1 6397 92 THE ROLE OF TRANSPOSABLE ELEMENTS IN AGING AND CANCER. TRANSPOSABLE ELEMENTS (TES) CONSTITUTE A LARGE PORTION OF THE HUMAN GENOME. VARIOUS MECHANISMS AT THE TRANSCRIPTION AND POST-TRANSCRIPTION LEVELS DEVELOPED TO SUPPRESS TE ACTIVITY IN HEALTHY CONDITIONS. HOWEVER, A GROWING BODY OF EVIDENCE SUGGESTS THAT TE DYSREGULATION IS INVOLVED IN VARIOUS HUMAN DISEASES, INCLUDING AGE-RELATED DISEASES AND CANCER. IN THIS REVIEW, WE EXPLAINED HOW SENSING TES BY THE IMMUNE SYSTEM COULD INDUCE INNATE IMMUNE RESPONSES, CHRONIC INFLAMMATION, AND FOLLOWING AGE-RELATED DISEASES. WE ALSO NOTED THAT INFLAMMAGEING AND EXOGENOUS CARCINOGENS COULD TRIGGER THE UPREGULATION OF TES IN PRECANCEROUS CELLS. INCREASED INFLAMMATION COULD ENHANCE EPIGENETIC PLASTICITY AND UPREGULATION OF EARLY DEVELOPMENTAL TES, WHICH REWIRES THE TRANSCRIPTIONAL NETWORKS AND GIFT THE SURVIVAL ADVANTAGE TO THE PRECANCEROUS CELLS. IN ADDITION, UPREGULATED TES COULD INDUCE GENOME INSTABILITY, ACTIVATION OF ONCOGENES, OR INHIBITION OF TUMOR SUPPRESSORS AND CONSEQUENT CANCER INITIATION AND PROGRESSION. SO, WE SUGGEST THAT TES COULD BE CONSIDERED THERAPEUTIC TARGETS IN AGING AND CANCER. 2023 2 6571 24 TRANSPOSABLE ELEMENTS CROSS KINGDOM BOUNDARIES AND CONTRIBUTE TO INFLAMMATION AND AGEING: SOMATIC ACQUISITION OF FOREIGN TRANSPOSABLE ELEMENTS AS A CATALYST OF GENOME INSTABILITY, EPIGENETIC DYSREGULATION, INFLAMMATION, SENESCENCE, AND AGEING. THE DE-REPRESSION OF TRANSPOSABLE ELEMENTS (TES) IN MAMMALIAN GENOMES IS THOUGHT TO CONTRIBUTE TO GENOME INSTABILITY, INFLAMMATION, AND AGEING, YET IS VIEWED AS A CELL-AUTONOMOUS EVENT. IN CONTRAST TO MAMMALIAN CELLS, PROKARYOTES CONSTANTLY EXCHANGE GENETIC MATERIAL THROUGH TES, CROSSING BOTH CELL AND SPECIES BARRIERS, CONTRIBUTING TO RAPID MICROBIAL EVOLUTION AND DIVERSITY IN COMPLEX COMMUNITIES SUCH AS THE MAMMALIAN GUT. HERE, IT IS PROPOSED THAT TES RELEASED FROM PROKARYOTES IN THE MICROBIOME OR FROM PATHOGENIC INFECTIONS REGULARLY CROSS THE KINGDOM BARRIER TO THE SOMATIC CELLS OF THEIR EUKARYOTIC HOSTS. IT IS PROPOSED THIS HORIZONTAL TRANSFER OF TES FROM MICROBE TO HOST IS A STOCHASTIC, ONGOING CATALYST OF GENOME DESTABILIZATION, RESULTING IN STRUCTURAL AND EPIGENETIC VARIATIONS, AND ACTIVATION OF WELL-EVOLVED HOST DEFENSE MECHANISMS CONTRIBUTING TO INFLAMMATION, SENESCENCE, AND BIOLOGICAL AGEING. IT IS PROPOSED THAT INNATE IMMUNITY PATHWAYS DEFEND AGAINST THE HORIZONTAL ACQUISITION OF MICROBIAL TES, AND THAT ACTIVATION OF THIS PATHWAY DURING HORIZONTAL TRANSPOSON TRANSFER PROMOTES CHRONIC INFLAMMATION DURING AGEING. FINALLY, IT IS SUGGESTED THAT HORIZONTAL ACQUISITION OF PROKARYOTIC TES INTO MAMMALIAN GENOMES HAS BEEN MASKED AND SUBSEQUENTLY UNDER-REPORTED DUE TO FLAWS IN CURRENT SEQUENCING PIPELINES, AND NEW STRATEGIES TO UNCOVER THESE EVENTS ARE PROPOSED. 