONAL AND POST-TRANSCRIPTIONAL LEVELS, EXERTING THEIR ACTIVITIES BOTH IN THE NUCLEAR AND CYTOPLASMIC COMPARTMENTS. THANKS TO HIGH-THROUGHPUT SEQUENCING TECHNIQUES, SEVERAL LNCRNAS HAVE BEEN SHOWN TO FAVOR THE ESTABLISHMENT OF CHRONIC HBV INFECTION, TO CHANGE THE HOST TRANSCRIPTOME TO ESTABLISH A PRO-CARCINOGENIC ENVIRONMENT, AND TO DIRECTLY PARTICIPATE IN HCC DEVELOPMENT AND PROGRESSION. IN THIS REVIEW, WE SUMMARIZE CURRENT KNOWLEDGE ON THE ROLE OF LNCRNAS IN HBV INFECTION AND HBV-RELATED LIVER CARCINOGENESIS AND DISCUSS THE POTENTIAL OF LNCRNAS AS PREDICTIVE OR DIAGNOSTIC BIOMARKERS. 2021 9 17 18 5' FLANKING REGION OF VAR GENES NUCLEATE HISTONE MODIFICATION PATTERNS LINKED TO PHENOTYPIC INHERITANCE OF VIRULENCE TRAITS IN MALARIA PARASITES. IN THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM ANTIGENIC VARIATION FACILITATES LONG-TERM CHRONIC INFECTION OF THE HOST. THIS IS ACHIEVED BY SEQUENTIAL EXPRESSION OF A SINGLE MEMBER OF THE 60-MEMBER VAR FAMILY. HERE WE SHOW THAT THE 5' FLANKING REGION NUCLEATES EPIGENETIC EVENTS STRONGLY LINKED TO THE MAINTENANCE OF MONO-ALLELIC VAR GENE EXPRESSION PATTERN DURING PARASITE PROLIFERATION. TRI- AND DIMETHYLATION OF HISTONE H3 LYSINE 4 PEAK IN THE 5' UPSTREAM REGION OF TRANSCRIBED VAR AND DURING THE POISED STATE (NON-TRANSCRIBED PHASE OF VAR GENES DURING THE 48 H ASEXUAL LIFE CYCLE), 'BOOKMARKING' THIS MEMBER FOR RE-ACTIVATION AT THE ONSET OF THE NEXT CYCLE. HISTONE H3 LYSINE 9 TRIMETHYLATION ACTS AS AN ANTAGONIST TO LYSINE 4 METHYLATION TO ESTABLISH STABLY SILENT VAR GENE STATES ALONG THE 5' FLANKING AND CODING REGION. FURTHERMORE, WE SHOW THAT COMPETITION EXISTS BETWEEN H3K9 METHYLATION AND H3K9 ACETYLATION IN THE 5' FLANKING REGION AND THAT THESE MARKS CONTRIBUTE EPIGENETICALLY TO REPRESSING OR ACTIVATING VAR GENE EXPRESSION. OUR WORK POINTS TO A PIVOTAL ROLE OF THE HISTONE METHYL MARK WRITING AND READING MACHINERY IN THE PHENOTYPIC INHERITANCE OF VIRULENCE TRAITS IN THE MALARIA PARASITE. 2007 10 1218 26 CRISPR INTERFERENCE OF A CLONALLY VARIANT GC-RICH NONCODING RNA FAMILY LEADS TO GENERAL REPRESSION OF VAR GENES IN PLASMODIUM FALCIPARUM. THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM USES MUTUALLY EXCLUSIVE EXPRESSION OF THE PFEMP1-ENCODING VAR GENE FAMILY TO EVADE THE HOST IMMUNE SYSTEM. DESPITE PROGRESS IN THE MOLECULAR UNDERSTANDING OF THE DEFAULT SILENCING MECHANISM, THE ACTIVATION MECHANISM OF THE UNIQUELY EXPRESSED VAR MEMBER REMAINS ELUSIVE. A GC-RICH NONCODING RNA (NCRNA) GENE FAMILY HAS COEVOLVED WITH PLASMODIUM