2023
Cancer Relevance of Circulating Antibodies Against LINE-1 Antigens in Humans
Vylegzhanina A, Bespalov I, Novototskaya-Vlasova K, Hall B, Gleiberman A, Yu H, Leontieva O, Leonova K, Kurnasov O, Osterman A, Dy G, Komissarov A, Vasilieva E, Gehlhausen J, Iwasaki A, Ambrosone C, Tsuji T, Matsuzaki J, Odunsi K, Andrianova E, Gudkov A. Cancer Relevance of Circulating Antibodies Against LINE-1 Antigens in Humans. Cancer Research Communications 2023, 3: 2256-2267. PMID: 37870410, PMCID: PMC10631453, DOI: 10.1158/2767-9764.crc-23-0289.Peer-Reviewed Original ResearchMeSH KeywordsAutoantibodiesHumansImmunoglobulin GLong Interspersed Nucleotide ElementsNeoplasmsRetroelementsConceptsL1 antigenCancer typesDisease stage 1Discovery of autoantibodiesHigh IgG titersTumor-associated antigensDetermination of immunoreactivityTumor immunoreactivityCirculating AntibodiesIgG titersAntibody responseImmune responseLiver cancerReactive IgGHealthy individualsCurable cancer typesImmune systemAntigenNormal tissuesPatientsCancerEarly detectionElevated levelsCarcinogenic processAutoantibodiesRegulation of gene editing using T-DNA concatenation
Dickinson L, Yuan W, LeBlanc C, Thomson G, Wang S, Jacob Y. Regulation of gene editing using T-DNA concatenation. Nature Plants 2023, 9: 1398-1408. PMID: 37653336, PMCID: PMC11193869, DOI: 10.1038/s41477-023-01495-w.Peer-Reviewed Original ResearchConceptsT-DNA copy numberLong terminal repeatGene editingCopy numberT-DNA copiesPlant gene editingT-DNA structureTransfer DNAT-DNADNA repeatsAgrobacterium tumefaciensDNA repairSingle copyGene targetingExogenous DNATerminal repeatMolecular determinantsArabidopsisLarge concatemersRepeatsDNAEditingCopiesRad17Retrotransposons
2022
Structures of a mobile intron retroelement poised to attack its structured DNA target
Chung K, Xu L, Chai P, Peng J, Devarkar S, Pyle A. Structures of a mobile intron retroelement poised to attack its structured DNA target. Science 2022, 378: 627-634. PMID: 36356138, PMCID: PMC10190682, DOI: 10.1126/science.abq2844.Peer-Reviewed Original ResearchConceptsGroup II intronsCryo-electron microscopy structureDNA targetsStem-loop motifMicroscopy structureGenetic diversificationDNA substratesForward splicingRetroelementsAncient elementsDNA targetingIntronsTertiary complexRibozymeRetrotransposonsGenomeRetrotranspositionSplicingComplexesRNPDNAMotifTargetDiversificationTargetingHijacking of transcriptional condensates by endogenous retroviruses
Asimi V, Sampath Kumar A, Niskanen H, Riemenschneider C, Hetzel S, Naderi J, Fasching N, Popitsch N, Du M, Kretzmer H, Smith ZD, Weigert R, Walther M, Mamde S, Meierhofer D, Wittler L, Buschow R, Timmermann B, Cisse II, Ameres SL, Meissner A, Hnisz D. Hijacking of transcriptional condensates by endogenous retroviruses. Nature Genetics 2022, 54: 1238-1247. PMID: 35864192, PMCID: PMC9355880, DOI: 10.1038/s41588-022-01132-w.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsEmbryonic Stem CellsEndogenous RetrovirusesHeterochromatinMammalsMiceNuclear BodiesRetroelementsConceptsTranscriptional condensatesEndogenous retrovirusesMurine embryonic stem cellsSingle-cell RNA-seq analysisKnockout mouse embryosRNA-seq analysisEmbryonic stem cellsMost endogenous retrovirusesERV RNAsPhase-separated dropletsNascent RNAPluripotency genesPluripotent lineageRNA polymeraseTranscription factorsReconstitution systemTriggers dissociationERV lociMouse embryosMediator coactivatorSelective degradationDisease contextsStem cellsRNASpecific depletion
2021
Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions
