2025
H3K4me3 amplifies transcription at intergenic active regulatory elements.
Yu H, Zhang Y, Liao Z, Walters B, Lesch B. H3K4me3 amplifies transcription at intergenic active regulatory elements. Genes & Development 2025 PMID: 40825666, DOI: 10.1101/gad.352841.125.Peer-Reviewed Original ResearchRNA polymerase activityIntergenic regionRegulatory elementsPolymerase activityHistone H3 lysine 4Trimethylation of histone H3 lysine 4Active regulatory elementsTranscriptionally active promotersH3 lysine 4Pervasive transcriptionIntergenic lociMammalian genomesHistone modificationsLysine 4Epigenetic editingH3K4me3TranscriptionGenomeRNAActivity promotionLociHistoneShed lightRegionPromoterChanges in the FXR-cistrome and alterations in bile acid physiology in Wilson disease
Wooton-Kee C, Yalamanchili H, Mohamed I, Hassan M, Setchell K, Rivas M, Coskun A, Putluri V, Putluri N, Jalal P, Schilsky M, Moore D. Changes in the FXR-cistrome and alterations in bile acid physiology in Wilson disease. Hepatology Communications 2025, 9: e0707. PMID: 40408300, PMCID: PMC12106221, DOI: 10.1097/hc9.0000000000000707.Peer-Reviewed Original ResearchConceptsWild-type miceFarnesoid X receptorWilson's diseaseNon-parenchymal cellsDistal intergenic regionsLiver bile acid concentrationWD patientsHealthy controlsMetabolic target genesFarnesoid X Receptor RegulationBile salt export pumpIntergenic regionFXR activationAutosomal recessive disorderBile acid homeostasisBile acid physiologyFarnesoid X receptor activationPromoter regionHomeostasis pathwaysBile acid metabolismDecreasing FXR activityTarget genesBile acid profilesMarker genesStress pathwaysComprehensive mutational analysis of the sequence–function relationship within a viral internal ribosome entry site
Grunseich S, Strobel S. Comprehensive mutational analysis of the sequence–function relationship within a viral internal ribosome entry site. Nucleic Acids Research 2025, 53: gkaf445. PMID: 40421802, PMCID: PMC12107430, DOI: 10.1093/nar/gkaf445.Peer-Reviewed Original ResearchConceptsCrPV-IRESIRES functionViral internal ribosome entry siteNext-generation sequencing methodsInternal ribosome entry siteSequence-function relationshipsCricket paralysis virusRibosome entry siteCell-free systemComprehensive mutational analysisMechanism of translationHigh-throughput methodRibosome contactsIntergenic regionRNA elementsTranslation initiationSequence requirementsIRES elementsMutation databaseEukaryotic extractsInitiation factorsSequencing methodsExpressed proteinsHelical regionsMutation analysis
2024
Innovative application of CRISPR for eliminating Ustiloxin in Cordyceps militaris: Enhancing food safety and quality
Liu M, Wang A, Meng G, Liu Q, Yang Y, Wang M, Wang Z, Wang F, Dong C. Innovative application of CRISPR for eliminating Ustiloxin in Cordyceps militaris: Enhancing food safety and quality. LWT 2024, 204: 116420. PMID: 39119199, PMCID: PMC11308680, DOI: 10.1016/j.lwt.2024.116420.Peer-Reviewed Original ResearchFood safetyEnhanced food safetyAgronomic charactersMycotoxin productionBiosynthetic gene clusterFunctional foodsPost-translationally modified peptideCyclopeptide mycotoxinsFruiting bodiesGenome resequencingUstiloxinGenome miningIntergenic regionApplications of CRISPRGene clusterOff-target eventsCore genesPost-translationallySimultaneous deletionMycotoxinsFoodUstiloxin BCordyceps militarisCRISPR/Cas9 systemCRISPR technologyExploring the relationship between admixture and genetic susceptibility to attention deficit hyperactivity disorder in two Latin American cohorts
