2025
Transgenic expression of endoplasmic reticulum proteins in C. elegans neurons is prone to causing ER stress
Park J, Yogev S. Transgenic expression of endoplasmic reticulum proteins in C. elegans neurons is prone to causing ER stress. MicroPublication Biology 2025, 2025: 10.17912/micropub.biology.001547. PMID: 40519643, PMCID: PMC12163624, DOI: 10.17912/micropub.biology.001547.Peer-Reviewed Original ResearchER-associated degradationER stressLevels of ER stressOrganelle-specific markersC. elegans neuronsEndoplasmic reticulum proteinEndomembrane systemOrganelle biologyOrganelle markersIndividual organellesFluorescent proteinTransgenic markersOrganellesProteinPhenotypeMarkersEndomembraneExpressionTransgene expressionLow levelsBiologyStressETS emerges to heat up adipose
Rodeheffer M. ETS emerges to heat up adipose. Genes & Development 2025 PMID: 40389324, DOI: 10.1101/gad.352966.125.Peer-Reviewed Original ResearchTranscription factor bindingE26 transformation-specific (ETS) transcription factorsPromoter chromatin accessibilityChromatin accessibilityFactor bindingTranscription factorsHistone acetylationAdipose biologyGene expressionETV4HistoneTranscriptionGenesUCP1AcetylationE26AdipogenesisBindingBiologyThermogenesisExpressionAdiposeThe application of irreversible genomic states to define and trace ancient cell type homologies
Simakov O, Wagner G. The application of irreversible genomic states to define and trace ancient cell type homologies. EvoDevo 2025, 16: 5. PMID: 40319312, PMCID: PMC12049793, DOI: 10.1186/s13227-025-00242-w.Peer-Reviewed Original ResearchImpact gene expressionGenomic stateCell typesGene expressionGene regulatory networksHomologous cell typesBranching animalsGenomic charactersRegulatory elementsRegulatory networksRegulatory signaturesMorphological traitsHomologyPhenotypic levelMolecular signaturesOntogenetic originGenesMorphological featuresNon-functionalCellsHypothesis articleGenomeExpressionTraitsTypeHypothalamic PNOC/NPY neurons constitute mediators of leptin-controlled energy homeostasis
Solheim M, Stroganov S, Chen W, Subagia P, Bauder C, Wnuk-Lipinski D, Del Río-Martín A, Sotelo-Hitschfeld T, Beddows C, Klemm P, Dodd G, Lundh S, Secher A, Wunderlich F, Steuernagel L, Brüning J. Hypothalamic PNOC/NPY neurons constitute mediators of leptin-controlled energy homeostasis. Cell 2025, 188: 3550-3566.e22. PMID: 40273910, DOI: 10.1016/j.cell.2025.04.001.Peer-Reviewed Original ResearchConceptsLeptin's anorectic effectsDiet-induced hyperphagiaNeuropeptide Y (NPYAgouti-related peptideChemogenetic activationAnorectic effectLeptin regulates appetiteBody weightArcuate nucleusLEPR expressionHyperphagiaLeptin actionSuppress appetiteObese backgroundLeptinObesity therapeuticsObesityNeuronsEnergy homeostasisWeight gainNPYNeurocircuitryAppetiteExpressionPNoCsEukaryotic Microproteins
Jaunbocus N, Ebenki V, Su H, Slavoff S. Eukaryotic Microproteins. Annual Review Of Biochemistry 2025, 94: 1-28. PMID: 40245354, PMCID: PMC12207985, DOI: 10.1146/annurev-biochem-080124-012840.Peer-Reviewed Original ResearchH3.1K27M-induced misregulation of the TONSOKU-H3.1 pathway causes genomic instability
Yuan W, Huang Y, LeBlanc C, Poulet A, De Luna Vitorino F, Valsakumar D, Dean R, Garcia B, van Wolfswinkel J, Voigt P, Jacob Y. H3.1K27M-induced misregulation of the TONSOKU-H3.1 pathway causes genomic instability. Nature Communications 2025, 16: 3547. PMID: 40229276, PMCID: PMC11997104, DOI: 10.1038/s41467-025-58892-2.Peer-Reviewed Original ResearchConceptsGenomic instabilityChromatin-based mechanismsHistone mark H3K27me3DNA damageH3K27MChromatin maturityGenome integrityNascent chromatinCell identityHistone H3Transcriptional programsH3.1 variantsGenomic alterationsDNAGenomeHistoneH3K27M expressionTumors of patientsEctopic activityATXR5ATXR6ExpressionCellsChromatinReduced Notch signaling in hypothalamic endothelial cells mediates obesity-induced alterations in glucose uptake and insulin signaling