SPECIES THAT EXPRESS VAR GENES. HERE, WE SHOW THAT THIS NCRNA FAMILY IS TRANSCRIBED IN A CLONALLY VARIANT MANNER, WITH PREDOMINANT TRANSCRIPTION OF A SINGLE MEMBER OCCURRING WHEN THE NCRNA IS LOCATED ADJACENT TO AND UPSTREAM OF AN ACTIVE VAR GENE. WE DEVELOPED A SPECIFIC CRISPR INTERFERENCE (CRISPRI) STRATEGY THAT ALLOWED FOR THE TRANSCRIPTIONAL REPRESSION OF ALL GC-RICH MEMBERS. A LACK OF GC-RICH NCRNA TRANSCRIPTION LED TO THE DOWNREGULATION OF THE ENTIRE VAR GENE FAMILY IN RING-STAGE PARASITES. STRIKINGLY, IN MATURE BLOOD-STAGE PARASITES, THE GC-RICH NCRNA CRISPRI AFFECTED THE TRANSCRIPTION PATTERNS OF OTHER CLONALLY VARIANT GENE FAMILIES, INCLUDING THE DOWNREGULATION OF ALL PFMC-2TM MEMBERS. WE PROVIDE EVIDENCE FOR THE KEY ROLE OF GC-RICH NCRNA TRANSCRIPTION IN VAR GENE ACTIVATION AND DISCOVERED A MOLECULAR LINK BETWEEN THE TRANSCRIPTIONAL CONTROL OF VARIOUS CLONALLY VARIANT MULTIGENE FAMILIES INVOLVED IN PARASITE VIRULENCE. THIS WORK OPENS NEW AVENUES FOR ELUCIDATING THE MOLECULAR PROCESSES THAT CONTROL IMMUNE EVASION AND PATHOGENESIS IN P. FALCIPARUMIMPORTANCEPLASMODIUM FALCIPARUM IS THE DEADLIEST MALARIA PARASITE SPECIES, ACCOUNTING FOR THE VAST MAJORITY OF DISEASE CASES AND DEATHS. THE VIRULENCE OF THIS PARASITE IS RELIANT UPON THE MUTUALLY EXCLUSIVE EXPRESSION OF CYTOADHERENCE PROTEINS ENCODED BY THE 60-MEMBER VAR GENE FAMILY. ANTIGENIC VARIATION OF THIS MULTIGENE FAMILY SERVES AS AN IMMUNE EVASION MECHANISM, ULTIMATELY LEADING TO CHRONIC INFECTION AND PATHOGENESIS. UNDERSTANDING THE REGULATION MECHANISM OF ANTIGENIC VARIATION IS KEY TO DEVELOPING NEW THERAPEUTIC AND CONTROL STRATEGIES. OUR STUDY UNCOVERS A NOVEL LAYER IN THE EPIGENETIC REGULATION OF TRANSCRIPTION OF THIS FAMILY OF VIRULENCE GENES BY MEANS OF A MULTIGENE-TARGETING CRISPR INTERFERENCE APPROACH. 2020 11 2481 40 EPIGENETIC UPREGULATION OF LNCRNAS AT 13Q14.3 IN LEUKEMIA IS LINKED TO THE IN CIS DOWNREGULATION OF A GENE CLUSTER THAT TARGETS NF-KB. NON-CODING RNAS ARE MUCH MORE COMMON THAN PREVIOUSLY THOUGHT. HOWEVER, FOR THE VAST MAJORITY OF NON-CODING RNAS, THE CELLULAR FUNCTION REMAINS ENIGMATIC. THE TWO LONG NON-CODING RNA (LNCRNA) GENES DLEU1 AND DLEU2 MAP TO A CRITICAL REGION AT CHROMOSOMAL BAND 13Q14.3 THAT IS RECURRENTLY DELETED IN SOLID TUMORS AND HEMATOPOIETIC MALIGNANCIES LIKE CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). WHILE NO POINT MUTATIONS HAVE BEEN FOUND IN THE PROTEIN CODING CANDIDATE GENES AT 13Q14.3, THEY ARE DEREGULATED IN MALIGNANT CELLS, SUGGESTING AN EPIGENETIC TUMOR SUPPRESSOR