2020 3 6752 27 WIDESPREAD EXONIZATION OF TRANSPOSABLE ELEMENTS IN HUMAN CODING SEQUENCES IS ASSOCIATED WITH EPIGENETIC REGULATION OF TRANSCRIPTION. TRANSPOSABLE ELEMENTS (TES) HAVE LONG BEEN REGARDED AS SELFISH OR JUNK DNA HAVING LITTLE OR NO ROLE IN THE REGULATION OR FUNCTIONING OF THE HUMAN GENOME. HOWEVER, OVER THE PAST SEVERAL YEARS THIS VIEW CAME TO BE CHALLENGED AS SEVERAL STUDIES PROVIDED ANECDOTAL AS WELL AS GLOBAL EVIDENCE FOR THE CONTRIBUTION OF TES TO THE REGULATORY AND CODING NEEDS OF HUMAN GENES. IN THIS STUDY, WE EXPLORED THE INCORPORATION AND EPIGENETIC REGULATION OF CODING SEQUENCES DONATED BY TES USING GENE EXPRESSION AND OTHER ANCILLARY GENOMICS DATA FROM TWO HUMAN HEMATOPOIETIC CELL-LINES: GM12878 (A LYMPHOBLASTOID CELL LINE) AND K562 (A CHRONIC MYELOGENOUS LEUKEMIA CELL LINE). IN EACH CELL LINE, WE FOUND SEVERAL THOUSAND INSTANCES OF TES DONATING CODING SEQUENCES TO HUMAN GENES. WE COMPARED THE TRANSCRIPTOME ASSEMBLY OF THE RNA SEQUENCING (RNA-SEQ) READS WITH AND WITHOUT THE AID OF A REFERENCE TRANSCRIPTOME AND FOUND THAT THE PERCENTAGE OF GENES THAT INCORPORATE TES IN THEIR CODING SEQUENCES IS SIGNIFICANTLY GREATER THAN THAT OBTAINED FROM THE REFERENCE TRANSCRIPTOME ASSEMBLIES USING REFSEQ AND GENCODE GENE MODELS. WE ALSO USED HISTONE MODIFICATIONS CHROMATIN IMMUNOPRECIPITATION SEQUENCING (CHIP-SEQ) DATA, CAP ANALYSIS OF GENE EXPRESSION (CAGE) DATA AND DNASEI HYPERSENSITIVITY SITE (DHS) DATA TO DEMONSTRATE THE EPIGENETIC REGULATION OF THE TE DERIVED CODING SEQUENCES. OUR RESULTS SUGGEST THAT TES FORM A SIGNIFICANTLY HIGHER PERCENTAGE OF CODING SEQUENCES THAN REPRESENTED IN GENE ANNOTATION DATABASES AND THESE TE DERIVED SEQUENCES ARE EPIGENETICALLY REGULATED IN ACCORDANCE WITH THEIR EXPRESSION IN THE TWO CELL TYPES. 2013 4 3644 28 INCREASED LEVELS OF ENDOGENOUS RETROVIRUSES TRIGGER FIBROINFLAMMATION AND PLAY A ROLE IN KIDNEY DISEASE DEVELOPMENT. INFLAMMATION IS A COMMON FEATURE OF ALL FORMS OF CHRONIC KIDNEY DISEASE; HOWEVER, THE UNDERLYING MECHANISM REMAINS POORLY UNDERSTOOD. EVOLUTIONARILY INHERITED ENDOGENOUS RETROVIRUSES (ERVS) HAVE THE POTENTIAL TO TRIGGER AN IMMUNE REACTION. COMPREHENSIVE RNA-SEQUENCING OF CONTROL AND DISEASED KIDNEYS FROM HUMAN AND MOUSE DISEASE MODELS INDICATED HIGHER EXPRESSION OF TRANSPOSABLE ELEMENTS (TES) AND ERVS IN DISEASED KIDNEYS. LOSS OF CYTOSINE METHYLATION CAUSING EPIGENETIC DEREPRESSION LIKELY CONTRIBUTES TO AN INCREASE IN ERV LEVELS. GENETIC DELETION/PHARMACOLOGICAL INHIBITION OF DNA METHYLTRANSFERASE 1 (DNMT1) INDUCES ERV EXPRESSION. IN CULTURED KIDNEY TUBULE CELLS, ERVS ELICIT THE ACTIVATION OF CYTOSOLIC NUCLEOTIDE SENSORS SUCH AS RIG-I, MDA5, AND STING. ERVS EXPRESSIONS IN KIDNEY TUBULES TRIGGER RIG-I/STING, AND CYTOKINE EXPRESSION, AND CORRELATE WITH THE PRESENCE OF IMMUNE CELLS. GENETIC DELETION OF RIG-I OR STING OR TREATMENT WITH REVERSE TRANSCRIPTASE INHIBITOR AMELIORATES KIDNEY FIBROINFLAMMATION. OUR DATA INDICATE AN IMPORTANT ROLE OF EPIGENETIC DEREPRESSION-INDUCED ERV ACTIVATION TRIGGERING RENAL FIBROINFLAMMATION. 