1 1218 145 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 2 340 51 ALTERATIONS IN LOCAL CHROMATIN ENVIRONMENT ARE INVOLVED IN SILENCING AND ACTIVATION OF SUBTELOMERIC VAR GENES IN PLASMODIUM FALCIPARUM. PLASMODIUM FALCIPARUM ERYTHROCYTE MEMBRANE PROTEIN 1 (PFEMP1), ENCODED BY THE VAR GENE FAMILY, UNDERGOES ANTIGENIC VARIATION AND PLAYS AN IMPORTANT ROLE IN CHRONIC INFECTION AND SEVERE MALARIA. ONLY A SINGLE VAR GENE IS TRANSCRIBED PER PARASITE, AND EPIGENETIC CONTROL MECHANISMS ARE FUNDAMENTAL IN THIS STRATEGY OF MUTUALLY EXCLUSIVE TRANSCRIPTION. WE SHOW THAT SUBTELOMERIC UPSB VAR GENE PROMOTERS CARRIED ON EPISOMES ARE SILENCED BY DEFAULT, AND THAT PROMOTER ACTIVATION IS SUFFICIENT TO SILENCE ALL OTHER FAMILY MEMBERS. HOWEVER, THEY ARE ACTIVE BY DEFAULT WHEN PLACED DOWNSTREAM OF A SECOND ACTIVE VAR PROMOTER, UNDERSCORING THE SIGNIFICANCE OF LOCAL CHROMATIN ENVIRONMENT AND NUCLEAR COMPARTMENTALIZATION IN VAR PROMOTER REGULATION. NATIVE CHROMATIN COVERING THE SPE2-REPEAT ARRAY IN UPSB PROMOTERS IS RESISTANT TO NUCLEASE DIGESTION, AND INSERTION OF THESE REGULATORY ELEMENTS INTO A HETEROLOGOUS PROMOTER CAUSES LOCAL ALTERATIONS IN NUCLEOSOMAL ORGANIZATION AND PROMOTER REPRESSION. OUR FINDINGS SUGGEST A COMMON LOGIC UNDERLYING THE TRANSCRIPTIONAL CONTROL OF ALL VAR GENES, AND HAVE IMPORTANT IMPLICATIONS FOR OUR UNDERSTANDING OF THE EPIGENETIC PROCESSES INVOLVED IN THE REGULATION OF THIS MAJOR VIRULENCE GENE FAMILY. 2007 3 2091 47 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 4 6179 43 THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM CAN SENSE ENVIRONMENTAL CHANGES AND RESPOND BY ANTIGENIC SWITCHING. THE PRIMARY ANTIGENIC AND VIRULENCE DETERMINANT OF THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM IS A VARIANT SURFACE PROTEIN CALLED PFEMP1. DIFFERENT FORMS OF PFEMP1 ARE ENCODED BY A MULTICOPY GENE FAMILY CALLED VAR, AND SWITCHING BETWEEN ACTIVE GENES ENABLES THE PARASITES TO EVADE THE ANTIBODY RESPONSE OF THEIR HUMAN HOSTS. VAR GENE SWITCHING IS KEY FOR THE MAINTENANCE OF CHRONIC INFECTIONS; HOWEVER, WHAT CONTROLS SWITCHING IS UNKNOWN, ALTHOUGH IT HAS BEEN SUGGESTED TO OCCUR AT A CONSTANT FREQUENCY WITH LITTLE OR NO ENVIRONMENTAL INFLUENCE. VAR GENE TRANSCRIPTION IS CONTROLLED EPIGENETICALLY THROUGH THE ACTIVITY OF HISTONE METHYLTRANSFERASES (HMTS). STUDIES IN MODEL SYSTEMS HAVE SHOWN THAT METABOLISM AND EPIGENETIC CONTROL OF GENE EXPRESSION ARE LINKED THROUGH THE AVAILABILITY OF INTRACELLULAR S-ADENOSYLMETHIONINE (SAM), THE PRINCIPAL METHYL DONOR IN BIOLOGICAL METHYLATION MODIFICATIONS, WHICH CAN FLUCTUATE BASED ON NUTRIENT AVAILABILITY. TO DETERMINE WHETHER ENVIRONMENTAL CONDITIONS AND CHANGES IN METABOLISM CAN