2025
Drosophila Modulo is essential for transposon silencing and developmental robustness
Parikh R, Nayak D, Lin H, Gangaraju V. Drosophila Modulo is essential for transposon silencing and developmental robustness. Journal Of Biological Chemistry 2025, 301: 108210. PMID: 39848495, PMCID: PMC11879677, DOI: 10.1016/j.jbc.2025.108210.Peer-Reviewed Original ResearchPIWI-interacting RNAsTransposable elementsDevelopmental robustnessTE silencingSilencing of transposable elementsP-element induced wimpy testisPreserving genome integrityHistone 3 lysineIntrinsic genetic variationPost-transcriptional silencingMammalian nucleolinTransposon RNAsTransposon silencingPiRNA functionPiwi-piRNATE activityGenomic sitesMaternal germlineArgonaute 3Genome integrityTranscriptional silencingGenetic variationEpigenetic regulationPiwiBinding protein
2024
Autonomous transposons tune their sequences to ensure somatic suppression
Ilık İ, Glažar P, Tse K, Brändl B, Meierhofer D, Müller F, Smith Z, Aktaş T. Autonomous transposons tune their sequences to ensure somatic suppression. Nature 2024, 626: 1116-1124. PMID: 38355802, PMCID: PMC10901741, DOI: 10.1038/s41586-024-07081-0.Peer-Reviewed Original ResearchConceptsTransposable elementsSAFB proteinsPiwi-interacting RNA pathwayRNA-basedIntronic transposed elementsRNA processing signalsPre-mRNA processingIntronic spaceNested genesPostmeiotic spermatidsAutonomous transposonsDNA transposonsRNA pathwaysCassette exonsSplicing codeSplicing eventsGenome integrityTE exonizationHuman genesL1 elementsRNA synthesisHost genesTissue-specificSAFBSomatic cellsThe Role of RAG in V(D)J Recombination
Xiao J, Martin E, Wang K, Schatz D. The Role of RAG in V(D)J Recombination. 2024 DOI: 10.1016/b978-0-128-24465-4.00019-3.Peer-Reviewed Original ResearchRecombination signal sequencesRecombination activating geneV(D)J recombinationDNA cleavageConserved sequence elementsNonhomologous end-joining pathwayLymphoid-specific proteinsAntigen receptor gene segmentsEnd-joining pathwayPair of hairpinsReceptor gene segmentsTransposable elementsDomain architectureSequence elementsLocus structureSignal sequenceTransposition mechanismTranscriptional regulationJawed vertebratesTransposase activityActive genesPosttranslational modificationsEnhancer elementsProtein structureCell cycle
2023
Transposable elements cause the loss of self‐incompatibility in citrus
Hu J, Liu C, Du Z, Guo F, Song D, Wang N, Wei Z, Jiang J, Cao Z, Shi C, Zhang S, Zhu C, Chen P, Larkin R, Lin Z, Xu Q, Ye J, Deng X, Bosch M, Franklin‐Tong V, Chai L. Transposable elements cause the loss of self‐incompatibility in citrus. Plant Biotechnology Journal 2023, 22: 1113-1131. PMID: 38038155, PMCID: PMC11022811, DOI: 10.1111/pbi.14250.Peer-Reviewed Original ResearchConceptsMiniature inverted-repeat transposable elementsMiniature inverted-repeat transposable element insertionSelf-incompatibilityTransposable elementsS-locusS-RNaseS-RNase-based SI systemPromoter regionLoss of self-incompatibilityPromote genetic diversityS-RNase allelesPrezygotic mechanismsGenetic diversityInbreeding depressionSelf-compatibleNucleotide mutationsFlowering plantsLoss of SiTransgenic experimentsBreeding strategiesCitrus genusAllelesSI phenotypePromoterCitrus
2022
LINE-1 activation in the cerebellum drives ataxia
Takahashi T, Stoiljkovic M, Song E, Gao XB, Yasumoto Y, Kudo E, Carvalho F, Kong Y, Park A, Shanabrough M, Szigeti-Buck K, Liu ZW, Kristant A, Zhang Y, Sulkowski P, Glazer PM, Kaczmarek LK, Horvath TL, Iwasaki A. LINE-1 activation in the cerebellum drives ataxia. Neuron 2022, 110: 3278-3287.e8. PMID: 36070749, PMCID: PMC9588660, DOI: 10.1016/j.neuron.2022.08.011.Peer-Reviewed Original ResearchConceptsLINE-1 activationL1 activationAtaxia telangiectasia patientsNuclear element-1Transposable elementsEpigenetic silencersHuman genomeL1 promoterMolecular regulatorsDNA damagePurkinje cell dysfunctionElement 1First direct evidenceTelangiectasia patientsDirect targetingCerebellar expressionNeurodegenerative diseasesDisease etiologyCalcium homeostasis