MECHANISM. WE THEREFORE CHARACTERIZED THE EPIGENETIC MAKEUP OF 13Q14.3 IN CLL CELLS AND FOUND HISTONE MODIFICATIONS BY CHROMATIN-IMMUNOPRECIPITATION (CHIP) THAT ARE ASSOCIATED WITH ACTIVATED TRANSCRIPTION AND SIGNIFICANT DNA-DEMETHYLATION AT THE TRANSCRIPTIONAL START SITES OF DLEU1 AND DLEU2 USING 5 DIFFERENT SEMI-QUANTITATIVE AND QUANTITATIVE METHODS (APRIMES, BIOCOBRA, MCIP, MASSARRAY, AND BISULFITE SEQUENCING). THESE EPIGENETIC ABERRATIONS WERE CORRELATED WITH TRANSCRIPTIONAL DEREGULATION OF THE NEIGHBORING CANDIDATE TUMOR SUPPRESSOR GENES, SUGGESTING A COREGULATION IN CIS OF THIS GENE CLUSTER. WE FOUND THAT THE 13Q14.3 GENES IN ADDITION TO THEIR PREVIOUSLY KNOWN FUNCTIONS REGULATE NF-KB ACTIVITY, WHICH WE COULD SHOW AFTER OVEREXPRESSION, SIRNA-MEDIATED KNOCKDOWN, AND DOMINANT-NEGATIVE MUTANT GENES BY USING WESTERN BLOTS WITH PREVIOUSLY UNDESCRIBED ANTIBODIES, BY A CUSTOMIZED ELISA AS WELL AS BY REPORTER ASSAYS. IN ADDITION, WE PERFORMED AN UNBIASED SCREEN OF 810 HUMAN MIRNAS AND IDENTIFIED THE MIR-15/16 FAMILY OF GENES AT 13Q14.3 AS THE STRONGEST INDUCERS OF NF-KB ACTIVITY. IN SUMMARY, THE TUMOR SUPPRESSOR MECHANISM AT 13Q14.3 IS A CLUSTER OF GENES CONTROLLED BY TWO LNCRNA GENES THAT ARE REGULATED BY DNA-METHYLATION AND HISTONE MODIFICATIONS AND WHOSE MEMBERS ALL REGULATE NF-KB. THEREFORE, THE TUMOR SUPPRESSOR MECHANISM IN 13Q14.3 UNDERLINES THE ROLE BOTH OF EPIGENETIC ABERRATIONS AND OF LNCRNA GENES IN HUMAN TUMORIGENESIS AND IS AN EXAMPLE OF COLOCALIZATION OF A FUNCTIONALLY RELATED GENE CLUSTER. 2013 12 6047 35 THE COMPUTATIONAL ANALYSIS CONDUCTED ON MIRNA TARGET SITES IN ASSOCIATION WITH SNPS AT 3'UTR OF ADHD-IMPLICATED GENES. BACKGROUND: ATTENTION-DEFICIT/HYPERACTIVITY DISORDER (ADHD) IS A FREQUENT CHRONIC NEUROPSYCHIATRIC DISORDER IN WHICH DIFFERENT FACTORS INCLUDING ENVIRONMENTAL, GENETIC, AND EPIGENETIC FACTORS PLAY AN IMPORTANT ROLE IN ITS PATHOGENESIS. ONE OF THE EFFECTIVE EPIGENETIC FACTORS IS RECOGNIZED AS MICRORNAS (MIRNAS). ON THE OTHER HAND, IT HAS BEEN INDICATED THAT THE SINGLE NUCLEOTIDE POLYMORPHISM (SNPS) PRESENT WITHIN 3'UTR (3' UNTRANSLATED REGION) OF MRNAS CAN INFLUENCE THE REGULATION OF MIRNA-MEDIATED GENE AND SUSCEPTIBILITY TO A DIVERSITY OF HUMAN DISEASES. METHODS: THE PURPOSE OF THIS STUDY WAS TO ANALYZE THE SNPS WITHIN THE 3'UTR OF MIRNA TARGET GENES ASSOCIATED WITH ADHD. 3'UTR GENETIC VARIANTS WERE IDENTIFIED IN ALL GENES ASSOCIATED WITH ADHD USING DISGENET, DBGAP, OVID, DAVID, WEB OF KNOWLEDGE, AND SNPS DATABASES. MIRNA'S TARGET PREDICTION DATABASES WERE APPLIED IN ORDER TO PREDICT THE MIRNA BINDING SITES. 