2024
Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion
Yuan T, Yan H, Li K, Surovtsev I, King M, Mochrie S. Cohesin distribution alone predicts chromatin organization in yeast via conserved-current loop extrusion. Genome Biology 2024, 25: 293. PMID: 39543681, PMCID: PMC11566905, DOI: 10.1186/s13059-024-03432-2.Peer-Reviewed Original ResearchConceptsTopologically associating domainsLoop extrusionTopologically associating domains boundariesNon-vertebrate eukaryotesChIP-seq dataChromatin spatial organizationTree of lifeHi-C mapsBinds CTCFCohesin distributionTAD boundariesCTCF sitesChromatin organizationDNA sequencesCTCFCohesinYeastChromatinSpatial organizationEukaryotesGenomeResultsToVertebratesExtrusion factorsOrganizationIdentifying topologically associating domains using differential kernels
Maisuradze L, King M, Surovtsev I, Mochrie S, Shattuck M, O’Hern C. Identifying topologically associating domains using differential kernels. PLOS Computational Biology 2024, 20: e1012221. PMID: 39008525, PMCID: PMC11249266, DOI: 10.1371/journal.pcbi.1012221.Peer-Reviewed Original ResearchConceptsTopologically associating domainsHi-C mapsFalse discovery rateChromatin conformation capture techniquesEnhancer-promoter interactionsLow false discovery rateSelf-interacting regionsStructure of chromatinRegulate gene expressionAverage contact probabilitiesHi-CLocus IDNA transcriptionGene expressionChromatinDiscovery rateContact probabilityBiological phenomenaState-of-the-artKernel-based techniqueComputer visionReplicationCorrelated changesDisease statesCapture techniquesThe condensation of HP1α/Swi6 imparts nuclear stiffness
Williams J, Surovtsev I, Schreiner S, Chen Z, Raiymbek G, Nguyen H, Hu Y, Biteen J, Mochrie S, Ragunathan K, King M. The condensation of HP1α/Swi6 imparts nuclear stiffness. Cell Reports 2024, 43: 114373. PMID: 38900638, PMCID: PMC11348953, DOI: 10.1016/j.celrep.2024.114373.Peer-Reviewed Original ResearchSingle-molecule imagingBiomolecular condensatesSeparation-of-function alleleHeterochromatin protein HP1aChromatin-bound moleculesHigh-resolution live-cell imagingLive-cell imagingCondensationHeterochromatin domainsMethylated nucleosomesSwi6Nuclear stiffnessForce spectroscopyChromatin meshworkCellular organizationCell mechanicsDynamic poolEffect of loops on the mean-square displacement of Rouse-model chromatin
Yuan T, Yan H, Bailey M, Williams J, Surovtsev I, King M, Mochrie S. Effect of loops on the mean-square displacement of Rouse-model chromatin. Physical Review E 2024, 109: 044502. PMID: 38755928, DOI: 10.1103/physreve.109.044502.Peer-Reviewed Original ResearchConceptsStretching exponentConsistent with recent experimentsTopologically associating domainsMean square displacementRecent experimentsLoop extrusionExponent valuesTAD formationTree of lifeDynamics of chromatinExponentEffects of loopChromatin lociChromatin dynamicsRouse modelChromatin organizationChromatin mobilityGene locusContact mapsDynamicsChromatinLoopPolymer dynamicsLociPolymer simulations
2023
An ESCRT grommet cooperates with a diffusion barrier to maintain nuclear integrity
Ader N, Chen L, Surovtsev I, Chadwick W, Rodriguez E, King M, Lusk C. An ESCRT grommet cooperates with a diffusion barrier to maintain nuclear integrity. Nature Cell Biology 2023, 25: 1465-1477. PMID: 37783794, PMCID: PMC11365527, DOI: 10.1038/s41556-023-01235-4.Peer-Reviewed Original ResearchConceptsSpindle pole body proteinNuclear envelope barrierESCRT-III proteinsNuclear pore complexSpindle pole bodyNucleocytoplasmic compartmentalizationESCRT functionPore complexPole bodyDistinct complementNuclear compartmentNuclear integrityTransport proteinsMolecular mechanismsRemodelling mechanismProteinBody proteinLoops and the activity of loop extrusion factors constrain chromatin dynamics