INFLUENCE VAR GENE EXPRESSION, P. FALCIPARUM WAS CULTURED IN MEDIA WITH ALTERED CONCENTRATIONS OF NUTRIENTS INVOLVED IN SAM METABOLISM. WE FOUND THAT CONDITIONS THAT INFLUENCE LIPID METABOLISM INDUCE VAR GENE SWITCHING, INDICATING THAT PARASITES CAN RESPOND TO CHANGES IN THEIR ENVIRONMENT BY ALTERING VAR GENE EXPRESSION PATTERNS. GENETIC MODIFICATIONS THAT DIRECTLY MODIFIED EXPRESSION OF THE ENZYMES THAT CONTROL SAM LEVELS SIMILARLY LED TO PROFOUND CHANGES IN VAR GENE EXPRESSION, CONFIRMING THAT CHANGES IN SAM AVAILABILITY MODULATE VAR GENE SWITCHING. THESE OBSERVATIONS DIRECTLY CHALLENGE THE PARADIGM THAT ANTIGENIC VARIATION IN P. FALCIPARUM FOLLOWS AN INTRINSIC, PROGRAMED SWITCHING RATE, WHICH OPERATES INDEPENDENTLY OF ANY EXTERNAL STIMULI. 2023 5 1219 53 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 6 6695 38 VARIANT GENE EXPRESSION AND ANTIGENIC VARIATION BY MALARIA PARASITES. MALARIA IS A SIGNIFICANT THREAT THROUGHOUT THE DEVELOPING WORLD. AMONG THE MOST FASCINATING ASPECTS OF THE PROTOZOAN PARASITES RESPONSIBLE FOR THIS DISEASE ARE THE METHODS THEY EMPLOY TO AVOID THE IMMUNE SYSTEM AND PERPETUATE CHRONIC INFECTIONS. KEY AMONG THESE IS ANTIGENIC VARIATION: BY SYSTEMATICALLY ALTERING ANTIGENS THAT ARE DISPLAYED TO THE HOST'S IMMUNE SYSTEM, THE PARASITE RENDERS THE ADAPTIVE IMMUNE RESPONSE INEFFECTIVE. FOR PLASMODIUM FALCIPARUM, THE SPECIES RESPONSIBLE FOR THE MOST SEVERE FORM OF HUMAN MALARIA, THIS PROCESS INVOLVES A COMPLICATED MOLECULAR MECHANISM THAT RESULTS IN CONTINUOUSLY CHANGING PATTERNS OF VARIANT-ANTIGEN-ENCODING GENE EXPRESSION. ALTHOUGH MANY FEATURES OF THIS PROCESS REMAIN OBSCURE, SIGNIFICANT PROGRESS HAS BEEN MADE IN RECENT YEARS TO DECIPHER VARIOUS MOLECULAR ASPECTS OF THE REGULATORY CASCADE THAT CAUSES CHRONIC INFECTION. 2017 7 17 46 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 8 129 59 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 9 3827 54 INVESTIGATION OF HETEROCHROMATIN PROTEIN 1 FUNCTION IN THE MALARIA PARASITE PLASMODIUM FALCIPARUM USING A CONDITIONAL DOMAIN DELETION AND SWAPPING APPROACH. THE HUMAN MALARIA PARASITE PLASMODIUM FALCIPARUM ENCODES A SINGLE ORTHOLOG OF HETEROCHROMATIN PROTEIN 1 (PFHP1) THAT PLAYS A CRUCIAL ROLE IN THE EPIGENETIC REGULATION OF VARIOUS SURVIVAL-RELATED PROCESSES. PFHP1 IS ESSENTIAL FOR PARASITE PROLIFERATION AND THE HERITABLE SILENCING OF GENES LINKED TO ANTIGENIC VARIATION, HOST CELL INVASION, AND SEXUAL CONVERSION. HERE, WE EMPLOYED CRISPR/CAS9-MEDIATED GENOME EDITING COMBINED WITH THE DICRE/LOXP SYSTEM TO INVESTIGATE HOW THE PFHP1 CHROMODOMAIN (CD), HINGE DOMAIN, AND CHROMOSHADOW DOMAIN (CSD) CONTRIBUTE TO OVERALL PFHP1 FUNCTION. WE SHOW THAT THE 76 C-TERMINAL