2025
CREATE: cell-type-specific cis-regulatory element identification via discrete embedding
Cui X, Yin Q, Gao Z, Li Z, Chen X, Lv H, Chen S, Liu Q, Zeng W, Jiang R. CREATE: cell-type-specific cis-regulatory element identification via discrete embedding. Nature Communications 2025, 16: 4607. PMID: 40382355, PMCID: PMC12085597, DOI: 10.1038/s41467-025-59780-5.Peer-Reviewed Original ResearchConceptsCis-regulatory elementsPrediction of cis-regulatory elementsCell-type-specific cis-regulatory elementsChromatin interaction dataGene regulatory landscapeCell type-specific functionsGene regulatory mechanismsComplex biological traitsLarge-scale predictionGenome sequenceChromatin accessibilitySequence-basedBiological traitsRegulatory codeRegulatory dynamicsRegulatory mechanismsCell typesRegulatory landscapeInteraction dataChromatinGenesIdentificationSequenceSilencingTraits
2024
Comparative single-cell multiome identifies evolutionary changes in neural progenitor cells during primate brain development
Liu Y, Luo X, Sun Y, Chen K, Hu T, You B, Xu J, Zhang F, Cheng Q, Meng X, Yan T, Li X, Qi X, He X, Guo X, Li C, Su B. Comparative single-cell multiome identifies evolutionary changes in neural progenitor cells during primate brain development. Developmental Cell 2024, 60: 414-428.e8. PMID: 39481377, DOI: 10.1016/j.devcel.2024.10.005.Peer-Reviewed Original ResearchEvolutionary changesDistal regulatory elementsGene regulatory mechanismsExtracellular matrixSingle-cell multiomicsProgenitor cellsTranscriptional divergenceEvolutionary divergenceChromatin regionsChromatin accessibilityNeural progenitorsRegulatory elementsSequence changesTranscriptional rewiringGenetic mechanismsMouse prefrontal cortexRegulatory mechanismsPrefrontal cortexHuman neural progenitorsHuman-specific featuresUpper-layer neuronsNeural progenitor cellsChromatinCellular propertiesProgenitor proliferationTopologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk
Nakamura T, Ueda J, Mizuno S, Honda K, Kazuno A, Yamamoto H, Hara T, Takata A. Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk. Cell Genomics 2024, 4: 100488. PMID: 38280381, PMCID: PMC10879036, DOI: 10.1016/j.xgen.2024.100488.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingASD genesWhole-genome sequencing dataTopologically associating domainsInfluence multiple genesGene regulatory mechanismsASD-associated genesGenetic architectureASD heritabilityMultiple genesASD probandsPromoter variantsGenesAutism spectrum disorder riskHuman induced pluripotent stem cellsPromoterPluripotent stem cellsTADStudies of autism spectrum disorderVariantsAutism spectrum disorderStem cellsSequenceProbandsHeritability
2013
A High-Resolution Enhancer Atlas of the Developing Telencephalon
Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JL. A High-Resolution Enhancer Atlas of the Developing Telencephalon. Cell 2013, 152: 895-908. PMID: 23375746, PMCID: PMC3660042, DOI: 10.1016/j.cell.2012.12.041.Peer-Reviewed Original ResearchConceptsForebrain enhancersDistant-acting enhancersGene regulatory mechanismsTransgenic mouse embryosEnhancer architectureVivo enhancerEpigenomic analysisRegulatory sequencesMouse embryosRegulatory mechanismsTelencephalon developmentMammalian telencephalonVivo expressionEnhancerCritical roleDeveloping TelencephalonSequenceNeurodevelopmental disordersTelencephalonCortex tissueVivo activityGenesEmbryosSpeciesAtlas
2012
Nanoparticle-based artificial RNA silencing machinery for antiviral therapy
Wang Z, Liu H, Yang S, Wang T, Liu C, Cao Y. Nanoparticle-based artificial RNA silencing machinery for antiviral therapy. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 12387-12392. PMID: 22802676, PMCID: PMC3412013, DOI: 10.1073/pnas.1207766109.Peer-Reviewed Original ResearchConceptsFundamental gene regulatory mechanismsHepatitis C virusGene regulatory mechanismsCultured cellsTarget RNA cleavageSequence-specific mannerCellular interferon responseFunctional genomicsHuman hepatoma cellsRNA interferenceArtificial RNARegulatory mechanismsMouse modelRNA cleavageCultured human hepatoma cellsSpecific mannerHCV RNA levelsRNAXenotransplantation mouse modelHepatoma cellsInterferon responsePotent antiviral activityRNA levelsMachineryProteinase activity
2007
Down-Regulation of IL-7Rα Expression in Human T Cells via DNA Methylation
Kim HR, Hwang KA, Kim KC, Kang I. Down-Regulation of IL-7Rα Expression in Human T Cells via DNA Methylation. The Journal Of Immunology 2007, 178: 5473-5479. PMID: 17442928, DOI: 10.4049/jimmunol.178.9.5473.Peer-Reviewed Original ResearchConceptsJurkat T cellsDNA methylationGene expressionGene promoterIL-7Ralpha expressionT cellsPromoter activityImportant gene regulatory mechanismGene regulatory mechanismsGene promoter constructsHuman CD8Gene promoter activityIL-7Cell survival responseT cell developmentT cell subsetsIL-7Rα expressionRegulatory mechanismsPromoter constructsCell developmentMethylationLuciferase reporterHuman T cellsSurvival responseDown regulationThe role for DNA methylation in differentially regulating IL-7 receptor alpha expression by human T cells (94.22)
Kang I, Hwang K, Kim K, Kim H. The role for DNA methylation in differentially regulating IL-7 receptor alpha expression by human T cells (94.22). The Journal Of Immunology 2007, 178: s174-s174. DOI: 10.4049/jimmunol.178.supp.94.22.Peer-Reviewed Original ResearchJurkat T cellsDNA methylationGene promoterT cellsGene expressionImportant gene regulatory mechanismHuman CD8IL-7Gene regulatory mechanismsGene promoter constructsCell survival responseReceptor alpha expressionT cell subsetsT cell developmentHuman T cellsRegulatory mechanismsPromoter activityPromoter constructsCell developmentCell subsetsIL-7RaMethylationCD8Luciferase reporterAlpha expression
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