2021
Structural insights into the evolution of the RAG recombinase
Liu C, Zhang Y, Liu CC, Schatz DG. Structural insights into the evolution of the RAG recombinase. Nature Reviews Immunology 2021, 22: 353-370. PMID: 34675378, DOI: 10.1038/s41577-021-00628-6.Peer-Reviewed Original ResearchConceptsRAG recombinaseComparative genome analysisGenomes of eukaryotesProtein-DNA complexesSingle amino acid mutationAntigen receptor genesMolecular domesticationRag familyAmino acid mutationsJawed vertebratesVertebrate immunityTransposable elementsEvolutionary adaptationGenome analysisStructural biologyDNA bindingStructural insightsGene 1Acid mutationsCleavage activityRecombinaseReceptor geneStructural evidenceRecombinationAdaptive immunityStructural analyses of an RNA stability element interacting with poly(A)
Torabi SF, Chen YL, Zhang K, Wang J, DeGregorio SJ, Vaidya AT, Su Z, Pabit SA, Chiu W, Pollack L, Steitz JA. Structural analyses of an RNA stability element interacting with poly(A). Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2026656118. PMID: 33785601, PMCID: PMC8040590, DOI: 10.1073/pnas.2026656118.Peer-Reviewed Original ResearchConceptsRNA stability elementCis-acting RNA elementsGlobal conformational changesRich internal loopCryo-electron microscopyRice transposable elementsDiverse genomesDouble-helical regionsSmall-angle X-ray scatteringEne motifTransposable elementsGlobal structural changesRNA interactionsRNA stabilityBioinformatics studiesRNA elementsStability elementShort helixConformational changesDecay pathwaysInternal loopBiochemical structureTriplex structureBindingMotifPopulation genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements
Crava C, Varghese F, Pischedda E, Halbach R, Palatini U, Marconcini M, Gasmi L, Redmond S, Afrane Y, Ayala D, Paupy C, Carballar‐Lejarazu R, Miesen P, van Rij R, Bonizzoni M. Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements. Molecular Ecology 2021, 30: 1594-1611. PMID: 33432714, PMCID: PMC8048955, DOI: 10.1111/mec.15798.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsArboviral vector Aedes aegyptiEndogenous viral elementsPopulation genomicsGenomic architectureViral elementsVector Aedes aegyptiPiRNA-mediated silencingNonretroviral RNA virusesGenome-wide screenHorizontal gene transferSequence-specific mechanismWild-caught mosquitoesA. aegyptiEndogenization eventsAedes aegyptiAdaptive evolutionPiRNA clustersEukaryotic cellsGermline cellsTransposable elementsGeographical populationsHost genomeHost functionsCognate virus
2020
PIWI–piRNA pathway-mediated transposable element repression in Hydra somatic stem cells
Teefy BB, Siebert S, Cazet JF, Lin H, Juliano CE. PIWI–piRNA pathway-mediated transposable element repression in Hydra somatic stem cells. RNA 2020, 26: 550-563. PMID: 32075940, PMCID: PMC7161359, DOI: 10.1261/rna.072835.119.Peer-Reviewed Original ResearchConceptsPIWI-piRNA pathwayTE expressionSomatic stem cellsTransposable elementsTE transcriptsStem cellsFreshwater cnidarianSmall RNA pathwaysTransposable element repressionSomatic cell lineagesGermline of animalsInterstitial stem cellsStem cell populationInterstitial lineageSomatic piRNAsDegradome sequencingEpithelial cellsAncestral functionRNA pathwaysGermline piRNAsPIWI proteinsTE repressionGermline competenceSequence signaturesRNA immunoprecipitation
2019
Transcriptome-wide piRNA profiling in human brains for aging genetic factors.