Chandrasekaran S, Espeso-Gil S, Loh YE, Javidfar B, Kassim B, Zhu Y, Zhang Y, Dong Y, Bicks LK, Li H, Rajarajan P, Peter CJ, Sun D, Agullo-Pascual E, Iskhakova M, Estill M, Lesch BJ, Shen L, Jiang Y, Akbarian S. Neuron-specific chromosomal megadomain organization is adaptive to recent retrotransposon expansions. Nature Communications 2021, 12: 7243. PMID: 34903713, PMCID: PMC8669064, DOI: 10.1038/s41467-021-26862-z.Peer-Reviewed Original ResearchConceptsCellular stress response genesOpen chromatin domainsChromatin domain organizationRepeat-rich sequencesStress response genesRetrotransposon expansionsSPRET/EiJChromatin domainsChromosomal architectureChromosomal conformationDomain organizationAdult mouse cerebral cortexMurine germlineTranscriptional dysregulationResponse genesRegulatory mechanismsMus musculusMature neuronsNeuronal ablationStrong enrichmentMouse cerebral cortexSequenceSETDB1Single moleculesGermlineKDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements
Zhang SM, Cai WL, Liu X, Thakral D, Luo J, Chan LH, McGeary MK, Song E, Blenman KRM, Micevic G, Jessel S, Zhang Y, Yin M, Booth CJ, Jilaveanu LB, Damsky W, Sznol M, Kluger HM, Iwasaki A, Bosenberg MW, Yan Q. KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements. Nature 2021, 598: 682-687. PMID: 34671158, PMCID: PMC8555464, DOI: 10.1038/s41586-021-03994-2.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell Line, TumorDNA-Binding ProteinsEpigenesis, GeneticGene SilencingHeterochromatinHistone-Lysine N-MethyltransferaseHumansInterferon Type IJumonji Domain-Containing Histone DemethylasesMaleMelanomaMiceMice, Inbred C57BLMice, KnockoutNuclear ProteinsRepressor ProteinsRetroelementsTumor EscapeConceptsImmune checkpoint blockadeImmune evasionCheckpoint blockadeImmune responseAnti-tumor immune responseRobust adaptive immune responseTumor immune evasionAnti-tumor immunityAdaptive immune responsesType I interferon responseDNA-sensing pathwayMouse melanoma modelImmunotherapy resistanceMost patientsCurrent immunotherapiesTumor immunogenicityImmune memoryMelanoma modelCytosolic RNA sensingRole of KDM5BConsiderable efficacyInterferon responseImmunotherapyEpigenetic therapyBlockadeMachine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia
Zhu X, Zhou B, Pattni R, Gleason K, Tan C, Kalinowski A, Sloan S, Fiston-Lavier AS, Mariani J, Petrov D, Barres BA, Duncan L, Abyzov A, Vogel H, Moran J, Vaccarino F, Tamminga C, Levinson D, Urban A. Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia. Nature Neuroscience 2021, 24: 186-196. PMID: 33432196, PMCID: PMC8806165, DOI: 10.1038/s41593-020-00767-4.Peer-Reviewed Original ResearchMeSH KeywordsAdaptor Proteins, Signal TransducingAdultCation Transport ProteinsEmbryonic DevelopmentFemaleGenomeHeLa CellsHigh-Throughput Nucleotide SequencingHumansLong Interspersed Nucleotide ElementsMachine LearningMental DisordersMutagenesis, InsertionalNeurogliaNeuronsPregnancyRetroelementsSchizophreniaConceptsBrain developmentPossible pathological effectsAnatomical distributionBilateral distributionHuman neuronsNervous systemHuman nervous systemNeuropsychiatric diseasesNeuropsychiatric disordersGliaPathological effectsNeuronsSomatic L1 insertionsWhole-genome sequencingHuman brainSomatic retrotransposition
2020
Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria
Vallota-Eastman A, Arrington E, Meeken S, Roux S, Dasari K, Rosen S, Miller J, Valentine D, Paul B. Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria. BMC Genomics 2020, 21: 664. PMID: 32977771, PMCID: PMC7517822, DOI: 10.1186/s12864-020-07052-5.Peer-Reviewed Original ResearchConceptsDiversity-generating retroelementsFilamentous strains of cyanobacteriaEnvironmental stressCore cellular processesUnique domain architectureStrains of cyanobacteriaCell-cell attachmentLigand-binding moduleSignal responseCyanobacterial genomesMonophyletic cladeArchaeal lineagesIntragenomic duplicationsLigand-binding domainDomain architectureCyanobacterial generaFilamentous strainsRegulatory networksFilamentous cyanobacteriaRegulatory genesHypervariable proteinsCellular processesRetroelementsCyanobacteriaRegulatory pathways