124 SNPS WITH MAF>0.05 WERE IDENTIFIED LOCATED IN THE BINDING SITE OF THE MIRNA OF 35 GENES AMONGST 51 GENES ASSOCIATED WITH ADHD. RESULTS: BIOINFORMATICS ANALYSIS PREDICTED 81 MRE (MIRNA RECOGNITION ELEMENTS)-CREATING SNPS, 101 MRE-BREAKING SNPS, 61 MRE-ENHANCING SNPS, AND FINALLY PREDICTED 41 MREDECREASING SNPS IN THE 3'UTR OF ADHD-IMPLICATED GENES. THESE CANDIDATE SNPS WITHIN THESE GENES MIRNA BINDING SITES CAN ALTER THE MIRNAS BINDING, AND CONSEQUENTLY, LEAD TO MRNA GENE REGULATION. CONCLUSION: THEREFORE, THESE MIRNA AND MRE-SNPS MAY PLAY IMPORTANT ROLES IN ADHD, AND BECAUSE OF THAT, THEY WOULD BE VALUABLE FOR FURTHER INVESTIGATION IN THE FIELD OF FUNCTIONAL VERIFICATION. 2020 13 5120 33 POSSIBLE EPIGENETIC REGULATORY EFFECT OF DYSREGULATED CIRCULAR RNAS IN EPILEPSY. CIRCULAR RNAS (CIRCRNAS) INVOLVE IN THE EPIGENETIC REGULATION AND ITS MAJOR MECHANISM IS THE SEQUESTRATION OF THE TARGET MICRO RNAS (MIRNAS). WE HYPOTHESIZED THAT CIRCRNAS MIGHT BE RELATED WITH THE PATHOPHYSIOLOGY OF CHRONIC EPILEPSY AND EVALUATED THE ALTERED CIRCRNA EXPRESSIONS AND THEIR POSSIBLE REGULATORY EFFECTS ON THEIR TARGET MIRNAS AND MRNAS IN A MOUSE EPILEPSY MODEL. THE CIRCRNA EXPRESSION PROFILE IN THE HIPPOCAMPUS OF THE PILOCARPINE MICE WAS ANALYZED AND COMPARED WITH CONTROL. THE CORRELATION BETWEEN THE EXPRESSION OF MIRNA BINDING SITES (MIRNA RESPONSE ELEMENTS, MRE) IN THE DYSREGULATED CIRCRNAS AND THE EXPRESSION OF THEIR TARGET MIRNAS WAS EVALUATED. AS MIRNAS ALSO INHIBIT THEIR TARGET MRNAS, CIRCRNA-MIRNA-MRNA REGULATORY NETWORK, COMPRISED OF DYSREGULATED RNAS THAT TARGETS ONE ANOTHER WERE SEARCHED. FOR THE IDENTIFIED NETWORKS, BIOINFORMATICS ANALYSES WERE PERFORMED. AS THE RESULT, FORTY-THREE CIRCRNAS WERE DYSREGULATED IN THE HIPPOCAMPUS (UP-REGULATED, 26; DOWN-REGULATED, 17). THE CHANGE IN THE EXPRESSION OF MRE IN THOSE CIRCRNAS NEGATIVELY CORRELATED WITH THE CHANGE IN THE RELEVANT TARGET MIRNA EXPRESSION (R = -0.461, P<0.001), SUPPORTING THAT CIRCRNAS INHIBIT THEIR TARGET MIRNA. 333 DYSREGULATED CIRCRNA-MIRNA-MRNA NETWORKS WERE IDENTIFIED. GENE ONTOLOGY AND PATHWAY ANALYSES DEMONSTRATED THAT THE UP-REGULATED MRNAS IN THOSE NETWORKS WERE CLOSELY RELATED TO THE MAJOR PROCESSES IN EPILEPSY. AMONG THEM, STRING ANALYSIS IDENTIFIED 37 KEY MRNAS WITH ABUNDANT (>/=4) INTERACTIONS WITH OTHER DYSREGULATED TARGET MRNAS. THE DYSREGULATION OF THE CIRCRNAS WHICH HAD MULTIPLE INTERACTIONS WITH KEY MRNAS WERE VALIDATED BY PCR. WE CONCLUDED THAT DYSREGULATED CIRCRNAS MIGHT HAVE A PATHOPHYSIOLOGIC ROLE IN CHRONIC EPILEPSY BY REGULATING MULTIPLE DISEASE RELEVANT MRNAS VIA CIRCRNA-MIRNA-MRNA INTERACTIONS. 