2024
A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals
Konstantinidou P, Loubalova Z, Ahrend F, Friman A, Almeida M, Poulet A, Horvat F, Wang Y, Losert W, Lorenzi H, Svoboda P, Miska E, van Wolfswinkel J, Haase A. A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals. Cell Reports 2024, 43: 114777. PMID: 39302833, PMCID: PMC11615739, DOI: 10.1016/j.celrep.2024.114777.Peer-Reviewed Original ResearchPIWI-interacting RNAsPiwi-interacting RNA clustersPiRNA clustersPiRNA biologySilencing mobile genetic elementsGenomic piRNA clustersSingle-stranded precursorsMobile genetic elementsSafeguarding genome integrityGerm cell biologySpecies-specific variationGenome invadersTranscriptional readthroughTransposon insertionGenetic elementsGenome integrityRetroviral invasionMolecular mechanismsCell biologyRNAMammalsSpeciesBiologyTransposonReadthroughThe Upstream Sequence Transcription Complex dictates nucleosome positioning and promoter accessibility at piRNA genes in the C. elegans germ line
Paniagua N, Roberts C, Gonzalez L, Monedero-Alonso D, Reinke V. The Upstream Sequence Transcription Complex dictates nucleosome positioning and promoter accessibility at piRNA genes in the C. elegans germ line. PLOS Genetics 2024, 20: e1011345. PMID: 38985845, PMCID: PMC11262695, DOI: 10.1371/journal.pgen.1011345.Peer-Reviewed Original ResearchPiRNA genesPiRNA clustersGenomic domainsC. elegans germ lineUpstream sequence transcription complexSmall RNA pathwaysGermline-specific expressionGlobal genome organizationPiRNA precursorsPiRNA pathwayChromosome IVGenome organizationRNA pathwaysChromatin stateTranscribed genesNucleosome positioningNucleosome densityGenome integrityTranscriptional regulationTranscription complexC. elegansPiRNAsGerm lineISW-1Nucleosomal environment
2021
Population 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
Improved reference genome of the arboviral vector Aedes albopictus
Palatini U, Masri RA, Cosme LV, Koren S, Thibaud-Nissen F, Biedler JK, Krsticevic F, Johnston JS, Halbach R, Crawford JE, Antoshechkin I, Failloux AB, Pischedda E, Marconcini M, Ghurye J, Rhie A, Sharma A, Karagodin DA, Jenrette J, Gamez S, Miesen P, Masterson P, Caccone A, Sharakhova MV, Tu Z, Papathanos PA, Van Rij RP, Akbari OS, Powell J, Phillippy AM, Bonizzoni M. Improved reference genome of the arboviral vector Aedes albopictus. Genome Biology 2020, 21: 215. PMID: 32847630, PMCID: PMC7448346, DOI: 10.1186/s13059-020-02141-w.Peer-Reviewed Original ResearchConceptsArboviral vector Aedes albopictusSex-determining locusFirst physical mapAsian tiger mosquito Aedes albopictusTiger mosquito Aedes albopictusMosquito Aedes albopictusAedes albopictusPiRNA clustersDiverse AeGenome assemblyInnovative control measuresReference genomeAccurate DNA sequencesNovel microRNAsImmunity genesPhysical mapDNA sequencesGenetic manipulationViral insertionVector Aedes albopictusExpression dataGenomeAlbopictus populationsSequencing methodsAdaptation potential
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
2014
The C. elegans SNAPc Component SNPC-4 Coats piRNA Domains and Is Globally Required for piRNA Abundance
Kasper DM, Wang G, Gardner KE, Johnstone TG, Reinke V. The C. elegans SNAPc Component SNPC-4 Coats piRNA Domains and Is Globally Required for piRNA Abundance. Developmental Cell 2014, 31: 145-158. PMID: 25373775, PMCID: PMC4223638, DOI: 10.1016/j.devcel.2014.09.015.Peer-Reviewed Original ResearchConceptsRNA genesPIWI-interacting RNA (piRNA) pathwayTransfer RNA genesSmall RNA genesDiscrete genomic regionsDNA-binding subunitSmall nuclear RNAPiRNA abundanceRNA pathwaysPiRNA genesChromatin organizationPiRNA clustersPiRNA expressionProtein complexesGenomic regionsCoordinated expressionNuclear RNAExpression environmentForeign sequencesGenesExpressionDomainPiRNAsLocalizationTransposon
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