Garzón Rodríguez N, Briceño-Balcázar I, Nicolini H, Martínez-Magaña J, Genis-Mendoza A, Flores-Lázaro J, Villatoro Velázquez J, Bustos Gamiño M, Medina-Mora M, Quiroz-Padilla M. Exploring the relationship between admixture and genetic susceptibility to attention deficit hyperactivity disorder in two Latin American cohorts. Journal Of Human Genetics 2024, 69: 373-380. PMID: 38714835, PMCID: PMC11269173, DOI: 10.1038/s10038-024-01246-5.Peer-Reviewed Original ResearchGenome-wide association analysisSingle-nucleotide polymorphismsSingle-nucleotide variantsSingle-nucleotideRisk-associated lociGenome-wide significanceRisk single-nucleotide polymorphismsAttention deficit hyperactivity disorderLocal ancestryAssociation lociIntergenic regionAdmixture proportionsAncestral componentsGenomic ancestryAssociation analysisAncestry levelsEuropean ancestryGenetic associationEuropean componentDeficit hyperactivity disorderAncestryGenomeGenesGenetic susceptibilityHyperactivity disorderThe discovery of novel noncoding RNAs in 50 bacterial genomes
Narunsky A, Higgs G, Torres B, Yu D, de Andrade G, Kavita K, Breaker R. The discovery of novel noncoding RNAs in 50 bacterial genomes. Nucleic Acids Research 2024, 52: 5152-5165. PMID: 38647067, PMCID: PMC11109978, DOI: 10.1093/nar/gkae248.Peer-Reviewed Original ResearchBacterial genomesDomains of lifeIntergenic regionNcRNA classesGC-rich intergenic regionsBacterial domain of lifeIndividual bacterial genomesStructured noncoding RNAsNovel noncoding RNAsProtein coding genesNoncoding RNAsNcRNA motifsRiboswitch candidatesBacterial domainRiboswitch classesCoding genesGene regulationCellular processesCytidine nucleotidesBacterial speciesGenomeComputational pipelineNcRNAsDiverse functionsGenes
2023
Comparative Genomics of Bacillus subtilis Phages Related to phiNIT1 from Desert Soils of the Southwest United States
Vill A, Delesalle V, Magness L, Chaudhry B, Lichty K, Strine M, Guffey A, DeCurzio J, Krukonis G. Comparative Genomics of Bacillus subtilis Phages Related to phiNIT1 from Desert Soils of the Southwest United States. PHAGE 2023, 4: 173-180. PMID: 40134794, PMCID: PMC11932518, DOI: 10.1089/phage.2023.0027.Peer-Reviewed Original ResearchGenomic structureBacillus phagesBacillus subtilis phageGram-positive bacteriumPathogenic Bacillus speciesDiverse genomesIntergenic regionSequence similarityGenetic diversityRepeat sequencesProtein familyRepresentative phagesPhageB. subtilisBacillus subtilisHost rangeBacillus speciesGenomeVirion structureCapsid structureDesert soilsTail lengthSequenceMyovirusesLysis assayGenome-wide Association Study for AKI
Bhatraju P, Stanaway I, Palmer M, Menon R, Schaub J, Menez S, Srivastava A, Wilson F, Kiryluk K, Palevsky P, Naik A, Sakr S, Jarvik G, Parikh C, Ware L, Ikizler T, Siew E, Chinchilli V, Coca S, Garg A, Go A, Kaufman J, Kimmel P, Himmelfarb J, Wurfel M. Genome-wide Association Study for AKI. Kidney360 2023, 4: 870-880. PMID: 37273234, PMCID: PMC10371295, DOI: 10.34067/kid.0000000000000175.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGene locusAssociation studiesSingle-cell RNA sequencing dataHealthy living donorsLoop of HenleThick ascending limbWide significant associationsGenetic variantsGenome-wide significanceRNA sequencing dataKidney biopsyCommon genetic riskLiving donorsSubsequent sequelaeSerial evaluationFunctional annotationIntergenic regionAscending limbGene expressionSequencing dataRisk of AKIKidney biopsy tissueProximal tubular epithelial cellsMember 1 gene
