2025
The retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity
Wood T, Henriques W, Cullen H, Romero M, Blengini C, Sarathy S, Sorkin J, Bekele H, Jin C, Kim S, Wang X, Laureau R, Chemiakine A, Khondker R, Isola J, Stout M, Gennarino V, Mogessie B, Jain D, Schindler K, Suh Y, Wiedenheft B, Berchowitz L. The retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity. Nature Aging 2025, 5: 765-779. PMID: 40263616, PMCID: PMC12180178, DOI: 10.1038/s43587-025-00852-y.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesTranscription factor MYBL1Gonadal tissueMale gonadal tissueRNA intermediateEvolutionary innovationHuman genomeAssociation studiesHost genomeProtein self-assemblyDevelopmental regulationCapsid geneCapsid-like structuresHuman cellsCapsid formationYears ago4,5RetrotransposonsGenomeSequenceGenesRNAReproductive capacityPNMA1Reproductive functionMouse model
2023
Regulation 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 complexRibozymeRetrotransposonsGenomeRetrotranspositionSplicingComplexesRNPDNAMotifTargetDiversificationTargetingA rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A
Simon M, Yang J, Gigas J, Earley E, Hillpot E, Zhang L, Zagorulya M, Tombline G, Gilbert M, Yuen S, Pope A, Van Meter M, Emmrich S, Firsanov D, Athreya A, Biashad S, Han J, Ryu S, Tare A, Zhu Y, Hudgins A, Atzmon G, Barzilai N, Wolfe A, Moody K, Garcia B, Thomas D, Robbins P, Vijg J, Seluanov A, Suh Y, Gorbunova V. A rare human centenarian variant of SIRT6 enhances genome stability and interaction with Lamin A. The EMBO Journal 2022, 41: embj2021110393. PMID: 36215696, PMCID: PMC9627671, DOI: 10.15252/embj.2021110393.Peer-Reviewed Original ResearchConceptsMono-ADP-ribosyl transferasesLamin A/CAshkenazi JewishSirtuin 6DNA double-strand break repairDouble-strand break repairImproving genome maintenanceAJ individualsGenome maintenanceGenome stabilityLINE1 retrotransposonsTarget sequenceBreak repairDeacetylase activityCellular pathwaysNAD+ concentrationMetabolic regulationLamin ACancer cellsKill cancer cellsHuman longevityAllelesRetrotransposonsGenomeDeacylase
2021
Investigating the Potential Roles of SINEs in the Human Genome
Zhang X, Pratt H, Weng Z. Investigating the Potential Roles of SINEs in the Human Genome. Annual Review Of Genomics And Human Genetics 2021, 22: 1-20. PMID: 33792357, DOI: 10.1146/annurev-genom-111620-100736.Peer-Reviewed Original ResearchConceptsShort interspersed nuclear elementsHuman genomePol II-transcribed genesFunctional regulatory elementsGene-rich regionsRNA polymerase IIIProximity to genesInterspersed nuclear elementsRegulate gene expressionPotential regulatory functionsSINE RNAsNonautonomous retrotransposonsPolymerase IIIGene regulationRegulatory elementsAutonomous retroelementsGenomeNuclear elementsGene expressionGenesRNARNA levelsPolPotential roleRetrotransposons
2018
DNA melting initiates the RAG catalytic pathway
Ru H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H. DNA melting initiates the RAG catalytic pathway. Nature Structural & Molecular Biology 2018, 25: 732-742. PMID: 30061602, PMCID: PMC6080600, DOI: 10.1038/s41594-018-0098-5.Peer-Reviewed Original ResearchConceptsRecombination signal sequencesDNA meltingCryo-EM structureBase-specific contactsSignal sequenceDNA transpositionSubstrate bindingRetroviral integrationRAG endonucleaseDimer openingTerminal sequenceGTG sequenceDNA cleavageScissile phosphateDNAUniversal mechanismPiston-like movementSequenceActive siteHeptamerRetrotransposonsCatalytic pathwayTransposonComplexesEndonuclease
2015
Adaption by Rewiring Epigenetic Landscapes
Liu Y, Xiao A. Adaption by Rewiring Epigenetic Landscapes. Cell Stem Cell 2015, 17: 249-250. PMID: 26340521, PMCID: PMC4710369, DOI: 10.1016/j.stem.2015.08.015.Peer-Reviewed Original Research
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
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
2003
The Pathway for DNA Recognition and RNA Integration by a Group II Intron Retrotransposon
Aizawa Y, Xiang Q, Lambowitz AM, Pyle AM. The Pathway for DNA Recognition and RNA Integration by a Group II Intron Retrotransposon. Molecular Cell 2003, 11: 795-805. PMID: 12667460, DOI: 10.1016/s1097-2765(03)00069-8.Peer-Reviewed Original ResearchConceptsGroup II intron RNPsIntron-encoded proteinTarget site specificityMobile genetic elementsIntron invasionDNA recognitionDNA bindingGenetic elementsConformational changesDuplex DNADNA targetsSite specificityDNAStrand DNAComplex cascadeReverse transcriptionRNPInvasionRetrotransposonsSplicingTranscriptionProteinKinetic frameworkPathwayCascade
1991
A New Member of a Family of Site-Specific Retrotransposons Is Present in the Spliced Leader RNA Genes of Trypanosoma cruzi
Villanueva M, Williams S, Beard C, Richards F, Aksoy S. A New Member of a Family of Site-Specific Retrotransposons Is Present in the Spliced Leader RNA Genes of Trypanosoma cruzi. Molecular And Cellular Biology 1991, 11: 6139-6148. DOI: 10.1128/mcb.11.12.6139-6148.1991.Peer-Reviewed Original ResearchA New Member of a Family of Site-Specific Retrotransposons Is Present in the Spliced Leader RNA Genes of Trypanosoma cruzi
Villanueva M, Williams S, Beard C, Richards F, Aksoy S. A New Member of a Family of Site-Specific Retrotransposons Is Present in the Spliced Leader RNA Genes of Trypanosoma cruzi. Molecular And Cellular Biology 1991, 11: 6139-6148. DOI: 10.1128/mcb.11.12.6139-6148.1991.Peer-Reviewed Original ResearchOpen reading frameAmino acid homologySL RNAReading frameLong open reading frameSpliced leader RNA genesExtensive amino acid homologySpliced leader RNAPol genes of retrovirusesOverall amino acid homologyLow copy numberPol open reading frameEndonuclease domainLeader RNAGene sequencesTrypanosomatid speciesGene locusRetrotransposonsCopy numberCrithidia fasciculataTruncated versionFunctional roleIdentical sitesHomologyPol gene
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