RESIDUES ARE RESPONSIBLE FOR TARGETING PFHP1 TO THE NUCLEUS. FURTHERMORE, WE REVEAL THAT EACH OF THE THREE FUNCTIONAL DOMAINS OF PFHP1 ARE REQUIRED FOR HETEROCHROMATIN FORMATION, GENE SILENCING, AND MITOTIC PARASITE PROLIFERATION. FINALLY, WE DISCOVERED THAT THE HINGE DOMAIN AND CSD OF HP1 ARE FUNCTIONALLY CONSERVED BETWEEN P. FALCIPARUM AND P. BERGHEI, A RELATED MALARIA PARASITE INFECTING RODENTS. IN SUMMARY, OUR STUDY PROVIDES NEW INSIGHTS INTO PFHP1 FUNCTION AND OFFERS A TOOL FOR FURTHER STUDIES ON EPIGENETIC REGULATION AND LIFE CYCLE DECISION IN MALARIA PARASITES.IMPORTANCE MALARIA IS CAUSED BY UNICELLULAR PLASMODIUM SPECIES PARASITES THAT REPEATEDLY INVADE AND REPLICATE INSIDE RED BLOOD CELLS. SOME BLOOD-STAGE PARASITES EXIT THE CELL CYCLE AND DIFFERENTIATE INTO GAMETOCYTES THAT ARE ESSENTIAL FOR MALARIA TRANSMISSION VIA THE MOSQUITO VECTOR. EPIGENETIC CONTROL MECHANISMS ALLOW THE PARASITES TO ALTER THE EXPRESSION OF SURFACE ANTIGENS AND TO BALANCE THE SWITCH BETWEEN PARASITE MULTIPLICATION AND GAMETOCYTE PRODUCTION. THESE PROCESSES ARE CRUCIAL TO ESTABLISH CHRONIC INFECTION AND OPTIMIZE PARASITE TRANSMISSION. HERE, WE PERFORMED A MUTATIONAL ANALYSIS OF HETEROCHROMATIN PROTEIN 1 (HP1) IN P. FALCIPARUM WE DEMONSTRATE THAT ALL THREE DOMAINS OF THIS PROTEIN ARE INDISPENSABLE FOR THE PROPER FUNCTION OF HP1 IN PARASITE MULTIPLICATION, HETEROCHROMATIN FORMATION, AND GENE SILENCING. MOREOVER, EXPRESSION OF CHIMERIC PROTEINS REVEALED THE FUNCTIONAL CONSERVATION OF HP1 PROTEINS BETWEEN DIFFERENT PLASMODIUM SPECIES. THESE RESULTS PROVIDE NEW INSIGHT INTO THE FUNCTION AND EVOLUTION OF HP1 AS AN ESSENTIAL EPIGENETIC REGULATOR OF PARASITE SURVIVAL. 2021 10 4490 27 MONOCYTE EPIGENETICS AND INNATE IMMUNITY TO MALARIA: YET ANOTHER LEVEL OF COMPLEXITY? CHILDREN UNDER THE AGE OF 5 YEARS LIVING IN AREAS OF MODERATE TO HIGH MALARIA TRANSMISSION ARE HIGHLY SUSCEPTIBLE TO CLINICAL MALARIA WITH FEVER THAT PROMPTS TREATMENT OF BLOOD STAGE INFECTION WITH ANTI-MALARIAL DRUGS. IN CONTRAST, OLDER SCHOOL AGE CHILDREN FREQUENTLY EXPERIENCE SUBCLINICAL MALARIA, I.E. CHRONIC PLASMODIUM FALCIPARUM PARASITEMIA WITHOUT FEVER OR OTHER CLINICAL SYMPTOMS. THE ROLE OF INNATE IMMUNE CELLS IN REGULATING INFLAMMATION AT A LEVEL THAT IS SUFFICIENT TO CONTROL THE PARASITE BIOMASS, WHILE AT THE SAME TIME MAINTAINING A DISEASE-TOLERANT CLINICAL PHENOTYPE, I.E., SUBCLINICAL MALARIA, IS NOT WELL UNDERSTOOD. RECENT STUDIES SUGGEST THAT HOST EPIGENETIC MECHANISMS UNDERLIE THE INNATE IMMUNE HOMEOSTASIS ASSOCIATED WITH SUBCLINICAL MALARIA. THIS CURRENT OPINION ARTICLE PRESENTS EVIDENCE SUPPORTING THE NOTION THAT MODIFICATIONS OF THE HOST MONOCYTE/MACROPHAGE EPIGENOME REGULATE INNATE IMMUNE FUNCTIONS PERTINENT TO SUBCLINICAL MALARIA. 