2022
Abstract WMP107: Back To The Future: Recurrent Stroke Genome Wide Association Study
Aldridge C, Armstrong N, Sunmonu N, Hsu F, Keene K, Sale M, Worrall B. Abstract WMP107: Back To The Future: Recurrent Stroke Genome Wide Association Study. Stroke 2022, 53: awmp107-awmp107. DOI: 10.1161/str.53.suppl_1.wmp107.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsCadherin-8Novel single nucleotide polymorphismsBiallelic single nucleotide polymorphismsGenome wide association studiesGenetic Reference PanelTOPMed imputation serverRecurrent strokeImputation ServerIntergenic regionAssociation studiesChromosome 1Ancestry distributionReference panelImputation qualityCox proportional hazards modelsNucleotide polymorphismsPopulation ancestryGenotyped samplesTOPMedMixed ancestryProportional hazards modelPotential new insightsChromosomeGenes
2021
Identification of novel locus associated with coronary artery aneurysms and validation of loci for susceptibility to Kawasaki disease
Hoggart C, Shimizu C, Galassini R, Wright V, Shailes H, Bellos E, Herberg J, Pollard A, O’Connor D, Choi S, Seaby E, Menikou S, Hibberd M, Sallah N, Burgner D, Brogan P, Patel H, Kim J, Tremoulet A, Salo E, van Stijn D, Kuijpers T, Burns J, Levin M. Identification of novel locus associated with coronary artery aneurysms and validation of loci for susceptibility to Kawasaki disease. European Journal Of Human Genetics 2021, 29: 1734-1744. PMID: 33772158, PMCID: PMC7994355, DOI: 10.1038/s41431-021-00838-5.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesIntergenic regionNovel lociChromosome 20q13Second genome-wide association studyEuropean genome-wide association studyValidation of lociJapanese genome-wide association studiesGWAS summary dataAssociated lociGenomic regionsGenome dataPutative lociDifferent genesRisk allelesAssociation studiesEuropean descentLociGenetic variantsAllelesSNVsWider significanceGenesSusceptibilityCASP3Multi-omics analysis to identify susceptibility genes for colorectal cancer
Yuan Y, Bao J, Chen Z, Villanueva A, Wen W, Wang F, Zhao D, Fu X, Cai Q, Long J, Shu X, Zheng D, Moreno V, Zheng W, Lin W, Guo X. Multi-omics analysis to identify susceptibility genes for colorectal cancer. Human Molecular Genetics 2021, 30: 321-330. PMID: 33481017, PMCID: PMC8485221, DOI: 10.1093/hmg/ddab021.Peer-Reviewed Original ResearchMeSH KeywordsCarcinogenesisCell Line, TumorCell ProliferationColorectal NeoplasmsDNA MethylationGene Expression Regulation, NeoplasticGenetic Association StudiesGenetic Predisposition to DiseaseGenomeGenome-Wide Association StudyHumansNerve Tissue ProteinsPolymorphism, Single NucleotideRepressor ProteinsRisk FactorsTranscriptomeConceptsGenome-wide association studiesMulti-omics analysisSusceptibility genesTarget genesPutative target genesGWAS-identified variantsMost genetic variantsDNA methylation dataNovel susceptibility genesGenotype-Tissue ExpressionGenetic risk lociPutative susceptibility genesGene regulationIntergenic regionPathogenic dysregulationCancer Genome AtlasEpithelial-mesenchymal transitionRisk lociGene expressionMethylation dataAssociation studiesGenesCell behaviorGenetic variantsGenome Atlas
2019
Effects of Common and Rare Chromosome 4 GABAergic Gene Variation on Alcohol Use and Antisocial Behavior.