Mao Q, Fan L, Wang X, Lin X, Cao Y, Zheng C, Zhang Y, Zhang H, Garcia-Milian R, Kang L, Shi J, Yu T, Wang K, Zuo L, Li CR, Guo X, Luo X. Transcriptome-wide piRNA profiling in human brains for aging genetic factors. 2019, 4 PMID: 32149191, PMCID: PMC7059831.Peer-Reviewed Original ResearchPIWI-interacting RNAsTransposable elementsAge-associated genesCritical genetic determinantsGenomic integrityExpression regulationCancer stem cellsMicroarray technologyGenetic determinantsStem cellsExpression levelsRenewal capacityMolecular featuresBiological systemsPotential roleGenetic factorsYears of survivalUnderlying mechanismHuman prefrontal cortexGermlineGenesRNADisease statusMultiple testingPrefrontal cortexN(6)-Methyladenine in eukaryotes
Alderman MH, Xiao AZ. N(6)-Methyladenine in eukaryotes. Cellular And Molecular Life Sciences 2019, 76: 2957-2966. PMID: 31143960, PMCID: PMC6857450, DOI: 10.1007/s00018-019-03146-w.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsTranscriptome-wide piRNA profiling in human gastric cancer
Lin X, Xia Y, Hu D, Mao Q, Yu Z, Zhang H, Li C, Chen G, Liu F, Zhu W, Shi Y, Zhang H, Zheng J, Sun T, Xu J, Chao HH, Zheng X, Luo X. Transcriptome-wide piRNA profiling in human gastric cancer. Oncology Reports 2019, 41: 3089-3099. PMID: 30896887, PMCID: PMC6448102, DOI: 10.3892/or.2019.7073.Peer-Reviewed Original ResearchConceptsPIWI-interacting RNAsTransposable elementsHuman gastric cancerProtein-coding genesNon-coding RNAsCancer risk SNPsPiRNA expressionNearest geneWhole transcriptomeCancer stem cellsDNA variantsIndefinite capacityDifferential expressionAdjacent non-tumorous tissuesStem cellsHuman stomachRegulatory effectsGenesRNANon-tumorous tissuesExpressionMolecular featuresBiological systemsGastric cancerTranscriptome
2018
Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
Böhme U, Otto TD, Cotton JA, Steinbiss S, Sanders M, Oyola SO, Nicot A, Gandon S, Patra KP, Herd C, Bushell E, Modrzynska KK, Billker O, Vinetz JM, Rivero A, Newbold CI, Berriman M. Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals. Genome Research 2018, 28: 547-560. PMID: 29500236, PMCID: PMC5880244, DOI: 10.1101/gr.218123.116.Peer-Reviewed Original ResearchConceptsAvian malaria speciesLTR retrotransposonsHigh-quality draft genome sequenceClades of parasitesComplete LTR retrotransposonsLineage-specific evolutionNovel gene familyOrthologs of genesMalaria parasite genomeAvian malaria parasitesAmino acid divergenceDraft genome sequenceInvasion-related genesAvian lineagesMalaria speciesProtein homologsGene familyMultigene familyPhylogenetic positionTransposable elementsBird speciesParasite genomePhylogenetic analysisGenome sequenceAvian malaria
2017
Activity of Retrotransposons in Stem Cells and Differentiated Cells
Macia A, Tejwani L, Mesci P, Muotri A, Garcia-Perez J. Activity of Retrotransposons in Stem Cells and Differentiated Cells. 2017, 127-156. DOI: 10.1007/978-3-319-48344-3_6.Peer-Reviewed Original ResearchTransposable elementsSelfish DNAHuman genomeTE insertionsEarly embryonic developmental stagesActivity of TEsActivity of retrotransposonsActivity of L1New TE insertionsEmbryonic developmental stagesHuman transposable elementsMammalian genomesGenome stabilityEukaryotic genomesNew genesGenomic regulationGenomic rearrangementsGenomeLINE-1sDifferentiated cellsGerm cellsDevelopmental stagesMobile elementsNew copiesStem cellsNew insights into the evolutionary origins of the recombination‐activating gene proteins and V(D)J recombination