2022 11 5096 45 PLASMODIUM FALCIPARUM SET2 DOMAIN IS ALLOSTERICALLY REGULATED BY ITS PHD-LIKE DOMAIN TO METHYLATE AT H3K36. THE ANTIGENIC VARIATION IS AN ESSENTIAL MECHANISM EMPLOYED BY THE MALARIA PARASITE TO ESTABLISH A CHRONIC INFECTION IN HUMANS. THREE MAJOR VIRULENT PROTEINS EMP1, RIFINS, AND STEVOR HAVE BEEN IMPLICATED IN CONTRIBUTING TO THE ANTIGENIC VARIATION PROCESS AND ARE ENCODED BY MULTIGENE FAMILIES IN PLASMODIUM SPP. THE KEY VIRULENCE FACTOR PFEMP1 IS ENCODED BY VAR GENES, AND IT EXHIBITS A MUTUALLY EXCLUSIVE TRANSCRIPTIONAL SWITCHING BETWEEN VAR GENES, ENSURING AN INDIVIDUAL PARASITE ONLY TRANSCRIBES A SINGLE VAR GENE AT A TIME. EXPRESSION OF VAR GENES IS TIGHTLY REGULATED BY TWO HISTONE EPIGENETIC METHYLATION MARKS H3K36ME3 AND H3K9ME3, OF WHICH THE H3K36ME3 MARK IS HIGHLY ENRICHED ON TRANSCRIPTION START SITES (TSSS) OF SUPPRESSED VAR GENES IN P. FALCIPARUM. HOWEVER, THE MECHANISMS OF H3K36ME3 MARK PROPAGATION ON ALL THE 59 VAR GENES OF P. FALCIPARUM ARE NOT KNOWN. HERE, WE HAVE IDENTIFIED A PHD (PLANT HOMEODOMAIN-LIKE DOMAIN) LIKE DOMAIN PRESENT WITHIN THE PFSET2 PROTEIN THAT SPECIFICALLY BINDS TO THE H3K36ME2 MARK, AN INTERMEDIATE PRODUCT OF THE H3K36ME3 MARK FORMATION ON THE NUCLEOSOME. SURPRISINGLY, WE HAVE FOUND THAT PHD - H3K36ME2 INTERACTION LEADS TO STIMULATION OF SET2 DOMAIN ACTIVITY ON THE NUCLEOSOME SUBSTRATES. THE ALLOSTERIC STIMULATION OF THE PFSET2 DOMAIN BY PHD-LIKE DOMAIN PRESENT WITHIN THE SAME PROTEIN SUGGESTS A NOVEL MECHANISM OF H3K36ME3 MARK PROPAGATION ON VAR GENES OF P. FALCIPARUM. THIS STUDY PROPOSES ALLOSTERIC REGULATION OF PFSET2 PROTEIN BY H3K36ME2 MARK AS AN ESSENTIAL MECHANISM OF VAR GENES SUPPRESSION TO ENSURE SUCCESSFUL ANTIGENIC VARIATION BY THE MALARIA PARASITE. 2021 12 2055 31 EPIGENETIC CONTROL DURING LYMPHOID DEVELOPMENT AND IMMUNE RESPONSES: ABERRANT REGULATION, VIRUSES, AND CANCER. METHYLATION OF CYTOSINES CONTROLS A NUMBER OF BIOLOGIC PROCESSES SUCH AS IMPRINTING AND X CHROMOSOMAL INACTIVATION. DNA HYPERMETHYLATION IS CLOSELY ASSOCIATED WITH TRANSCRIPTIONAL SILENCING, WHILE DNA HYPOMETHYLATION IS ASSOCIATED WITH TRANSCRIPTIONAL ACTIVATION. HYPOACETYLATION OF HISTONES LEADS TO COMPACT CHROMATIN WITH REDUCED ACCESSIBILITY TO THE TRANSCRIPTIONAL MACHINERY. METHYL-CPG BINDING PROTEINS CAN RECRUIT COREPRESSORS AND HISTONE DEACETYLASES; THUS, THE INTERPLAY BETWEEN THESE EPIGENETIC MECHANISMS REGULATES GENE ACTIVATION. METHYLATION HAS BEEN IMPLICATED AS AN IMPORTANT MECHANISM DURING IMMUNE DEVELOPMENT, CONTROLLING VDJ RECOMBINATION, LINEAGE-SPECIFIC EXPRESSION OF CELL SURFACE ANTIGENS, AND TRANSCRIPTIONAL REGULATION OF CYTOKINE GENES DURING IMMUNE RESPONSES. ABERRATIONS IN EPIGENETIC MACHINERY, EITHER BY GENETIC MUTATIONS OR BY SOMATIC CHANGES SUCH AS VIRAL INFECTIONS, ARE ASSOCIATED WITH EARLY ALTERATIONS IN CHRONIC DISEASES SUCH AS IMMUNODEFICIENCY AND CANCER. 