Deak J, Gizer I, Otto J, Bizon C, Wilhelmsen K. Effects of Common and Rare Chromosome 4 GABAergic Gene Variation on Alcohol Use and Antisocial Behavior. Journal Of Studies On Alcohol And Drugs 2019, 80: 585-593. PMID: 31790348, PMCID: PMC6900988, DOI: 10.15288/jsad.2019.80.585.Peer-Reviewed Original ResearchConceptsVariant associationsCommon variant associationsRare variant association testsRare variant signalsGene-based analysisRare variant associationsMolecular genetic studiesSingle variant analysisIntergenic regionRare variationAlcohol use disorderTop associationsSequencing dataVariant contributionsGenetic studiesAlcoholism (COGA) sampleGenetic sequencing dataReceptor geneUse disordersVariant signalsGene variationTypes of variationConfer riskStrong associationSignificant associationIdentification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation
Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, Lopes FL. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLOS ONE 2019, 14: e0222329. PMID: 31513639, PMCID: PMC6742455, DOI: 10.1371/journal.pone.0222329.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsCpG islandsDNA methylationReference genome sequence assemblyDatabase of SNPsCpG sitesBull Genomes ProjectGenome sequence assemblyDivergent feed efficiencyBovine phenotypesEpigenetic polymorphismEpigenetic controlEpigenetic regulationIntergenic regionNearby genesMethylation targetsGenomic sequencesMethylation patternsSequence assemblyGenome ProjectMethylation profilesMethylation sitesSNP databaseDifferential expressionVariant annotationGenome‐wide analyses of psychological resilience in U.S. Army soldiers
Stein MB, Choi KW, Jain S, Campbell‐Sills L, Chen C, Gelernter J, He F, Heeringa SG, Maihofer AX, Nievergelt C, Nock MK, Ripke S, Sun X, Kessler RC, Smoller JW, Ursano RJ. Genome‐wide analyses of psychological resilience in U.S. Army soldiers. American Journal Of Medical Genetics Part B Neuropsychiatric Genetics 2019, 180: 310-319. PMID: 31081985, PMCID: PMC6551278, DOI: 10.1002/ajmg.b.32730.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGenome-wide significant lociGenome-wide significant associationGenome-wide analysisCommon variant heritabilityGenome-wide significanceIntergenic regionSecond geneSignificant lociGenetic basisMolecular basisKinase 2Association studiesMember 5Genetic determinantsDoublecortin familyLociBiological basisPolygenic risk scoresNew avenuesGenome‐wide Discovery of Rare Riboswitches in Bacteria
Arachchilage G, Atilho R, Stav S, Higgs G, Breaker R. Genome‐wide Discovery of Rare Riboswitches in Bacteria. The FASEB Journal 2019, 33: 778.8-778.8. DOI: 10.1096/fasebj.2019.33.1_supplement.778.8.Peer-Reviewed Original ResearchRiboswitch candidatesBacterial genomesGC-rich intergenic regionsDifferent bacterial genomesGenome-wide discoverySequenced bacterial genomesNascent RNA transcriptsRiboswitch classesThiamin biosynthesisRiboswitch aptamerStructured ncRNAsNcRNA classesIntergenic regionHydroxymethylpyrimidine pyrophosphateRiboswitchBioinformatics pipelineRNA transcriptsTranscription processComputational pipelinePhysiological pathwaysConformational changesNcRNAsGenomeFASEB JournalHoward Hughes Medical Institute
2018
17p12 Influences Hematoma Volume and Outcome in Spontaneous Intracerebral Hemorrhage