2023 5 374 31 AN ENDOSIRNA-BASED REPRESSION MECHANISM COUNTERACTS TRANSPOSON ACTIVATION DURING GLOBAL DNA DEMETHYLATION IN EMBRYONIC STEM CELLS. ERASURE OF DNA METHYLATION AND REPRESSIVE CHROMATIN MARKS IN THE MAMMALIAN GERMLINE LEADS TO RISK OF TRANSCRIPTIONAL ACTIVATION OF TRANSPOSABLE ELEMENTS (TES). HERE, WE USED MOUSE EMBRYONIC STEM CELLS (ESCS) TO IDENTIFY AN ENDOSIRNA-BASED MECHANISM INVOLVED IN SUPPRESSION OF TE TRANSCRIPTION. IN ESCS WITH DNA DEMETHYLATION INDUCED BY ACUTE DELETION OF DNMT1, WE SAW AN INCREASE IN SENSE TRANSCRIPTION AT TES, RESULTING IN AN ABUNDANCE OF SENSE/ANTISENSE TRANSCRIPTS LEADING TO HIGH LEVELS OF ARGONAUTE2 (AGO2)-BOUND SMALL RNAS. INHIBITION OF DICER OR AGO2 EXPRESSION REVEALED THAT SMALL RNAS ARE INVOLVED IN AN IMMEDIATE RESPONSE TO DEMETHYLATION-INDUCED TRANSPOSON ACTIVATION, WHILE THE DEPOSITION OF REPRESSIVE HISTONE MARKS FOLLOWS AS A CHRONIC RESPONSE. IN VIVO, WE ALSO FOUND TE-SPECIFIC ENDOSIRNAS PRESENT DURING PRIMORDIAL GERM CELL DEVELOPMENT. OUR RESULTS SUGGEST THAT ANTISENSE TE TRANSCRIPTION IS A "TRAP" THAT ELICITS AN ENDOSIRNA RESPONSE TO RESTRAIN ACUTE TRANSPOSON ACTIVITY DURING EPIGENETIC REPROGRAMMING IN THE MAMMALIAN GERMLINE. 2017 6 6570 27 TRANSPOSABLE ELEMENTS AND THEIR POTENTIAL ROLE IN COMPLEX LUNG DISORDER. TRANSPOSABLE ELEMENTS (TES) ARE A CLASS OF MOBILE GENETIC ELEMENTS (MGES) THAT WERE LONG REGARDED AS JUNK DNA, WHICH MAKE UP APPROXIMATELY 45% OF THE GENOME. ALTHOUGH MOST OF THESE ELEMENTS ARE RENDERED INACTIVE BY MUTATIONS AND OTHER GENE SILENCING MECHANISMS, TES SUCH AS LONG INTERSPERSED NUCLEAR ELEMENTS (LINES) ARE STILL ACTIVE AND TRANSLOCATE WITHIN THE GENOME. DURING TRANSPOSITION, THEY MAY CREATE LESIONS IN THE GENOME, THEREBY ACTING AS EPIGENETIC MODIFIERS. APPROXIMATELY 65 DISEASE-CAUSING LINE INSERTION EVENTS HAVE BEEN REPORTED THUS FAR; HOWEVER, ANY POSSIBLE ROLE OF TES IN COMPLEX DISORDERS IS NOT WELL ESTABLISHED. CHRONIC OBSTRUCTIVE PULMONARY DISEASE (COPD) IS ONE SUCH COMPLEX DISEASE THAT IS PRIMARILY CAUSED BY CIGARETTE SMOKING. ALTHOUGH THE EXACT MOLECULAR MECHANISM UNDERLYING COPD REMAINS UNCLEAR, OXIDATIVE STRESS IS THOUGHT TO BE THE MAIN FACTOR IN THE PATHOGENESIS OF COPD. IN THIS REVIEW, WE EXPLORE THE POTENTIAL ROLE OF OXIDATIVE STRESS IN EPIGENETIC ACTIVATION OF TES SUCH AS LINES AND THE SUBSEQUENT CASCADE OF MOLECULAR DAMAGE. RECENT ADVANCEMENTS IN SEQUENCING AND COMPUTATION HAVE EASED THE IDENTIFICATION OF MOBILE ELEMENTS. THEREFORE, A COMPARATIVE STUDY ON THE ACTIVITY OF THESE ELEMENTS AND MARKERS FOR GENOME INSTABILITY WOULD GIVE MORE INSIGHT ON THE RELATIONSHIP BETWEEN MGES AND COMPLEX DISORDER SUCH AS COPD. 2013 7 825 24 CHARACTERIZATION OF FUNCTIONAL TRANSPOSABLE ELEMENT ENHANCERS IN ACUTE MYELOID LEUKEMIA. TRANSPOSABLE ELEMENTS (TES) HAVE BEEN SHOWN TO HAVE IMPORTANT GENE REGULATORY FUNCTIONS AND THEIR ALTERATION COULD LEAD TO DISEASE PHENOTYPES. ACUTE MYELOID LEUKEMIA (AML) DEVELOPS AS A CONSEQUENCE OF A SERIES OF GENETIC CHANGES IN HEMATOPOIETIC PRECURSOR CELLS, INCLUDING