2003 13 1283 27 DECIPHERING THE EPIGENETIC CODE OF T LYMPHOCYTES. THE MULTIPLE LINEAGES AND DIFFERENTIATION STATES THAT CONSTITUTE THE T-CELL COMPARTMENT ALL DERIVE FROM A COMMON THYMIC PRECURSOR. THESE DISTINCT TRANSCRIPTIONAL STATES ARE MAINTAINED BOTH IN TIME AND AFTER MULTIPLE ROUNDS OF CELL DIVISION BY THE CONCERTED ACTIONS OF A SMALL SET OF LINEAGE-DEFINING TRANSCRIPTION FACTORS THAT ACT IN CONJUNCTION WITH A SUITE OF CHROMATIN-MODIFYING ENZYMES TO ACTIVATE, REPRESS, AND FINE-TUNE GENE EXPRESSION. THESE CHROMATIN MODIFICATIONS COLLECTIVELY PROVIDE AN EPIGENETIC CODE THAT ALLOWS THE STABLE AND HERITABLE MAINTENANCE OF THE T-CELL PHENOTYPE. RECENTLY, IT HAS BECOME APPARENT THAT THE EPIGENETIC CODE REPRESENTS A THERAPEUTIC TARGET FOR A VARIETY OF IMMUNE CELL DISORDERS, INCLUDING LYMPHOMA AND ACUTE AND CHRONIC INFLAMMATORY DISEASES. HERE, WE REVIEW THE RECENT ADVANCES IN EPIGENETIC REGULATION OF GENE EXPRESSION, PARTICULARLY AS IT RELATES TO THE T-CELL DIFFERENTIATION AND FUNCTION. 2014 14 851 24 CHIP-SEQ ANALYSIS OF HUMAN CHRONIC MYELOID LEUKEMIA CELLS. MANY TRANSCRIPTION FACTORS, CHROMATIN-ASSOCIATED PROTEINS AND REGULATORY DNA ELEMENTS ARE GENETICALLY AND/OR EPIGENETICALLY ALTERED IN CANCER, INCLUDING CHRONIC MYELOID LEUKEMIA (CML). THIS LEADS TO DEREGULATION OF TRANSCRIPTION THAT IS OFTEN CAUSALLY LINKED TO THE TUMORIGENIC STATE. CHROMATIN-IMMUNOPRECIPITATION COUPLED WITH MASSIVELY PARALLEL DNA SEQUENCING (CHIP-SEQ) IS THE KEY TECHNOLOGY TO STUDY TRANSCRIPTION AS IT ALLOWS IN VIVO WHOLE-GENOME MAPPING OF EPIGENETIC MODIFICATIONS AND INTERACTIONS OF PROTEINS WITH DNA OR CHROMATIN. HOWEVER, NUMEROUS DNA/CHROMATIN-BINDING PROTEINS, INCLUDING EZH2, REMAIN DIFFICULT TO "CHIP," THUS YIELDING GENOME-WIDE BINDING MAPS OF ONLY SUBOPTIMAL QUALITY. HERE, WE DESCRIBE A CHIP-SEQ PROTOCOL OPTIMIZED FOR HIGH-QUALITY PROTEIN-GENOME BINDING MAPS THAT HAVE PROVEN ESPECIALLY USEFUL FOR STUDYING DIFFICULT TO 'CHIP' TRANSCRIPTION REGULATORY FACTORS IN CHRONIC MYELOID LEUKEMIA (CML) AND RELATED MALIGNANCIES. 2016 15 6706 24 VIRAL GENE PRODUCTS ACTIVELY PROMOTE LATENT INFECTION BY EPIGENETIC SILENCING MECHANISMS. MANY VIRUSES UNDERGO AN ACUTE INFECTION IN THE HOST ORGANISM AND THEN ARE CLEARED BY THE ENSUING HOST IMMUNE RESPONSE, BUT OTHER VIRUSES ESTABLISH A PERSISTENT INFECTION INVOLVING A LATENT INFECTION OR A CHRONIC INFECTION. LATENT INFECTION BY THE HERPESVIRUSES OR HUMAN IMMUNODEFICIENCY VIRUS INVOLVES EPIGENETIC SILENCING OF THE DNA GENOME