2019
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2
Zhou B, Ho S, Greer S, Spies N, Bell J, Zhang X, Zhu X, Arthur J, Byeon S, Pattni R, Saha I, Huang Y, Song G, Perrin D, Wong W, Ji H, Abyzov A, Urban A. Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2. Nucleic Acids Research 2019, 47: 3846-3861. PMID: 30864654, PMCID: PMC6486628, DOI: 10.1093/nar/gkz169.Peer-Reviewed Original ResearchConceptsGenome sequenceStructural variantsGenomic structural featuresSomatic genomic rearrangementsFunctional genomics dataAllele-specific expressionEntire chromosome armsIntegrated genome analysisCRISPR/Cas9Cell linesMain cell linesGenome structureEpigenomic characteristicsChromosome armsGenome analysisDNA methylationGenome characteristicsRetrotransposon insertionChromosomal segmentsGenomic rearrangementsGenomic dataRegulatory complexityCell line HepG2Copy numberLoss of heterozygosity
2018
MIWI2 targets RNAs transcribed from piRNA‐dependent regions to drive DNA methylation in mouse prospermatogonia
Watanabe T, Cui X, Yuan Z, Qi H, Lin H. MIWI2 targets RNAs transcribed from piRNA‐dependent regions to drive DNA methylation in mouse prospermatogonia. The EMBO Journal 2018, 37: embj201695329. PMID: 30108053, PMCID: PMC6138435, DOI: 10.15252/embj.201695329.Peer-Reviewed Original ResearchConceptsDNA methylationRetrotransposon sequencesSmall RNAsArgonaute/Piwi proteinsPiwi protein MIWI2Suppressive epigenetic marksMouse prospermatogoniaChromatin statePIWI proteinsUnderlying molecular mechanismsDiverse organismsEpigenetic marksPiRNA clustersNascent RNAEpigenetic regulationTranslational regulationMIWI2RNA degradationRepeat sequencesGene expressionMolecular mechanismsTarget RNAMethylationRNAPiRNAs
2017
Landscape and variation of novel retroduplications in 26 human populations
Zhang Y, Li S, Abyzov A, Gerstein MB. Landscape and variation of novel retroduplications in 26 human populations. PLOS Computational Biology 2017, 13: e1005567. PMID: 28662076, PMCID: PMC5510864, DOI: 10.1371/journal.pcbi.1005567.Peer-Reviewed Original ResearchConceptsParent genesSequencing dataHigh-coverage exomesLow-coverage whole-genome sequencing dataHuman populationWhole-genome sequencing dataExon-exon junctionsGenomes Phase 3Young L1 elementsPaired-end readsPotential disease associationsRetrotranspositional activityGenomic elementsNucleosome positioningPhylogenetic treeRetroduplicationExome sequencing dataReference genomeGenomic featuresInsertion eventsL1 elementsComprehensive discoveryPopulation markersSNP callingFunctional regions
2016
Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis
Liddicoat BJ, Hartner JC, Piskol R, Ramaswami G, Chalk AM, Kingsley PD, Sankaran VG, Wall M, Purton LE, Seeburg PH, Palis J, Orkin SH, Lu J, Li JB, Walkley CR. Adenosine-to-inosine RNA editing by ADAR1 is essential for normal murine erythropoiesis. Experimental Hematology 2016, 44: 947-963. PMID: 27373493, PMCID: PMC5035604, DOI: 10.1016/j.exphem.2016.06.250.Peer-Reviewed Original ResearchMeSH KeywordsAdenosineAdenosine DeaminaseAnimalsCluster AnalysisErythrocyte IndicesErythroid CellsErythropoiesisGene ExpressionGene Expression ProfilingGene Expression Regulation, DevelopmentalGene Knockout TechniquesGranulocytesHematopoietic Stem Cell TransplantationInosineInterferonsMiceMicroRNAsMyelopoiesisOrgan SpecificityPhenotypeReceptors, InterferonRetroelementsRNA EditingRNA-Binding ProteinsSignal TransductionTranscription, GeneticConceptsRNA editingErythroid cellsNormal erythropoiesisHematopoietic stem/progenitorsHematopoietic cell typesInnate immune signalingStem/progenitorsEditing eventsErythroid-specific transcriptsEssential functionsImmune signalingMurine erythropoiesisADAR1Cell deathCell typesMyeloid-restricted deletionEditingRNAMicroRNA levelsErythropoiesisCellsProfound activationTranscriptsSignalingAdenosineGenome-wide characterization of human L1 antisense promoter-driven transcripts