Carmona LM, Schatz DG. New insights into the evolutionary origins of the recombination‐activating gene proteins and V(D)J recombination. The FEBS Journal 2017, 284: 1590-1605. PMID: 27973733, PMCID: PMC5459667, DOI: 10.1111/febs.13990.Peer-Reviewed Original ResearchConceptsTransposable elementsEvolutionary originRAG proteinsAbsence of RAG2Independent evolutionary originsBasal chordate amphioxusRecombination-activating gene (RAG) proteinsFamily of transposasesAntigen receptor genesRAG transposonChordate amphioxusJawed vertebratesSequence similarityEvolutionary relativesProteins RAG1RAG genesGene proteinRAG1Gene segmentsDiverse arrayMechanistic linkProteinRAG2Adaptive immune systemDNA cleavage reaction
2016
Genome-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 promotersDiscovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination
Huang S, Tao X, Yuan S, Zhang Y, Li P, Beilinson HA, Zhang Y, Yu W, Pontarotti P, Escriva H, Le Petillon Y, Liu X, Chen S, Schatz DG, Xu A. Discovery of an Active RAG Transposon Illuminates the Origins of V(D)J Recombination. Cell 2016, 166: 102-114. PMID: 27293192, PMCID: PMC5017859, DOI: 10.1016/j.cell.2016.05.032.Peer-Reviewed Original ResearchConceptsRAG transposonAntigen receptor gene assemblyBasal extant chordateDNA transposon familiesVertebrate adaptive immunityRecombination signal sequencesExtant chordatesTarget site duplicationsTransposable elementsDNA recombinationSignal sequenceTransposon excisionGene assemblyProtoRAGTransposon familySite duplicationsCrucial eventTransposonRecombinationAdaptive immunityChordatesTIRLanceletsRAG1/2GermlineMyriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi
Tycowski KT, Shu MD, Steitz JA. Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi. Cell Reports 2016, 15: 1266-1276. PMID: 27134163, PMCID: PMC4864102, DOI: 10.1016/j.celrep.2016.04.010.Peer-Reviewed Original ResearchConceptsTransposable elementsCellular noncoding RNAsPotential evolutionary consequencesCis-acting RNA structuresIntron lossEvolutionary consequencesBioinformatic identificationTE transcriptsReporter transcriptFish speciesNoncoding RNAsElement RNAHorizontal transferRNA structureTransposase geneRich tractHuman cellsTriple helix formationBase triplesRNAEne coreTranscriptsTriple helixIntronlessGenomeIntegrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies
Lu Q, Powles RL, Wang Q, He BJ, Zhao H. Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies. PLOS Genetics 2016, 12: e1005947. PMID: 27058395, PMCID: PMC4825932, DOI: 10.1371/journal.pgen.1005947.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGWAS signalsComplex traitsFunctional annotationAssociation studiesHuman complex traitsFunctional regionsNon-coding regionsGWAS p-valuesWide association studyNovel biological insightsRelevant tissue typesEpigenetic annotationsGenomic functionsRegulatory machineryTransposable elementsHuman genomeGenoSkylineRisk lociBiological insightsIntegrative analysisGenetic studiesRegulatory miRNAPrioritization performanceSpecific annotationsCollaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination
Carmona LM, Fugmann SD, Schatz DG. Collaboration of RAG2 with RAG1-like proteins during the evolution of V(D)J recombination. Genes & Development 2016, 30: 909-917. PMID: 27056670, PMCID: PMC4840297, DOI: 10.1101/gad.278432.116.Peer-Reviewed Original ResearchConceptsRecombination-activating gene 1Transib transposaseAbsence of RAG2RAG1/RAG2Antigen receptor genesJawed vertebratesRAG2 proteinsTransposable elementsRAG1 proteinRegulatory featuresDNA substratesGene 1RAG2Receptor geneRecombination activityProteinRecombinationTransposaseAdaptive immunityVertebratesTransposonGenesEvolutionLow levelsOrigin
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