OR PROVIRAL GENOME, RESPECTIVELY. LATENT INFECTION WAS PREVIOUSLY THOUGHT TO BE A DEFAULT PATHWAY RESULTING FROM INFECTION OF A NONPERMISSIVE CELL, BUT RECENT STUDIES HAVE SHOWN THAT VIRAL GENE PRODUCTS CAN PROMOTE EPIGENETIC SILENCING AND LATENT INFECTION. THIS REVIEW WILL SUMMARIZE THE VIRAL GENE PRODUCTS THAT HAVE BEEN SHOWN TO PROMOTE EPIGENETIC SILENCING OF THE GENOMES AND THEIR POTENTIAL FOR THERAPEUTICS TO TARGET THESE VIRAL GENE PRODUCTS AND DISRUPT OR LOCK IN LATENT INFECTION. 2017 16 3949 35 LNCRNAS IN T LYMPHOCYTES: RNA REGULATION AT THE HEART OF THE IMMUNE RESPONSE. GENOME-WIDE ANALYSES IN THE LAST DECADE HAVE UNCOVERED THE PRESENCE OF A LARGE NUMBER OF LONG NON-PROTEIN-CODING TRANSCRIPTS THAT SHOW HIGHLY TISSUE- AND STATE-SPECIFIC EXPRESSION PATTERNS. HIGH-THROUGHPUT SEQUENCING ANALYSES IN DIVERSE SUBSETS OF IMMUNE CELLS HAVE REVEALED A COMPLEX AND DYNAMIC EXPRESSION PATTERN FOR THESE LONG NONCODING RNAS (LNCRNAS) THAT CORRELATE WITH THE FUNCTIONAL STATES OF IMMUNE CELLS. ALTHOUGH THE VAST MAJORITY OF LNCRNAS EXPRESSED IN IMMUNE CELLS REMAIN UNSTUDIED, FUNCTIONAL STUDIES PERFORMED ON A SMALL SUBSET HAVE INDICATED THAT THEIR STATE-SPECIFIC EXPRESSIONS PATTERN FREQUENTLY HAS A REGULATORY IMPACT ON THE FUNCTION OF IMMUNE CELLS. IN VIVO AND IN VITRO STUDIES HAVE POINTED TO THE INVOLVEMENT OF LNCRNAS IN A WIDE VARIETY OF CELLULAR PROCESSES, INCLUDING BOTH THE INNATE AND ADAPTIVE IMMUNE RESPONSE THROUGH MECHANISMS RANGING FROM EPIGENETIC AND TRANSCRIPTIONAL REGULATION TO SEQUESTRATION OF FUNCTIONAL MOLECULES IN SUBCELLULAR COMPARTMENTS. THIS REVIEW WILL FOCUS MAINLY ON THE ROLE OF LNCRNAS IN CD4(+) AND CD8(+) T CELLS, WHICH PLAY PIVOTAL ROLES IN ADAPTIVE IMMUNITY. RECENT STUDIES HAVE POINTED TO KEY PHYSIOLOGICAL FUNCTIONS FOR LNCRNAS DURING SEVERAL DEVELOPMENTAL AND FUNCTIONAL STAGES OF THE LIFE CYCLE OF LYMPHOCYTES. ALTHOUGH LNCRNAS PLAY IMPORTANT PHYSIOLOGICAL ROLES IN LYMPHOCYTIC RESPONSE TO ANTIGENIC STIMULATION, DIFFERENTIATION INTO EFFECTOR CELLS, AND SECRETION OF CYTOKINES, THEIR DYSREGULATED EXPRESSION CAN PROMOTE OR SUSTAIN PATHOLOGICAL STATES SUCH AS AUTOIMMUNITY, CHRONIC INFLAMMATION, CANCER, AND VIREMIA. THIS, TOGETHER WITH THEIR HIGHLY CELL TYPE-SPECIFIC EXPRESSION PATTERNS, MAKES LNCRNAS IDEAL THERAPEUTIC TARGETS AND UNDERSCORES THE NEED FOR ADDITIONAL STUDIES INTO THE ROLE OF THESE UNDERSTUDIED TRANSCRIPTS IN ADAPTIVE IMMUNE RESPONSE. 