Marini S, Devan WJ, Radmanesh F, Miyares L, Poterba T, Hansen BM, Norrving B, Jimenez-Conde J, Giralt-Steinhauer E, Elosua R, Cuadrado-Godia E, Soriano C, Roquer J, Kourkoulis CE, Ayres AM, Schwab K, Tirschwell DL, Selim M, Brown DL, Silliman SL, Worrall BB, Meschia JF, Kidwell CS, Montaner J, Fernandez-Cadenas I, Delgado P, Greenberg SM, Lindgren A, Matouk C, Sheth KN, Woo D, Anderson CD, Rosand J, Falcone GJ. 17p12 Influences Hematoma Volume and Outcome in Spontaneous Intracerebral Hemorrhage. Stroke 2018, 49: 1618-1625. PMID: 29915124, PMCID: PMC6085089, DOI: 10.1161/strokeaha.117.020091.Peer-Reviewed Original ResearchConceptsAssociation studiesGenome-wide association studiesNumerous copy number variantsSusceptibility risk lociWide association studyNovel biological pathwaysGenomic regionsIntergenic regionCopy number variantsRisk lociBiological pathwaysSusceptibility lociAssociation testingGenetic variantsNumber variantsEuropean ancestryLociReplicationDiscovery phaseVariantsAncestryImportant determinantPathwayTranslational studiesQuality controlHigh Throughput Validation of Orphan Riboswitch Candidates
Arachchilage G, Sherlock M, White N, Panchapakesan S, Breaker R. High Throughput Validation of Orphan Riboswitch Candidates. The FASEB Journal 2018, 32: lb18-lb18. DOI: 10.1096/fasebj.2018.32.1_supplement.lb18.Peer-Reviewed Original ResearchRiboswitch candidatesRiboswitch classesIntergenic regionCognate ligandsS-adenosylmethionineLong intergenic regionCis-acting genesDiscovery of riboswitchesExperimental Biology 2018 MeetingImportant biological pathwaysHigh-throughput validationHigh-throughput strategyS-adenosylhomocysteineComparative genomicsRecent bioinformaticsBacterial mRNAsLine probingRNA elementsRiboswitchGenetic validationReporter assaysBiological pathwaysComputational approachThroughput strategyFASEB Journal
2015
Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery
Greer CB, Tanaka Y, Kim YJ, Xie P, Zhang MQ, Park IH, Kim TH. Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery. Cell Reports 2015, 13: 1444-1455. PMID: 26549458, PMCID: PMC4934896, DOI: 10.1016/j.celrep.2015.10.013.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationCell Cycle ProteinsCell Line, TumorEpigenesis, GeneticHistone Deacetylase InhibitorsHistone DeacetylasesHSP90 Heat-Shock ProteinsHumansKineticsNuclear ProteinsProtein BindingProtein Processing, Post-TranslationalRNA Polymerase IITranscription Elongation, GeneticTranscription FactorsConceptsNegative elongation factorElongation factorEnhancer activityHeat shock protein 90 (HSP90) activityEnhancer RNA productionRNA polymerase IISame genomic siteElongation machinerySmall molecule inhibitorsGene bodiesTranscription elongationPolymerase IINascent transcriptionGenomic sitesIntergenic regionGene activationRNA productionEfficient elongationMolecule inhibitorsProtein 4TranscriptionPromoterHDACsEnhancerElongation
2014
Assessment of HbF QTLs Affecting Disease Severity and Genetic Analysis in Patients Homozygous for Codon 8 (–AA) β0-Thalassemia Mutation
Jiang Z, Huang S, Luo H, Akar N, Basak A, Al-Allawi N, Unal S, Gumruk F, Davis L, Morrison T, Campbell A, Gallagher P, Forget B, Steinberg M, Chui D. Assessment of HbF QTLs Affecting Disease Severity and Genetic Analysis in Patients Homozygous for Codon 8 (–AA) β0-Thalassemia Mutation. Blood 2014, 124: 2690. DOI: 10.1182/blood.v124.21.2690.2690.Peer-Reviewed Original ResearchQuantitative trait lociGene clusterIntergenic regionHbF quantitative trait lociΓ-globin gene expressionKb intergenic regionSevere phenotypeMild phenotypeHBS1L-MYB intergenic regionΒ-globin gene clusterGenome-wide SNP arraysMild disease phenotypeDisease phenotypeMinor alleleWhole-genome sequencingTrait lociHPFH mutationNovel SNPsGenetic analysisSNP arrayGene expressionΒ-hemoglobinopathiesGenome sequencingQTL genotypesWhole-exome sequencingRetrotransposons 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
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