MUTATIONS IN EPIGENETIC FACTORS. HERE, WE SET OUT TO STUDY THE GENE REGULATORY ROLE OF TES IN AML. WE FIRST EXPLORED THE EPIGENETIC LANDSCAPE OF TES IN AML PATIENTS USING ATAC-SEQ DATA. WE SHOW THAT A LARGE NUMBER OF TES IN GENERAL, AND MORE SPECIFICALLY MAMMALIAN-WIDE INTERSPERSED REPEATS (MIRS), ARE MORE ENRICHED IN AML CELLS THAN IN NORMAL BLOOD CELLS. WE OBTAINED A SIMILAR FINDING WHEN ANALYZING HISTONE MODIFICATION DATA IN AML PATIENTS. GENE ONTOLOGY ENRICHMENT ANALYSIS SHOWED THAT GENES NEAR MIRS IN OPEN CHROMATIN REGIONS ARE INVOLVED IN LEUKEMOGENESIS. TO FUNCTIONALLY VALIDATE THEIR REGULATORY ROLE, WE SELECTED 19 MIR REGIONS IN AML CELLS, AND TESTED THEM FOR ENHANCER ACTIVITY IN AN AML CELL LINE (KASUMI-1) AND A CHRONIC MYELOID LEUKEMIA (CML) CELL LINE (K562); THE RESULTS REVEALED SEVERAL MIRS TO BE FUNCTIONAL ENHANCERS. TAKEN TOGETHER, OUR RESULTS SUGGEST THAT TES ARE POTENTIALLY INVOLVED IN MYELOID LEUKEMOGENESIS AND HIGHLIGHT THESE SEQUENCES AS POTENTIAL CANDIDATES HARBORING AML-ASSOCIATED VARIATION. 2020 8 1174 27 CONTRIBUTION OF TRANSPOSABLE ELEMENTS TO TRANSGENERATIONAL EFFECTS OF CHRONIC RADIOACTIVE EXPOSURE OF NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER LIVING FOR A LONG TIME IN THE ZONE OF THE CHERNOBYL NUCLEAR DISASTER. THE ACCIDENT AT THE CHERNOBYL NUCLEAR POWER PLANT (CHNPP) LED TO THE NEGATIVE IMPACT OF CHRONIC RADIOACTIVE CONTAMINATION ON POPULATIONS OF ORGANISMS ASSOCIATED WITH THE TRANSGENERATIONAL TRANSMISSION OF GENOME INSTABILITY. WHEN THE DESTABILIZATION OF GENOME, DIFFERENT GENETIC DAMAGES OCCUR, THE ACCUMULATION OF WHICH LEADS TO THE FORMATION OF MUTATIONS, MORPHOLOGICAL ANOMALIES, AND MORTALITY IN THE OFFSPRING. THE MECHANISMS UNDERLYING THE MANIFESTATION OF TRANSGENERATIONAL EVENTS IN THE OFFSPRING OF IRRADIATED PARENTS ARE NOT WELL UNDERSTOOD. IN THIS STUDY, FOR THE FIRST TIME, THE FEATURES OF THE INFLUENCE OF TRANSPOSABLE ELEMENTS (TES) ON THE LONG-TERM BIOLOGICAL CONSEQUENCES OF THE CHNPP ARE CONSIDERED. IN THIS WORK, SPECIMENS OF D. MELANOGASTER OBTAINED FROM NATURAL POPULATIONS IN 2007 IN THE AREAS OF THE CHNPP WITH HETEROGENEOUS RADIOACTIVE CONTAMINATION WERE STUDIED. THE DESCENDANTS FROM THESE POPULATIONS WERE MAINTAINED IN LABORATORY (INBRED) CONDITIONS FOR 160 GENERATIONS. A STABLE TRANSGENERATIONAL TRANSMISSION OF DOMINANT LETHAL MUTATIONS (DLMS) TO THE OFFSPRING OF ALL STUDIED POPULATIONS WAS SHOWN. THE DLM FREQUENCIES STRONGLY WERE CORRELATED WITH THE LEVEL OF SURVIVAL OF OFFSPRING. THE MEAN FREQUENCIES OF RECESSIVE SEX-LINKED LETHAL MUTATIONS VARIED AT THE LEVEL OF SPONTANEOUS POINT MUTATIONS. THE SIMULTANEOUS PRESENCE OF P, HOBO AND I ELEMENTS INDICATES THAT THE STUDIED POPULATIONS DO NOT HAVE A DEFINITE CYTOTYPE, THEIR PHENOTYPIC STATUS IS UNSTABLE. THE BEHAVIOR OF TES IN THE GENOMES OF OFFSPRING DEPENDS NOT ONLY ON PARENTAL EXPOSURE, BUT ALSO ON ORIGIN OF POPULATION, DISTANCE TO THE CHNPP, AND INBRED CONDITIONS. THE OBTAINED RESULTS CONFIRM THE HYPOTHESIS THAT TES ARE INVOLVED IN TRANSGENERATIONAL TRANSMISSION AND ACCUMULATION OF MUTATIONS BY THE OFFSPRING OF IRRADIATED PARENTS. THE TES PATTERN PRESENT IN THE CHERNOBYL GENOMES OF D. MELANOGASTER IS A PECULIAR OF EPIGENETIC MECHANISM FOR THE REGULATION OF PLASTICITY AND ADAPTATION OF POPULATIONS LIVING FOR MANY GENERATIONS UNDER CONDITIONS OF A TECHNOGENICALLY CAUSED RADIATION BACKGROUND. 