2018 14 2091 25 EPIGENETIC DYSREGULATION OF VIRULENCE GENE EXPRESSION IN SEVERE PLASMODIUM FALCIPARUM MALARIA. CHRONIC INFECTIONS WITH THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM DEPEND ON ANTIGENIC VARIATION. P. FALCIPARUM ERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1), THE MAJOR ERYTHROCYTE SURFACE ANTIGEN MEDIATING PARASITE SEQUESTRATION IN THE MICROVASCULATURE, IS ENCODED IN PARASITES BY A HIGHLY DIVERSE FAMILY OF VAR GENES. ANTIGENIC SWITCHING IS MEDIATED BY CLONAL VARIATION IN VAR EXPRESSION, AND RECENT IN VITRO STUDIES HAVE DEMONSTRATED A ROLE FOR EPIGENETIC PROCESSES IN VAR REGULATION. EXPRESSION OF PARTICULAR PFEMP1 VARIANTS MAY RESULT IN PARASITE ENRICHMENT IN DIFFERENT TISSUES, A FACTOR IN THE DEVELOPMENT OF SEVERE DISEASE. HERE, WE STUDY IN VIVO HUMAN INFECTIONS AND PROVIDE EVIDENCE THAT INFECTION-INDUCED STRESS RESPONSES IN THE HOST CAN MODIFY PFEMP1 EXPRESSION VIA THE PERTURBATION OF EPIGENETIC MECHANISMS. OUR WORK SUGGESTS THAT SEVERE DISEASE MAY NOT BE THE DIRECT RESULT OF AN ADAPTIVE VIRULENCE STRATEGY TO MAXIMIZE PARASITE SURVIVAL BUT THAT IT MAY INDICATE A LOSS OF CONTROL OF THE CAREFULLY REGULATED PROCESS OF ANTIGENIC SWITCHING THAT MAINTAINS CHRONIC INFECTIONS. 2012 15 4583 18 N6-METHYLADENINE RNA METHYLATION EPIGENETIC MODIFICATION AND KIDNEY DISEASES. RNA METHYLATION MODIFICATION IS A RAPIDLY DEVELOPING FIELD IN EPIGENETICS. N6-METHYLADENSINE (M(6)A) IS THE MOST COMMON INTERNAL MODIFICATION IN EUKARYOTIC MRNA. M(6)A GROUP REGULATES RNA SPLICING, STABILITY, TRANSLOCATION, AND TRANSLATION. ENZYMES CATALYZING THIS PROCESS WERE TERMED AS WRITERS, ERASERS, AND READERS. RECENT STUDIES HAVE FOCUSED ON EXPLORING THE ROLE OF RNA METHYLATION IN HUMAN DISEASES. RNA METHYLATION MODIFICATIONS, PARTICULARLY M(6)A, PLAY IMPORTANT ROLES IN THE PATHOGENESIS OF KIDNEY DISEASES. IN THIS REVIEW, WE PROVIDE A BRIEF DESCRIPTION OF M(6)A AND SUMMARIZE THE IMPACT OF M(6)A ON ACUTE AND CHRONIC KIDNEY DISEASE (CKD) AND POSSIBLE FUTURE STUDY DIRECTIONS FOR THIS RESEARCH. 