Zhu Y, Mehlkop O, Backes H, Cremer A, Porniece M, Klemm P, Steuernagel L, Chen W, Johnen R, Wunderlich F, Jais A, Brüning J. Reduced Notch signaling in hypothalamic endothelial cells mediates obesity-induced alterations in glucose uptake and insulin signaling. Cell Reports 2025, 44: 115522. PMID: 40186867, DOI: 10.1016/j.celrep.2025.115522.Peer-Reviewed Original ResearchConceptsShort-term HFD feedingNotch signalingIntracellular domainGlucose uptakeBrain microvascular endothelial cellsNotch intracellular domainHFD feedingDownregulation of Notch signalingHigh-fat dietBlood-brain barrierReduced Notch signalingGLUT1 expressionInsulin signalingSystemic insulin sensitivityBlood-brain barrier permeabilityNotch activationInduced expressionObesity-induced alterationsCaveolae formationPleiotropic effectsEndothelial cellsMicrovascular endothelial cellsExpressionBlood-brain barrier functionCultured brain microvascular endothelial cellsGlomerular mesangial cells derived complement factor H regulates complement activation, influences cell proliferation, and maintains actin cytoskeleton
Li Y, Ni X, Li X, Kang Y, Yuan X, Xu G, Wang T, Li D, Shi S, Lv J, Zhao M, Zhang H, Zhu L. Glomerular mesangial cells derived complement factor H regulates complement activation, influences cell proliferation, and maintains actin cytoskeleton. International Immunopharmacology 2025, 154: 114544. PMID: 40157080, DOI: 10.1016/j.intimp.2025.114544.Peer-Reviewed Original ResearchConceptsActin cytoskeletonGlomerular mesangial cellsInfluence cell proliferationCell proliferationSingle-cell sequencing dataComplement factor HNon-canonical functionsExpression of Cdc42Mesangial cellsSequence dataCell motilityAffecting cell proliferationCytoskeletonRegulate complement activationRegulatory roleCanonical functionActinComplement activationIndependent of complement activationFactor HIgA1-containing immune complexesComplement proteinsCellsComplement-induced damageExpressionSynthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16
Nakamura A, Fulk E, Johnson C, Isaacs F. Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16. ACS Synthetic Biology 2025, 14: 943-953. PMID: 40048245, PMCID: PMC11934965, DOI: 10.1021/acssynbio.4c00869.Peer-Reviewed Original ResearchConceptsSynthetic genetic elementsExpression of heterologous pathwaysUptake systemCupriavidus necator H16Genome engineering technologiesHeterologous pathwaysHeterotrophic conditionsGenetic elementsChromosomal expressionTunable expressionInducible promoterGenetic engineering technologyModel microbesCarbon sourceGene expressionFacultative chemolithotrophsUptake pathwayH16PathwayLanding padExpressionGenomeGenesMicrobesChemolithotrophsGuidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR)
Loughran G, Andreev D, Terenin I, Namy O, Mikl M, Yordanova M, McManus C, Firth A, Atkins J, Fraser C, Ignatova Z, Iwasaki S, Kufel J, Larsson O, Leidel S, Mankin A, Mariotti M, Tanenbaum M, Topisirovic I, Vázquez-Laslop N, Viero G, Caliskan N, Chen Y, Clark P, Dinman J, Farabaugh P, Gilbert W, Ivanov P, Kieft J, Mühlemann O, Sachs M, Shatsky I, Sonenberg N, Steckelberg A, Willis A, Woodside M, Valasek L, Dmitriev S, Baranov P. Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR). Nature Structural & Molecular Biology 2025, 32: 418-430. PMID: 40033152, DOI: 10.1038/s41594-025-01492-x.Peer-Reviewed Original ResearchConceptsInternal ribosome entry siteGene expression reportersStop codon readthroughRibosome entry siteEukaryotic translationTranscription initiationAntisense transcriptsRegulatory elementsRibosomal frameshiftingCodon readthroughExpression reportersEntry siteDual reportersUnconventional mechanismSequencePolyadenylationMisinterpretation of dataExpressionReadthroughFrameshiftSplicingTranscriptionEvaluate published dataMinimal requirementsProteinS-Nitrosylation of CRTC1 in Alzheimer’s disease impairs CREB-dependent gene expression induced by neuronal activity