2022 9 5134 33 POTENTIAL HEALTH RISKS OF MRNA-BASED VACCINE THERAPY: A HYPOTHESIS. THERAPEUTIC APPLICATIONS OF SYNTHETIC MRNA WERE PROPOSED MORE THAN 30 YEARS AGO, AND ARE CURRENTLY THE BASIS OF ONE OF THE VACCINE PLATFORMS USED AT A MASSIVE SCALE AS PART OF THE PUBLIC HEALTH STRATEGY TO GET COVID-19 UNDER CONTROL. TO DATE, THERE ARE NO PUBLISHED STUDIES ON THE BIODISTRIBUTION, CELLULAR UPTAKE, ENDOSOMAL ESCAPE, TRANSLATION RATES, FUNCTIONAL HALF-LIFE AND INACTIVATION KINETICS OF SYNTHETIC MRNA, RATES AND DURATION OF VACCINE-INDUCED ANTIGEN EXPRESSION IN DIFFERENT CELL TYPES. FURTHERMORE, DESPITE THE ASSUMPTION THAT THERE IS NO POSSIBILITY OF GENOMIC INTEGRATION OF THERAPEUTIC SYNTHETIC MRNA, ONLY ONE RECENT STUDY HAS EXAMINED INTERACTIONS BETWEEN VACCINE MRNA AND THE GENOME OF TRANSFECTED CELLS, AND REPORTED THAT AN ENDOGENOUS RETROTRANSPOSON, LINE-1 IS UNSILENCED FOLLOWING MRNA ENTRY TO THE CELL, LEADING TO REVERSE TRANSCRIPTION OF FULL LENGTH VACCINE MRNA SEQUENCES, AND NUCLEAR ENTRY. THIS FINDING SHOULD BE A MAJOR SAFETY CONCERN, GIVEN THE POSSIBILITY OF SYNTHETIC MRNA-DRIVEN EPIGENETIC AND GENOMIC MODIFICATIONS ARISING. WE PROPOSE THAT IN SUSCEPTIBLE INDIVIDUALS, CYTOSOLIC CLEARANCE OF NUCLEOTIDE MODIFIED SYNTHETIC (NMS-MRNAS) IS IMPEDED. SUSTAINED PRESENCE OF NMS-MRNA IN THE CYTOPLASM DEREGULATES AND ACTIVATES ENDOGENOUS TRANSPOSABLE ELEMENTS (TES), CAUSING SOME OF THE MRNA COPIES TO BE REVERSE TRANSCRIBED. THE CYTOSOLIC ACCUMULATION OF THE NMS-MRNA AND THE REVERSE TRANSCRIBED CDNA MOLECULES ACTIVATES RNA AND DNA SENSORY PATHWAYS. THEIR CONCURRENT ACTIVATION INITIATES A SYNCHRONIZED INNATE RESPONSE AGAINST NON-SELF NUCLEIC ACIDS, PROMPTING TYPE-I INTERFERON AND PRO-INFLAMMATORY CYTOKINE PRODUCTION WHICH, IF UNREGULATED, LEADS TO AUTOINFLAMMATORY AND AUTOIMMUNE CONDITIONS, WHILE ACTIVATED TES INCREASE THE RISK OF INSERTIONAL MUTAGENESIS OF THE REVERSE TRANSCRIBED MOLECULES, WHICH CAN DISRUPT CODING REGIONS, ENHANCE THE RISK OF MUTATIONS IN TUMOUR SUPPRESSOR GENES, AND LEAD TO SUSTAINED DNA DAMAGE. SUSCEPTIBLE INDIVIDUALS WOULD THEN EXPECTEDLY HAVE AN INCREASED RISK OF DNA DAMAGE, CHRONIC AUTOINFLAMMATION, AUTOIMMUNITY AND CANCER. IN LIGHT OF THE CURRENT MASS ADMINISTRATION OF NMS-MRNA VACCINES, IT IS ESSENTIAL AND URGENT TO FULLY UNDERSTAND THE INTRACELLULAR CASCADES INITIATED BY CELLULAR UPTAKE OF SYNTHETIC MRNA AND THE CONSEQUENCES OF THESE MOLECULAR EVENTS. 