2023 16 4055 30 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 17 1720 22 DYSREGULATED N6-METHYLADENOSINE (M(6)A) PROCESSING IN HEPATOCELLULAR CARCINOMA. N6-METHYLADENOSINE (M(6)A) IS THE MOST THOROUGHLY STUDIED TYPE OF INTERNAL RNA MODIFICATION, AS THIS EPIGENETIC MODIFICATION IS THE MOST ABUNDANT IN EUKARYOTIC RNAS TO DATE. THIS MODIFICATION OCCURS IN VARIOUS TYPES OF RNAS AND PLAYS SIGNIFICANT ROLES IN DOMINANT RNA-RELATED PROCESSES, SUCH AS TRANSLATION, SPLICING, EXPORT AND DEGRADATION. THESE PROCESSES ARE CATALYZED BY THREE TYPES OF PROMINENT ENZYMES: WRITERS, ERASERS AND READERS. INCREASING EVIDENCE HAS SHOWN THAT M(6)A MODIFICATION IS VITAL FOR THE REGULATION OF GENE EXPRESSION, CARCINOGENESIS, TUMOR PROGRESSION AND OTHER ABNORMAL CHANGES, AND RECENT STUDIES HAVE SHOWN THAT M(6)A IS IMPORTANT IN THE DEVELOPMENT OF HEPATOCELLULAR CARCINOMA (HCC). HEREIN, WE SUMMARIZE THE NATURE AND REGULATORY MECHANISMS OF M(6)A MODIFICATION, INCLUDING ITS ROLE IN THE PATHOGENESIS OF HCC AND RELATED CHRONIC LIVER DISEASES. WE ALSO HIGHLIGHT THE CLINICAL SIGNIFICANCE AND FUTURE STRATEGIES INVOLVING RNA M(6)A MODIFICATIONS IN HCC. 2021 18 2971 24 GENETIC AND EPIGENETIC SILENCING OF MICRORNA-203 ENHANCES ABL1 AND BCR-ABL1 ONCOGENE EXPRESSION. THE MAMMALIAN GENOME CONTAINS SEVERAL HUNDRED MICRORNAS THAT REGULATE GENE EXPRESSION THROUGH MODULATION OF TARGET MRNAS. HERE, WE REPORT A FRAGILE CHROMOSOMAL REGION LOST IN SPECIFIC HEMATOPOIETIC MALIGNANCIES. THIS 7 MB REGION ENCODES ABOUT 12% OF ALL GENOMIC MICRORNAS, INCLUDING MIR-203. THIS MICRORNA IS ADDITIONALLY HYPERMETHYLATED IN SEVERAL HEMATOPOIETIC TUMORS, INCLUDING CHRONIC MYELOGENOUS LEUKEMIAS AND SOME ACUTE LYMPHOBLASTIC LEUKEMIAS. A PUTATIVE MIR-203 TARGET, ABL1, IS SPECIFICALLY ACTIVATED IN THESE HEMATOPOIETIC MALIGNANCIES IN SOME CASES AS A BCR-ABL1 FUSION PROTEIN (PHILADELPHIA CHROMOSOME). RE-EXPRESSION OF MIR-203 REDUCES ABL1 AND BCR-ABL1 FUSION PROTEIN LEVELS AND INHIBITS TUMOR CELL PROLIFERATION IN AN ABL1-DEPENDENT MANNER. THUS, MIR-203 FUNCTIONS AS A TUMOR SUPPRESSOR, AND RE-EXPRESSION OF THIS MICRORNA MIGHT HAVE THERAPEUTIC BENEFITS IN SPECIFIC HEMATOPOIETIC MALIGNANCIES. 2008 19 1568 31 DNA METHYLATION OF TUMOR-SUPPRESSOR MIRNA GENES IN CHRONIC LYMPHOCYTIC LEUKEMIA. DNA METHYLATION IS ONE OF THE MOST IMPORTANT EPIGENETIC MODIFICATIONS OF THE GENOME INVOLVED IN THE REGULATION OF NUMEROUS CELLULAR PROCESSES THROUGH GENE SILENCING WITHOUT ALTERING DNA SEQUENCES. MIRNAS, A CLASS OF SINGLE-STRANDED NONCODING RNAS OF 19-25 NUCLEOTIDES IN LENGTH, FUNCTION AS POST-TRANSCRIPTIONAL REGULATORS OF GENE EXPRESSION LEADING TO MRNA CLEAVAGE OR TRANSLATIONAL REPRESSION OF THEIR CORRESPONDING TARGET PROTEIN-CODING GENES. RECENTLY, DYSREGULATION OF TUMOR SUPPRESSOR MIRNAS MEDIATED BY PROMOTER DNA HYPERMETHYLATION IS IMPLICATED IN HUMAN CANCERS, INCLUDING B-CELL CHRONIC LYMPHOCYTIC LEUKEMIA (CLL). MOREOVER, IT APPEARS THAT METHYLATED MIRNA GENES COULD BE POTENTIAL BIOMARKERS FOR CLL DIAGNOSIS OR THERAPY. THIS REVIEW WILL HIGHLIGHT THE ROLE OF ABERRANT METHYLATION OF MIRNA GENES IN THE PATHOGENESIS OF CLL. 2015 20 5226 31 PRMT5 RESTRICTS HEPATITIS B VIRUS REPLICATION THROUGH EPIGENETIC REPRESSION OF COVALENTLY CLOSED CIRCULAR DNA TRANSCRIPTION AND INTERFERENCE WITH PREGENOMIC RNA ENCAPSIDATION. CHRONIC HEPATITIS B VIRUS (HBV) INFECTION REMAINS A MAJOR HEALTH PROBLEM WORLDWIDE. THE COVALENTLY CLOSED CIRCULAR DNA (CCCDNA) MINICHROMOSOME, WHICH SERVES AS THE TEMPLATE FOR THE TRANSCRIPTION OF VIRAL RNAS, PLAYS A KEY ROLE IN VIRAL PERSISTENCE. WHILE ACCUMULATING EVIDENCE SUGGESTS THAT CCCDNA TRANSCRIPTION IS REGULATED BY EPIGENETIC MACHINERY, PARTICULARLY THE ACETYLATION OF CCCDNA-BOUND HISTONE 3 (H3) AND H4, THE POTENTIAL CONTRIBUTIONS OF HISTONE METHYLATION AND RELATED HOST FACTORS REMAIN OBSCURE. HERE, BY SCREENING A SERIES OF METHYLTRANSFERASES AND DEMETHYLASES, WE IDENTIFIED PROTEIN ARGININE METHYLTRANSFERASE 5 (PRMT5) AS AN EFFECTIVE RESTRICTOR OF HBV TRANSCRIPTION AND REPLICATION. IN CELL CULTURE-BASED MODELS FOR HBV INFECTION AND IN LIVER TISSUES OF PATIENTS WITH CHRONIC HBV INFECTION, WE FOUND THAT SYMMETRIC DIMETHYLATION OF ARGININE 3 ON H4 ON CCCDNA WAS A REPRESSIVE MARKER OF CCCDNA TRANSCRIPTION AND WAS REGULATED BY PRMT5 DEPENDING ON ITS METHYLTRANSFERASE DOMAIN. MOREOVER, PRMT5-TRIGGERED SYMMETRIC DIMETHYLATION OF ARGININE 3 ON H4 ON THE CCCDNA MINICHROMOSOME INVOLVED AN INTERACTION WITH THE HBV CORE PROTEIN AND THE BRG1-BASED HUMAN SWI/SNF CHROMATIN REMODELER, WHICH RESULTED IN DOWN-REGULATION OF THE BINDING OF RNA POLYMERASE II TO CCCDNA. IN ADDITION TO THE INHIBITORY EFFECT ON CCCDNA TRANSCRIPTION, PRMT5 INHIBITED HBV CORE PARTICLE DNA PRODUCTION INDEPENDENTLY OF ITS METHYLTRANSFERASE ACTIVITY. FURTHER STUDY REVEALED THAT PRMT5 INTERFERED WITH PREGENOMIC RNA ENCAPSIDATION BY PREVENTING ITS INTERACTION WITH VIRAL POLYMERASE PROTEIN THROUGH BINDING TO THE REVERSE TRANSCRIPTASE-RIBONUCLEASE H REGION OF POLYMERASE, WHICH IS CRUCIAL FOR THE POLYMERASE-PREGENOMIC RNA INTERACTION. CONCLUSION: PRMT5 RESTRICTS HBV REPLICATION THROUGH A TWO-PART MECHANISM INCLUDING EPIGENETIC SUPPRESSION OF CCCDNA TRANSCRIPTION AND INTERFERENCE WITH PREGENOMIC RNA ENCAPSIDATION; THESE FINDINGS IMPROVE THE UNDERSTANDING OF EPIGENETIC REGULATION OF HBV TRANSCRIPTION AND HOST-HBV INTERACTION, THUS PROVIDING NEW INSIGHTS INTO TARGETED THERAPEUTIC INTERVENTION. (HEPATOLOGY 2017;66:398-415). 2017