Criscione SW, Theodosakis N, Micevic G, Cornish TC, Burns KH, Neretti N, Rodić N. Genome-wide characterization of human L1 antisense promoter-driven transcripts. BMC Genomics 2016, 17: 463. PMID: 27301971, PMCID: PMC4908685, DOI: 10.1186/s12864-016-2800-5.Peer-Reviewed Original ResearchConceptsL1 antisense promoterAntisense promoterChimeric transcriptsHuman genomeGenome-wide characterizationGene transcriptional start siteHuman-specific subfamilyTranscriptional start siteYY1 transcription factorRNA-seq dataGenic transcriptsAntisense promoter activitySense promoterCellular transcriptomeMultiple cell linesHistone modificationsL1 biologyNeighboring genesTransposable elementsGenBank ESTsAntisense transcriptsHuman genesTranscription factorsStart siteActive promoters
2014
Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline
Watanabe T, Cheng EC, Zhong M, Lin H. Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline. Genome Research 2014, 25: 368-380. PMID: 25480952, PMCID: PMC4352877, DOI: 10.1101/gr.180802.114.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsPiRNA pathwayRetrotransposon sequencesIntergenic regionMammalian PIWI-interacting RNAsRNA regulatory networkLate spermatocytesVivo functional analysisDegradation of mRNAUTR of mRNAsSlicer activityEukaryotic genomesLncRNA transcriptomeRegulatory networksRegulatory sequencesRepetitive sequencesPseudogenesMRNA stabilityFunctional analysisLncRNAsWidespread expressionSpermatid stageRetrotransposonsMRNATransposon
2013
Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division
Abyzov A, Iskow R, Gokcumen O, Radke DW, Balasubramanian S, Pei B, Habegger L, Consortium T, Lee C, Gerstein M. Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division. Genome Research 2013, 23: 2042-2052. PMID: 24026178, PMCID: PMC3847774, DOI: 10.1101/gr.154625.113.Peer-Reviewed Original ResearchConceptsCell divisionCorrect phylogenetic treeGenomes Project ConsortiumHuman populationTranscription of mRNARetroduplicationPhylogenetic treeParent genesGenomic integrationCell cycleG1 transitionMore copiesGenesRetrotranspositionHuman subpopulationsMultiple linesRetrogenesPseudogenesTranscriptionDivisionRNAVariantsProteinMRNACopies
2012
Impact of Retrotransposons in Pluripotent Stem Cells
Tanaka Y, Chung L, Park IH. Impact of Retrotransposons in Pluripotent Stem Cells. Molecules And Cells 2012, 34: 509-516. PMID: 23135636, PMCID: PMC3784326, DOI: 10.1007/s10059-012-0242-8.Peer-Reviewed Original Research
2011
A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster
Yin H, Sweeney S, Raha D, Snyder M, Lin H. A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster. PLOS Genetics 2011, 7: e1002380. PMID: 22194694, PMCID: PMC3240582, DOI: 10.1371/journal.pgen.1002380.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChromatin Assembly and DisassemblyChromatin ImmunoprecipitationChromosomal Proteins, Non-HistoneChromosome MappingDrosophila melanogasterDrosophila ProteinsEpigenesis, GeneticEuchromatinGenome, InsectHeterochromatinHigh-Throughput Nucleotide SequencingHistonesRepetitive Sequences, Nucleic AcidRetroelementsRNA Polymerase IITranscription Initiation SiteConceptsHeterochromatin protein 1aChromatin modificationsStart siteChromatin modification landscapeKey chromatin modificationKey histone marksCell typesDrosophila cell typesRNA polymerase IIAdult Drosophila melanogasterTranscriptional start siteDiverse cell typesTranscription start siteFunctionality of genesHigh-Resolution WholeEuchromatic marksHistone codeHistone marksModification landscapeDrosophila melanogasterPolymerase IIGenome mapChromatin immunoprecipitationRegulatory sequencesSplicing junctionsGenome Sequencing of Mouse Induced Pluripotent Stem Cells Reveals Retroelement Stability and Infrequent DNA Rearrangement during Reprogramming
Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM. Genome Sequencing of Mouse Induced Pluripotent Stem Cells Reveals Retroelement Stability and Infrequent DNA Rearrangement during Reprogramming. Cell Stem Cell 2011, 9: 366-373. PMID: 21982236, PMCID: PMC3975295, DOI: 10.1016/j.stem.2011.07.018.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell LineageCellular ReprogrammingChimeraDNA Copy Number VariationsFalse Negative ReactionsGene RearrangementGene SilencingGenomeGenomic InstabilityHumansInduced Pluripotent Stem CellsMiceMolecular Sequence DataMutagenesis, InsertionalOrgan SpecificityRetroelementsSequence Analysis, DNAConceptsPluripotent stem cellsClasses of SVsPaired-end DNA sequencingStem cellsGenomic structural variationMouse Induced Pluripotent Stem CellsStructural variationsDNA copy number variationsEmbryonic stem cellsMost iPSC linesMouse iPSC linesIPSC linesInduced pluripotent stem cellsCopy number variationsGenome stabilityGene-disrupting mutationsRecent microarray studiesDNA rearrangementsGenome sequencingSpontaneous mutationsMicroarray studiesDeleterious genetic mutationsNumber variationsDNA sequencingComplex rearrangementsRole for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus
Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway PD, Sasaki H. Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus. Science 2011, 332: 848-852. PMID: 21566194, PMCID: PMC3368507, DOI: 10.1126/science.1203919.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArgonaute ProteinsDNA MethylationGenomic ImprintingMaleMiceMice, Inbred C57BLMitochondrial ProteinsModels, GeneticMutationPhospholipase DProteinsras-GRF1Repetitive Sequences, Nucleic AcidRetroelementsRNA, Small InterferingRNA, UntranslatedSpermatogoniaTestisTranscription, GeneticConceptsRasgrf1 locusDNA methylationPIWI-interacting RNA (piRNA) pathwayDe novo DNA methylationMonoallelic gene expressionNovo DNA methylationParental germ lineDe novo methylationSequence-specific methylationDifferential DNA methylationRNA pathwaysGenomic imprintingNovo methylationRetrotransposon sequencesGerm lineNoncoding RNAsGene expressionDirect repeatsPiRNAsTarget RNADifferent lociMethylationLociRNASpecific sequencesMITOPLD Is a Mitochondrial Protein Essential for Nuage Formation and piRNA Biogenesis in the Mouse Germline
Watanabe T, Chuma S, Yamamoto Y, Kuramochi-Miyagawa S, Totoki Y, Toyoda A, Hoki Y, Fujiyama A, Shibata T, Sado T, Noce T, Nakano T, Nakatsuji N, Lin H, Sasaki H. MITOPLD Is a Mitochondrial Protein Essential for Nuage Formation and piRNA Biogenesis in the Mouse Germline. Developmental Cell 2011, 20: 364-375. PMID: 21397847, PMCID: PMC3062204, DOI: 10.1016/j.devcel.2011.01.005.Peer-Reviewed Original ResearchConceptsPiRNA biogenesisDerepression of retrotransposonsPrimary piRNA biogenesisSmall RNA biogenesisMutant germ cellsMitochondrial protein essentialMicrotubule-dependent localizationPiRNA pathwayDrosophila homologRNA biogenesisConserved roleMitoPLDDiverse speciesProtein essentialPerinuclear structuresMouse germlineOuter membraneBiogenesisGerm cellsMeiotic arrestPhospholipase DMetabolism/Phosphatidic acidMitochondriaMutant mice
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