2021 17 1562 32 DNA METHYLATION OF ENHANCER ELEMENTS IN MYELOID NEOPLASMS: THINK OUTSIDE THE PROMOTERS? GENE REGULATION THROUGH DNA METHYLATION IS A WELL DESCRIBED PHENOMENON THAT HAS A PROMINENT ROLE IN PHYSIOLOGICAL AND PATHOLOGICAL CELL-STATES. THIS EPIGENETIC MODIFICATION IS USUALLY GROUPED IN REGIONS DENOMINATED CPG ISLANDS, WHICH FREQUENTLY CO-LOCALIZE WITH GENE PROMOTERS, SILENCING THE TRANSCRIPTION OF THOSE GENES. RECENT GENOME-WIDE DNA METHYLATION STUDIES HAVE CHALLENGED THIS PARADIGM, DEMONSTRATING THAT DNA METHYLATION OF REGULATORY REGIONS OUTSIDE PROMOTERS IS ABLE TO INFLUENCE CELL-TYPE SPECIFIC GENE EXPRESSION PROGRAMS UNDER PHYSIOLOGIC OR PATHOLOGIC CONDITIONS. COUPLING GENOME-WIDE DNA METHYLATION ASSAYS WITH HISTONE MARK ANNOTATION HAS ALLOWED FOR THE IDENTIFICATION OF SPECIFIC EPIGENOMIC CHANGES THAT AFFECT ENHANCER REGULATORY REGIONS, REVEALING AN ADDITIONAL LAYER OF COMPLEXITY TO THE EPIGENETIC REGULATION OF GENE EXPRESSION. IN THIS REVIEW, WE SUMMARIZE THE NOVEL EVIDENCE FOR THE MOLECULAR AND BIOLOGICAL REGULATION OF DNA METHYLATION IN ENHANCER REGIONS AND THE DYNAMISM OF THESE CHANGES CONTRIBUTING TO THE FINE-TUNING OF GENE EXPRESSION. WE ALSO ANALYZE THE CONTRIBUTION OF ENHANCER DNA METHYLATION ON THE EXPRESSION OF RELEVANT GENES IN ACUTE MYELOID LEUKEMIA AND CHRONIC MYELOPROLIFERATIVE NEOPLASMS. THE CHARACTERIZATION OF THE ABERRANT ENHANCER DNA METHYLATION PROVIDES NOT ONLY A NOVEL PATHOGENIC MECHANISM FOR DIFFERENT TUMORS BUT ALSO HIGHLIGHTS NOVEL POTENTIAL THERAPEUTIC TARGETS FOR MYELOID DERIVED NEOPLASMS. 2019 18 6533 38 TRANSCRIPTIONAL REGULATION OF INFLAMMATORY GENES ASSOCIATED WITH SEVERE ASTHMA. THE 10% OF PATIENTS WITH THE MOST SEVERE ASTHMA ARE RESPONSIBLE FOR A LARGE PART OF HEALTHCARE EXPENDITURE AND MORBIDITY. UNDERSTANDING THE PROCESSES INVOLVED IS KEY IF NEW THERAPEUTIC APPROACHES ARE TO BE DEVELOPED. EVIDENCE IS ACCUMULATING THAT CHRONIC DISEASES SUCH AS ASTHMA ARE ASSOCIATED WITH TEMPORAL AND SPATIAL ALTERATIONS IN THE PATTERN OF INFLAMMATORY GENE EXPRESSION WITHIN THE AIRWAYS. EXPRESSION OF THESE GENES CAN BE REGULATED BY TRANSCRIPTIONAL, POSTTRANSCRIPTIONAL, TRANSLATIONAL AND EPIGENETIC MECHANISMS. IT IS WELL ESTABLISHED THAT BINDING OF ACTIVATED TRANSCRIPTION FACTORS TO SPECIFIC INDUCIBLE GENE PROMOTER SITES IS TIGHTLY CONTROLLED BY CHROMATIN STATE AS A RESULT OF HISTONE MODIFICATIONS, PARTICULARLY THE BALANCE BETWEEN HISTONE ACETYLATION AND DEACETYLATION [1]. THE INTERACTION BETWEEN TRANSCRIPTION FACTORS AND THE PROMOTER IS KEY TO THE DIVERSIFICATION OF GENE EXPRESSION IN A TIME DEPENDENT MANNER LEADING TO ALTERED GENE EXPRESSION PROFILES. ALTERATIONS OF THE ACCESSIBILITY OF TRANSCRIPTION FACTORS TO THE DNA CAN HAVE RESIDING EFFECTS UPON GENE TRANSCRIPTION. THIS REVIEW WILL FOCUS ON THE REGULATION OF SEVERAL GROUPS OF KEY GENES WHICH ARE INVOLVED IN CHRONIC AIRWAY INFLAMMATION AND REMODELLING IN ASTHMA DRAWING MAINLY FROM OUR EXPERIENCE OF STUDYING THESE PROCESSES IN AIRWAY SMOOTH MUSCLE CELLS. AN OVERVIEW IS SHOWN IN FIGURE 1. 