2023 10 3419 31 HUMAN LINE-1 RETROTRANSPOSONS: IMPACTS ON THE GENOME AND REGULATION BY HOST FACTORS. GENOME SEQUENCING REVEALED THAT NEARLY HALF OF THE HUMAN GENOME IS COMPRISED OF TRANSPOSABLE ELEMENTS. ALTHOUGH MOST OF THESE ELEMENTS HAVE BEEN RENDERED INACTIVE DUE TO MUTATIONS, FULL-LENGTH INTACT LONG INTERSPERSED ELEMENT-1 (LINE-1 OR L1) COPIES RETAIN THE ABILITY TO MOBILIZE THROUGH RNA INTERMEDIATES BY A SO-CALLED "COPY-AND-PASTE" MECHANISM, TERMED RETROTRANSPOSITION. L1 IS THE ONLY KNOWN AUTONOMOUS MOBILE GENETIC ELEMENT IN THE GENOME, AND ITS RETROTRANSPOSITION CONTRIBUTES TO INTER- OR INTRA-INDIVIDUAL GENETIC VARIATION WITHIN THE HUMAN POPULATION. HOWEVER, L1 RETROTRANSPOSITION ALSO POSES A THREAT TO GENOME INTEGRITY DUE TO GENE DISRUPTION AND CHROMOSOMAL INSTABILITY. MOREOVER, RECENT STUDIES SUGGEST THAT ABERRANT L1 EXPRESSION CAN IMPACT HUMAN HEALTH BY CAUSING DISEASES SUCH AS CANCER AND CHRONIC INFLAMMATION THAT MIGHT LEAD TO AUTOIMMUNE DISORDERS. TO COUNTERACT THESE ADVERSE EFFECTS, THE HOST CELLS HAVE EVOLVED MULTIPLE LAYERS OF DEFENSE MECHANISMS AT THE EPIGENETIC, RNA AND PROTEIN LEVELS. INTRIGUINGLY, SEVERAL HOST FACTORS HAVE ALSO BEEN REPORTED TO FACILITATE L1 RETROTRANSPOSITION, SUGGESTING THAT THERE IS COMPETITION BETWEEN NEGATIVE AND POSITIVE REGULATION OF L1 BY HOST FACTORS. HERE, WE SUMMARIZE THE KNOWN HOST PROTEINS THAT REGULATE L1 ACTIVITY AT DIFFERENT STAGES OF THE REPLICATION CYCLE AND DISCUSS HOW THESE FACTORS MODULATE DISEASE-ASSOCIATED PHENOTYPES CAUSED BY L1. 2022 11 3845 14 IS AGING A "RETRO"SPECTIVE EVENT? REACTIVATION OF ENDOGENOUS RETROVIRUSES (ERVS), THE RELICS OF ANCIENT INFECTIONS, HAS BEEN IMPLICATED IN A NUMBER OF DISEASE CONTEXTS. IN THIS ISSUE OF CELL, LIU ET AL. SHOW HOW REACTIVATION OF ERVS IN OLD AGE CAN INDUCE SENESCENCE. THIS AWAKENING OF ERVS IS ASSOCIATED WITH THEIR EPIGENETIC DEREPRESSION AND CONTRIBUTES TO AGE-ASSOCIATED CHRONIC INFLAMMATION. 2023 12 5344 23 RADIOBIOLOGICAL FEATURES IN OFFSPRING OF NATURAL POPULATIONS OF DROSOPHILA MELANOGASTER AFTER CHERNOBYL ACCIDENT. IN THEIR NATURAL HABITATS, POPULATIONS OF ORGANISMS ARE FACED WITH DIFFERENT LEVELS OF CHRONIC LOW-INTENSITY RADIATION, CAUSING A WIDE RANGE OF RADIOBIOLOGICAL EFFECTS (FROM RADIOSENSITIVITY TO RADIOADAPTIVE RESPONSE AND HORMESIS). IN THIS STUDY, SPECIMENS OF DROSOPHILA MELANOGASTER WERE SELECTED FROM TERRITORIES OF THE CHERNOBYL NUCLEAR POWER PLANT WITH DIFFERENT LEVELS OF RADIOACTIVE CONTAMINATION. THE ISOGENIC STOCKS DERIVED FROM THESE SPECIMENS REPRESENT THE GENETIC SYSTEMS OF CURRENT POPULATIONS AND MAKE IT POSSIBLE TO STUDY RADIORESISTANCE AND ITS MECHANISMS IN FUTURE GENERATIONS UNDER CONTROLLED LABORATORY CONDITIONS. PREVIOUS STUDIES HAVE SHOWN THAT TRANSGENERATIONAL RADIATION EFFECTS AT THE LEVEL OF LETHAL MUTATIONS AND SURVIVAL RATE ARE UNSTABLE AND DEPEND NOT ONLY ON THE LEVEL OF CHRONIC LOW-INTENSITY IRRADIATION, BUT ALSO ON OTHER FACTORS. A SINGLE ACUTE IRRADIATION EXPOSURE OF OFFSPRING WHOSE PARENTS INHABITED A SITE WITH A HIGHER LEVEL OF CHRONIC IRRADIATION MADE IT POSSIBLE TO REVEAL PRONOUNCED RADIORESISTANT