Zhang X, Vlkolinsky R, Wu C, Dolatabadi N, Scott H, Prikhodko O, Zhang A, Blanco M, Lang N, Piña-Crespo J, Nakamura T, Roberto M, Lipton S. S-Nitrosylation of CRTC1 in Alzheimer’s disease impairs CREB-dependent gene expression induced by neuronal activity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2418179122. PMID: 40014571, PMCID: PMC11892585, DOI: 10.1073/pnas.2418179122.Peer-Reviewed Original ResearchConceptsActivity-dependent gene expressionGene expressionAlzheimer's diseaseCREB-dependent gene expressionS-nitrosylationNitric oxide (NO)-related speciesTargets of S-nitrosylationNeuronal activity-dependent gene expressionPathogenesis of ADDecreased neurite lengthIncreased neuronal cell deathNeuronal cell deathSynaptic plasticityTranscriptional pathwaysCell deathCRISPR/Cas9 techniqueTranscription coactivator 1AD modelLong-term memory formationIncreased S-nitrosylationLong-term potentiationTherapeutic targetExpressionNeurite lengthCerebrocortical neuronsStructural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides
Hainzl T, Scortti M, Lindgren C, Grundström C, Krypotou E, Vázquez-Boland J, Sauer-Eriksson A. Structural basis of promiscuous inhibition of Listeria virulence activator PrfA by oligopeptides. Cell Reports 2025, 44: 115290. PMID: 39970044, DOI: 10.1016/j.celrep.2025.115290.Peer-Reviewed Original ResearchConceptsDNA-binding helix-turn-helix motifInhibit virulence gene expressionVirulence gene expressionPathogen Listeria monocytogenesPrfA activityVirulence factorsPrfAMaster regulatorsHydrophobic residuesInhibitory bindingGene expressionStructural basisBinding promiscuityPeptide bindingBinding sitesConformational changesPeptide residuesOligopeptidesPeptideInhibitory peptidesBindingPeptide backboneResiduesPromiscuous inhibitionExpressionA comprehensive spatio-cellular map of the human hypothalamus
Tadross J, Steuernagel L, Dowsett G, Kentistou K, Lundh S, Porniece M, Klemm P, Rainbow K, Hvid H, Kania K, Polex-Wolf J, Knudsen L, Pyke C, Perry J, Lam B, Brüning J, Yeo G. A comprehensive spatio-cellular map of the human hypothalamus. Nature 2025, 639: 708-716. PMID: 39910307, PMCID: PMC11922758, DOI: 10.1038/s41586-024-08504-8.Peer-Reviewed Original ResearchConceptsGenome-wide association study genesRare deleterious variantsHypothalamic cell typesCell typesSingle-nucleus sequencingBody mass indexTranscription mapDeleterious variantsNeuronal cell typesG protein-coupled receptorsStudy genesBiological functions1Spatial transcriptomicsTranscriptomic identityCellular componentsExpression levelsPro-opiomelanocortin neuronsHuman hypothalamusAssociated with body mass indexPopulation levelMetabolic disordersHypothalamic cellsExpressionNeuronal clustersTranscriptomeResolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment
Pal A, Noble M, Morales M, Pal R, Baumgartner M, Yang J, Yim K, Uebbing S, Noonan J. Resolving the three-dimensional interactome of human accelerated regions during human and chimpanzee neurodevelopment. Cell 2025, 188: 1504-1523.e27. PMID: 39889695, PMCID: PMC11928272, DOI: 10.1016/j.cell.2025.01.007.Peer-Reviewed Original Research
2024
RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs
Li Y, Liu X, Cheng F, Pan X, Yang Y. RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs. 2024, 00: 48-53. DOI: 10.1109/bibm62325.2024.10821865.Peer-Reviewed Original ResearchMultiple RNA-binding proteinsRNA-binding proteinsRNA transcriptsRNA-protein binding sitesRBP binding sitesFull-length transcriptsBinding sitesPredicted binding siteSequence dataRNA informationRNA fragmentsGene expressionTranscriptionRNASequence lengthSequenceSitesGenesProteinMachine learning methodsImbalanced labelsImbalanced dataData imbalanceFragmentsExpressionEvolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum
Marshall K, Stadtmauer D, Maziarz J, Wagner G, Lesch B. Evolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum. Developmental Cell 2024, 60: 646-664.e8. PMID: 39536760, PMCID: PMC11859772, DOI: 10.1016/j.devcel.2024.10.013.Peer-Reviewed Original ResearchPlacental mammalsLevel of transcriptionSingle-cell dataGene expression patternsMammalian spermatogenesisGene expression programsEpigenomic dataAdult testisEvolutionary innovationSpermatogenic cellsGene setsSpermatogenic developmentModel marsupialOpossum Monodelphis domesticaGene expressionExpression patternsGenesDevelopmental processesExpression programsSpermatogenesisMonodelphis domesticaMammalsDevelopmental timeCombination of featuresExpressionDetecting Boolean Asymmetric Relationships With a Loop Counting Technique and its Implications for Analyzing Heterogeneity Within Gene Expression Datasets
Zhou H, Lin W, Labra S, Lipton S, Elman J, Schork N, Rangan A. Detecting Boolean Asymmetric Relationships With a Loop Counting Technique and its Implications for Analyzing Heterogeneity Within Gene Expression Datasets. IEEE Transactions On Computational Biology And Bioinformatics 2024, 22: 27-38. PMID: 39471117, PMCID: PMC12037869, DOI: 10.1109/tcbb.2024.3487434.Peer-Reviewed Original ResearchSubsets of genesGene-gene relationshipsGene expression dataGene-gene interactionsGene expression datasetsRNA-sequencing data setsDetected biclustersExpression datasetsGene pathwaysSubsets of cellsGenesRegulatory effectsBiclusteringCorrelated expressionAsymmetric interactionsSymmetric interactionsInteractionExpressionCellsFunction and evolution of Ir52 receptors in mate detection in Drosophila
Luo Y, Talross G, Carlson J. Function and evolution of Ir52 receptors in mate detection in Drosophila. Current Biology 2024, 34: 5395-5408.e6. PMID: 39471807, PMCID: PMC11614688, DOI: 10.1016/j.cub.2024.10.001.Peer-Reviewed Original ResearchMating partnersCluster of genesPotential mating partnersSexually dimorphic neuronsCourtship behaviorEvolutionary timeMate detectionExpression systemFly legFruit flyFly speciesSpeciesBiological problemsTaste neuronsMatingPheromone extractsFliesReceptorsDrosophilaCourtshipGenesNeuronsPheromoneCircuit mappingExpressionMachine-guided design of cell-type-targeting cis-regulatory elements
Gosai S, Castro R, Fuentes N, Butts J, Mouri K, Alasoadura M, Kales S, Nguyen T, Noche R, Rao A, Joy M, Sabeti P, Reilly S, Tewhey R. Machine-guided design of cell-type-targeting cis-regulatory elements. Nature 2024, 634: 1211-1220. PMID: 39443793, PMCID: PMC11525185, DOI: 10.1038/s41586-024-08070-z.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsCell typesActivation of off-target cellsGene expressionCell type-specific expressionSynthetic cis-regulatory elementsCell-type specificityHuman genomeUnique cell typeTissue identityBiotechnological applicationsTissue specificityIn vitro validationCell linesCre activitySequenceGenesNatural sequenceDevelopmental timeExpressionCellsGenomeTested in vivoMotifOff-target cellsPhysalia gonodendra are not yet sexually mature when released
Oguchi K, Yamamoto G, Kohtsuka H, Dunn C. Physalia gonodendra are not yet sexually mature when released. Scientific Reports 2024, 14: 23011. PMID: 39362967, PMCID: PMC11450099, DOI: 10.1038/s41598-024-73611-5.Peer-Reviewed Original ResearchConceptsGerm cell maturationGene expression analysisGerm cell markersReproductive ecologySexual reproductionHaploid cellsGerm cellsReproductive biologyGonophoresExpression analysisRelated genesLife cycleGenesCell maturationGermConsistent with other studiesFlow cytometryPhysalia utriculusExpressionCnidariaCell markersCellsPhysaliaSpermHydrozoa
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