Yi Xie
Postdoctoral Associate in NeuroscienceAbout
Research
Publications
2024
Abstract 2121: SUV39H1 Mediated Regulation Of KLF4 And KDM4a Coordinate Smooth Muscle Cell Phenotypic Plasticity
Chatterjee P, Chakraborty R, Sizer A, Xie Y, Hwa J, Martin K. Abstract 2121: SUV39H1 Mediated Regulation Of KLF4 And KDM4a Coordinate Smooth Muscle Cell Phenotypic Plasticity. Arteriosclerosis Thrombosis And Vascular Biology 2024, 44 DOI: 10.1161/atvb.44.suppl_1.2121.Peer-Reviewed Original ResearchRNA-seqPhenotypic plasticityEpigenetic regulationH3K9me3 repressive marksRNA-seq transcriptomicsContractile genesEpigenetic transcriptional repressionCell phenotypic plasticityH3K9me3 markExpression of SUV39H1Repressive marksTranscriptional repressionChromatin immunoprecipitationHistone methyltransferaseDedifferentiation in vitroIn vivoSUV39H1 knockdownH3K9me3MRNA stabilitySUV39H1Gene expressionPlasticity of vascular smooth muscle cellsRegulation of Klf4GenesH3K9me3 expressionProtein oxidation of fucose environments (POFE) reveals fucose–protein interactions
Xie Y, Chen S, Alvarez M, Sheng Y, Li Q, Maverakis E, Lebrilla C. Protein oxidation of fucose environments (POFE) reveals fucose–protein interactions. Chemical Science 2024, 15: 5256-5267. PMID: 38577366, PMCID: PMC10988611, DOI: 10.1039/d3sc06432h.Peer-Reviewed Original ResearchProtein-protein interactionsCopper-catalyzed click chemistryFormation of hydroxyl radicalsCell membrane glycoproteinMembrane glycoproteinPost-translational modificationsLiquid chromatography coupled with tandem mass spectrometryTandem mass spectrometryClick chemistryBinding partnersGalectin-3-binding proteinProtein functionCellular processesMammalian cellsMass spectrometryOxidized peptidesFucose residuesHydroxyl radicalsLabeled probesBioorthogonal groupsLC-MS/MSAmino acidsProteinFucoseProtein oxidationTwo DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids
Frisbie V, Hashimoto H, Xie Y, De Luna Vitorino F, Baeza J, Nguyen T, Yuan Z, Kiselar J, Garcia B, Debler E. Two DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids. Nature Communications 2024, 15: 2467. PMID: 38503750, PMCID: PMC10951340, DOI: 10.1038/s41467-024-46637-6.Peer-Reviewed Original ResearchConceptsMotif VIDot1 enzymesMechanism of substrate recognitionH2B mono-ubiquitinationHistone H3 lysine 79Active-site loopH3 lysine 79Histone H3 lysineEnzyme-substrate complexMotif IVTri-methyltransferaseSubstrate recognitionMethylation kineticsMono-ubiquitinationLysine 79Substrate preferenceH3 lysineTri-methylationDOT1BAcid residuesDot1Ala residuesKinetoplastidsMotifBiochemical analysis
2023
Analysis of Cell Glycogen with Quantitation and Determination of Branching Using Liquid Chromatography–Mass Spectrometry
Chen S, Bouchibti Y, Xie Y, Chen Y, Chang V, Lebrilla C. Analysis of Cell Glycogen with Quantitation and Determination of Branching Using Liquid Chromatography–Mass Spectrometry. Analytical Chemistry 2023, 95: 12884-12892. PMID: 37584460, DOI: 10.1021/acs.analchem.3c02230.Peer-Reviewed Original ResearchConceptsUHPLC/QqQ-MSDegree of branchingUltra-high-performance liquid chromatography/triple quadrupole mass spectrometryLiquid chromatography/triple quadrupole mass spectrometryQuadrupole mass spectrometryLiquid chromatography-mass spectrometryChromatography-mass spectrometryPMP derivatizationStructure determinationMass spectrometryDetermination of branchesHep G2) cellsLinkage analysisGlycogen phenotypeToxic to cellsBiological samplesHuman hepatocellular carcinomaBiological functionsSucrose gradientsEnzyme resultsGlucose residuesEffect of insulinSpectrometryInsulin-resistant statesFunction of glycogen