2025
The mitotic ATR-Chk1 pathway promotes CDK1 activity for faithful chromosome segregation
Joo Y, Parrado C, Li W, Yang R, Black E, Bleichert F, Liu Y, Kabeche L. The mitotic ATR-Chk1 pathway promotes CDK1 activity for faithful chromosome segregation. Cell Reports 2025, 44: 116019. PMID: 40705605, PMCID: PMC12451630, DOI: 10.1016/j.celrep.2025.116019.Peer-Reviewed Original ResearchConceptsDNA damage responseCdk1 activityATR-Chk1 pathwayChromosome segregationATR-Chk1Aurora B activityResidual activityCheckpoint kinase 1Mitotic progressionCDK1 inhibitionDamage responseRad3-relatedCDK1Lagging chromosomesATR-Chk1 activationHuman cellsChromosomeKinase 1Ataxia telangiectasiaMitosisChk1DNA damageDNAB activityPartial loss
2024
Chk2 sustains PLK1 activity in mitosis to ensure proper chromosome segregation
Black E, Ramírez Parrado C, Trier I, Li W, Joo Y, Pichurin J, Liu Y, Kabeche L. Chk2 sustains PLK1 activity in mitosis to ensure proper chromosome segregation. Nature Communications 2024, 15: 10782. PMID: 39737931, PMCID: PMC11685634, DOI: 10.1038/s41467-024-54922-7.Peer-Reviewed Original ResearchConceptsPolo-like kinase 1Plk1 activityChromosome segregationMitotic polo-like kinase 1Mitotic chromosome segregationProtecting genome stabilitySensitivity to PLK1 inhibitorsMitotic cell divisionCheckpoint kinase 2Polo-like kinase 1 activityDNA damage repairGenome stabilityChromosome missegregationCytokinetic defectsCell divisionGenomic instabilityT-loopCell cycleKinase activityChromosome misalignmentMitotic errorsChk2Kinase 2Damage repairChromosome
2020
Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation
Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain P, Zhou H, Hodny Z, Reiter L, Liu Y. Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation. Molecular Systems Biology 2020, 16: msb199170. PMID: 32175694, PMCID: PMC7073818, DOI: 10.15252/msb.20199170.Peer-Reviewed Original ResearchConceptsProtein degradationGenome-wide correlation analysisGene dosage variationProtein abundance levelsStable isotope-labeled amino acidsIndividual protein isoformsSpecific biological processesAlternative splicing isoformsData-independent acquisition mass spectrometryIsotope-labeled amino acidsAcquisition mass spectrometryProtein degradation ratesIntron retentionCellular functionsProtein isoformsSplicing isoformsCellular organellesTranscriptome variabilitySame geneTurnover controlRegulatory mechanismsBiological processesSpecific mRNAsTight associationAbundance levels
2019
Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1
Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics 2019, 19: e1800438. PMID: 30901150, DOI: 10.1002/pmic.201800438.Peer-Reviewed Original ResearchConceptsChromosomal protein HMG-14DIA-MSDIA mass spectrometryPotential protein functionsCRISPR-Cas gene editingImmune regulation processesCancer cellsExtracellular proteomeChromatin structureHistone inactivationFunctional annotationProtein functionCellular functionsRegulation eventsImportant functional implicationsHMG 14Gene knockoutEnrichment analysisData-independent acquisitionHMGN1Protein deletionCRISPR experimentsGene editingStress pathwaysIndependent acquisitionMulti-omic measurements of heterogeneity in HeLa cells across laboratories
Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature Biotechnology 2019, 37: 314-322. PMID: 30778230, DOI: 10.1038/s41587-019-0037-y.Peer-Reviewed Original ResearchConceptsCell linesGenome-wide copy numberMulti-omic measurementsHuman cultured cellsProtein turnover ratesPhenotypic responsesGenomic variabilityDifferent cell linesHeLa variantsSpecific cell linesCopy numberHeLa cellsCultured cellsHeLa cell linePhenotypic variabilityProgressive divergenceTurnover rateCellsBiological variationTechnical variationUniform conditionsTranscriptomeProteomeSuccessive passagesLines
2017
A Class of Environmental and Endogenous Toxins Induces BRCA2 Haploinsufficiency and Genome Instability
Tan SLW, Chadha S, Liu Y, Gabasova E, Perera D, Ahmed K, Constantinou S, Renaudin X, Lee M, Aebersold R, Venkitaraman AR. A Class of Environmental and Endogenous Toxins Induces BRCA2 Haploinsufficiency and Genome Instability. Cell 2017, 169: 1105-1118.e15. PMID: 28575672, PMCID: PMC5457488, DOI: 10.1016/j.cell.2017.05.010.Peer-Reviewed Original ResearchConceptsBRCA2 haploinsufficiencyChromosomal aberrationsBRCA2 mutation carriersDNA replication forksReplication fork instabilityStructural chromosomal aberrationsRNA-DNA hybridsMutation carriersFork instabilityBRCA2 expressionEndogenous toxinsHeterozygous mutationsGenome instabilityReplication forksCellular proteinsDNA replicationCancer susceptibilityProteasomal degradationUbiquitous environmental toxinSingle copySpontaneous mutagenesisMechanisms of toxicityTransient exposureEnvironmental toxinsTumor suppressor
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