2011 19 3379 28 HIV LATENCY AND THE NONCODING RNA THERAPEUTIC LANDSCAPE. THE HUMAN IMMUNODEFICIENCY VIRUS (HIV) BELONGS TO THE SUBFAMILY OF LENTIVIRUSES THAT ARE CHARACTERIZED BY LONG INCUBATION PERIODS AND CHRONIC, PERSISTENT INFECTION. THE VIRUS INTEGRATES INTO THE GENOME OF INFECTED CD4+ CELLS AND, IN A SUBPOPULATION OF CELLS, ADOPTS A TRANSCRIPTIONALLY SILENT STATE, A PROCESS REFERRED TO A VIRAL LATENCY. THIS PROPERTY MAKES IT EXCEEDINGLY DIFFICULT TO THERAPEUTICALLY TARGET THE VIRUS AND ERADICATE INFECTION. IF LEFT UNTREATED, THE INEXORABLE DEMISE OF THE INFECTED INDIVIDUAL'S IMMUNE SYSTEM ENSUES, A CAUSAL RESULT OF ACQUIRED IMMUNODEFICIENCY SYNDROME (AIDS). LATENTLY INFECTED CELLS PROVIDE A RESERVOIR THAT MAINTAINS VIRAL INFECTION INDEFINITELY. IN THIS CHAPTER WE EXPLORE THE ROLE OF NONCODING RNAS IN HIV INFECTION AND IN THE ESTABLISHMENT AND MAINTENANCE OF VIRAL LATENCY. BOTH SHORT AND LONG NONCODING RNAS ARE ENDOGENOUS MODULATORS OF EPIGENETIC REGULATION IN HUMAN CELLS AND PLAY AN ACTIVE ROLE IN GENE EXPRESSION. LASTLY, WE EXPLORE THERAPEUTIC MODALITIES BASED ON EXPRESSED RNAS THAT ARE CAPABLE OF COUNTERING INFECTION, TRANSCRIPTIONALLY REGULATING THE VIRUS, AND SUPPRESSING OR ACTIVATING THE LATENT STATE. 2015 20 2600 28 EPIGENETICS REGULATION DURING VIRUS-HOST INTERACTION AND THEIR EFFECTS ON THE VIRUS AND HOST CELL. EPIGENETICS, A FIELD OF STUDY FOCUSED ON CELLULAR GENE REGULATION INDEPENDENT OF DNA SEQUENCE ALTERATIONS, ENCOMPASSES DNA METHYLATION, HISTONE MODIFICATION AND MICRORNA MODIFICATION. EPIGENETICS PROCESSES PLAY A PIVOTAL ROLE IN GOVERNING THE LIFE CYCLES OF VIRUSES, ENABLING THEIR TRANSMISSION, PERSISTENCE, AND MAINTENANCE WITH IN HOST ORGANISMS. THIS REVIEW EXAMINES THE EPIGENETICS REGULATION OF DIVERSE VIRUS INCLUDING ORTHOMOXYVIRUSES, CORONAVIRUS, RETROVIRIDAE, MONONEGAVIRALES, AND POXVIRUSES AMONG OTHERS. THE INVESTIGATION ENCOMPASSES TEN REPRESENTATIVE VIRUSES FROM THESE FAMILIES. DETAILED EXPLORATION OF THE EPIGENETIC MECHANISMS UNDERLYING EACH VIRUS TYPE, INVOLVING MIRNA MODIFICATION, HISTONE MODIFICATION AND DNA METHYLATION, SHEDS LIGHT ON THE INTRICATE AND MULTIFACETED EPIGENETIC INTERPLAY BETWEEN VIRUSES AND THEIR HOSTS. FURTHERMORE, THIS REVIEW INVESTIGATES THE INFLUENCE OF THESE EPIGENETIC PROCESSES ON INFECTION CYCLES, EMPHASIZING THE UTILIZATION OF EPIGENETICS BY VIRUSES SUCH AS EPSTEIN-BARR VIRUS AND HUMAN IMMUNODEFICIENCY VIRUS (HIV) TO REGULATE GENE EXPRESSION DURING CHRONIC OR LATENT INFECTIONS, CONTROL LATENCY, AND TRANSITION TO LYTIC INFECTION. FINALLY, THE PAPER EXPLORES THE NOVEL TREATMENTS POSSIBILITIES STEMMING FROM THIS EPIGENETIC UNDERSTANDING. 2023