FEATURES IN THE OFFSPRING. AND THE OFFSPRING WHOSE PARENTS WERE EXPOSED TO RADIATION LEVELS CLOSE TO THE NATURAL RADIATION BACKGROUND, ON THE CONTRARY, ACQUIRED RADIOSENSITIVE FEATURES. THEIR RESPONSE TO ACUTE EXPOSURE INCLUDES A HIGH-FREQUENCY OF LETHAL MUTATIONS AND A SHORT LIFESPAN. THE DIFFERENTIAL RESPONSE TO DIFFERENT LEVELS OF CHRONIC PARENTAL EXPOSURE IS CAUSED BY DIFFERENCES IN THE ACTIVITIES OF CERTAIN TRANSPOSONS THAT DESTABILIZE THE GENOME. OUR DATA CONTRIBUTE TO THE UNDERSTANDING OF GENETIC AND EPIGENETIC MECHANISMS (VIA TRANSPOSON ACTIVITY) OF THE EFFECT OF PARENTAL RADIATION EXPOSURE ON THE HEALTH AND ADAPTIVE POTENTIAL OF POPULATIONS AFFECTED BY THE TECHNOGENICALLY INCREASED RADIATION BACKGROUND. 2022 13 3798 25 INTERPLAY BETWEEN ACTIVATION OF ENDOGENOUS RETROVIRUSES AND INFLAMMATION AS COMMON PATHOGENIC MECHANISM IN NEUROLOGICAL AND PSYCHIATRIC DISORDERS. HUMAN ENDOGENOUS RETROVIRUSES (ERVS) ARE ANCESTORIAL RETROVIRAL ELEMENTS THAT WERE INTEGRATED INTO OUR GENOME THROUGH GERMLINE INFECTIONS AND INSERTIONS DURING EVOLUTION. THEY HAVE REPEATEDLY BEEN IMPLICATED IN THE AETIOLOGY AND PATHOPHYSIOLOGY OF NUMEROUS HUMAN DISORDERS, PARTICULARLY IN THOSE THAT AFFECT THE CENTRAL NERVOUS SYSTEM. IN ADDITION TO THE KNOWN ASSOCIATION OF ERVS WITH MULTIPLE SCLEROSIS AND AMYOTROPHIC LATERAL SCLEROSIS, A GROWING NUMBER OF STUDIES LINKS THE INDUCTION AND EXPRESSION OF THESE RETROVIRAL ELEMENTS WITH THE ONSET AND SEVERITY OF NEURODEVELOPMENTAL AND PSYCHIATRIC DISORDERS. ALTHOUGH THESE DISORDERS DIFFER IN TERMS OF OVERALL DISEASE PATHOLOGY AND CAUSALITIES, A CERTAIN DEGREE OF (SUBCLINICAL) CHRONIC INFLAMMATION CAN BE IDENTIFIED IN ALL OF THEM. BASED ON THESE COMMONALITIES, WE DISCUSS THE BIDIRECTIONAL RELATIONSHIP BETWEEN ERV EXPRESSION AND INFLAMMATION AND HIGHLIGHT THAT NUMEROUS ENTRY POINTS TO THIS RECIPROCAL SEQUENCE OF EVENTS EXIST, INCLUDING INITIAL INFECTIONS WITH ERV-ACTIVATING PATHOGENS, EXPOSURE TO NON-INFECTIOUS INFLAMMATORY STIMULI, AND CONDITIONS IN WHICH EPIGENETIC SILENCING OF ERV ELEMENTS IS DISRUPTED. 2023 14 1219 29 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 15 340 21 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 16 851 20 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 17 2124 23 EPIGENETIC IMPLICATION OF GENE-ADJACENT RETROELEMENTS IN HELICOBACTER PYLORI-INFECTED ADULTS. A CHRONIC INFLAMMATORY CONDITION OF GASTRIC MUCOSA CAN FACILITATE THE INFLUX OF NEW STEM CELLS INTO THE STOMACH. EPIGENETIC CODES, SUCH AS DNA METHYLATION, MAY BE RESPONSIBLE FOR THE STABLE MAINTENANCE OF EPIGENETIC PHENOTYPES ESTABLISHED IN THE NEW STOMACH-ADAPTED STEM CELLS. A NUMBER OF HYPOTHESES HAVE BEEN MADE FOR THE ROLE OF CPG-ISLAND METHYLATION, WHICH IS COMMON IN THE HELICOBACTER PYLORI-INFECTED STOMACH. HOWEVER, THEY COULD NOT EXPLAIN THE PLAUSIBLE ROLE OF CPG-ISLAND METHYLATION IN THE RE-ESTABLISHMENT OF EPIGENETIC PHENOTYPES. THESE ISLANDS ARE HIGHLY REPETITIVE SEQUENCES DENSELY METHYLATED THROUGHOUT THE HUMAN GENOME, THE SO-CALLED PARASITIC RETROELEMENTS, WHICH EXPAND A NUMBER OF CDNA COPIES WITH REVERSE TRANSCRIPTASE. THE DENSELY METHYLATED RETROELEMENTS ADJACENT TO THE HOST GENES CAN FORM THE TRANSITIONAL-CPG SITES AROUND GENE-CONTROL REGIONS THAT ARE BARELY METHYLATED. THIS REVIEW FOCUSES ON THE PUTATIVE ROLE OF TRANSITIONAL CPG METHYLATION IN THE ADAPTIVE DIFFERENTIATION OF NEW STEM CELLS IN THE H. PYLORI-INFECTED STOMACH. 2012 18 2091 22 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 19 1218 27 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 20 6126 35 THE EPIGENETIC MODIFIER PBRM1 RESTRICTS THE BASAL ACTIVITY OF THE INNATE IMMUNE SYSTEM BY REPRESSING RETINOIC ACID-INDUCIBLE GENE-I-LIKE RECEPTOR SIGNALLING AND IS A POTENTIAL PROGNOSTIC BIOMARKER FOR COLON CANCER. IT HAS LONG BEEN KNOWN THAT PATIENTS SUFFERING FROM INFLAMMATORY BOWEL DISEASE (IBD) HAVE AN INCREASED RISK OF DEVELOPING COLORECTAL CANCER (CRC). THE INNATE IMMUNE SYSTEM OF HOST CELLS PROVIDES A FIRST-LINE DEFENCE AGAINST PATHOGENIC INFECTION, WHEREAS AN UNCONTROLLED INFLAMMATORY RESPONSE UNDER HOMEOSTATIC CONDITIONS USUALLY LEADS TO PATHOLOGICAL CONSEQUENCES, AS EXEMPLIFIED BY THE CHRONIC INFLAMMATION OF IBD. THE KEY MOLECULES AND PATHWAYS KEEPING INNATE IMMUNITY IN CHECK ARE STILL POORLY DEFINED. HERE, WE REPORT THAT THE CHROMATIN REMODELLER POLYBROMO-1 (PBRM1) IS A REPRESSOR OF INNATE IMMUNE SIGNALLING MEDIATED BY RETINOIC ACID-INDUCIBLE GENE-I (RIG-I)-LIKE RECEPTORS (RLRS). KNOCKDOWN OF PBRM1 IN COLON CANCER CELLS INCREASED THE EXPRESSION OF TWO RECEPTOR GENES (RIG-I AND MDA5) AND UPREGULATED INTERFERON (IFN)-RELATED AND INFLAMMATION-RELATED GENE SIGNATURES. THE INNATE IMMUNE SIGNAL STIMULATED BY A DOUBLE-STRANDED RNA VIRAL MIMIC WAS EXAGGERATED BY PBRM1 SUPPRESSION. PBRM1 COOPERATED WITH POLYCOMB PROTEIN EZH2 TO DIRECTLY BIND THE CIS-REGULATORY ELEMENTS OF RIG-I AND MDA5, THEREBY SUPPRESSING THEIR TRANSCRIPTION. MOREOVER, UPREGULATION OF RIG-I AND MDA5 IS REQUIRED FOR IFN RESPONSE ACTIVATION INDUCED BY PBRM1 SILENCING. TRIM25, A PROTEIN STIMULATED BY THE RLR PATHWAY AND IFN PRODUCTION, PHYSICALLY INTERACTED WITH PBRM1 AND INDUCED PBRM1 PROTEIN DESTABILIZATION BY PROMOTING ITS UBIQUITINATION. THESE FINDINGS REVEAL A PBRM1-RLR REGULATORY CIRCUIT THAT CAN KEEP INNATE IMMUNE ACTIVITY AT A MINIMAL LEVEL IN RESTING CELLS, AND ALSO ENSURE A ROBUST INFLAMMATORY RESPONSE IN THE CASE OF PATHOGEN INVASION. PBRM1 WAS FOUND TO BE DOWNREGULATED IN PRIMARY TISSUES FROM PATIENTS WITH CRC OR IBD, AND ITS EXPRESSION CORRELATED NEGATIVELY WITH THAT OF RLR GENES AND INTERFERON-STIMULATED GENES IN CRC SAMPLES. LOWER PBRM1 EXPRESSION WAS ASSOCIATED WITH ADVANCED PATHOLOGICAL GRADE AND POORER SURVIVAL OF CRC PATIENTS, INDICATING THAT PBRM1 COULD SERVE AS A POTENTIAL PROGNOSTIC BIOMARKER FOR CRC. COPYRIGHT (C) 2017 PATHOLOGICAL SOCIETY OF GREAT BRITAIN AND IRELAND. PUBLISHED BY JOHN WILEY & SONS, LTD. 2018