Bailey M, Surovtsev I, Williams J, Yan H, Yuan T, Li K, Duseau K, Mochrie S, King M. Loops and the activity of loop extrusion factors constrain chromatin dynamics. Molecular Biology Of The Cell 2023, 34: ar78. PMID: 37126401, PMCID: PMC10398873, DOI: 10.1091/mbc.e23-04-0119.Peer-Reviewed Original ResearchConceptsChromatin dynamicsChromatin mobilityChromatin conformation capture experimentsINO80 chromatin remodelerSystematic genetic perturbationsDynamics of chromatinSWI/SNFChromatin fluctuationsCondensin complexRSC complexChromatin remodelersFission yeastChromosome structureChromatin polymerExtrusion factorsChromatin motionGenetic perturbationsThree-dimensional structureDNA structureChromatinCohesinPolymer simulationsIntroduction of loopsKey roleActive process
2021
Extrusion of chromatin loops by a composite loop extrusion factor
Yan H, Surovtsev I, Williams JF, Bailey MLP, King MC, Mochrie SGJ. Extrusion of chromatin loops by a composite loop extrusion factor. Physical Review E 2021, 104: 024414. PMID: 34525654, PMCID: PMC9112126, DOI: 10.1103/physreve.104.024414.Peer-Reviewed Original ResearchInterconnecting solvent quality, transcription, and chromosome folding in Escherichia coli
Xiang Y, Surovtsev IV, Chang Y, Govers SK, Parry BR, Liu J, Jacobs-Wagner C. Interconnecting solvent quality, transcription, and chromosome folding in Escherichia coli. Cell 2021, 184: 3626-3642.e14. PMID: 34186018, DOI: 10.1016/j.cell.2021.05.037.Peer-Reviewed Original ResearchCovariance distributions in single particle tracking
Bailey MLP, Yan H, Surovtsev I, Williams JF, King MC, Mochrie SGJ. Covariance distributions in single particle tracking. Physical Review E 2021, 103: 032405. PMID: 33862686, PMCID: PMC9115892, DOI: 10.1103/physreve.103.032405.Peer-Reviewed Original ResearchConceptsCovariance distributionLocalization noiseMultivariate Gaussian random variablesGaussian random variablesSkew-normal distributionStatistical propertiesDisplacement covarianceRandom variablesThird central momentHeterogeneous noiseAnomalous diffusionProbability distributionTheory-experiment discrepancyViscoelastic polymer solutionsCentral momentsParticle trajectoriesTheoretical meansTheoretical equationsMotionSingle modeRecent experimentsTheoryNoiseParticle trackingCovariance
2019
Is the Bacterial Cytoplasm a Poor Solvent for the Chromosome?
Xiang Y, Surovtsev I, Dufresne E, Jacobs-Wagner C. Is the Bacterial Cytoplasm a Poor Solvent for the Chromosome? Biophysical Journal 2019, 116: 320a. DOI: 10.1016/j.bpj.2018.11.1736.Peer-Reviewed Original Research
2018
mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding
Delarue M, Brittingham G, Pfeffer S, Surovtsev I, Pinglay S, Kennedy K, Schaffer M, Gutierrez J, Sang D, Poterewicz G, Chung J, Plitzko J, Groves J, Jacobs-Wagner C, Engel B, Holt L. mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding. Cell 2018, 174: 338-349.e20. PMID: 29937223, PMCID: PMC10080728, DOI: 10.1016/j.cell.2018.05.042.Peer-Reviewed Original ResearchSubcellular Organization: A Critical Feature of Bacterial Cell Replication
Surovtsev IV, Jacobs-Wagner C. Subcellular Organization: A Critical Feature of Bacterial Cell Replication. Cell 2018, 172: 1271-1293. PMID: 29522747, PMCID: PMC5870143, DOI: 10.1016/j.cell.2018.01.014.Peer-Reviewed Original ResearchConceptsSelf-replicating entitiesCellular lifeStructured genomesDynamic spatial patternsChallenge cellsIntracellular organellesCellular replicationCytoskeletal filamentsBacterial cellsUnique biological propertiesComplex internal organizationSpatial organizationSmall formsCell replicationActive transportLiving systemsBacteriaReplicationGenomeBiological propertiesCellsSpatial patternsOrganellesPowerful meansHallmark
2016
Replication fork passage drives asymmetric dynamics of a critical nucleoid‐associated protein in Caulobacter
Arias‐Cartin R, Dobihal GS, Campos M, Surovtsev IV, Parry B, Jacobs‐Wagner C. Replication fork passage drives asymmetric dynamics of a critical nucleoid‐associated protein in Caulobacter. The EMBO Journal 2016, 36: 301-318. PMID: 28011580, PMCID: PMC5286365, DOI: 10.15252/embj.201695513.Peer-Reviewed Original ResearchConceptsNucleoid-associated proteinsDNA replicationNovel nucleoid-associated proteinGene expressionReplication fork passageGlobal gene expressionCell cycle regulationDNA-binding activityCell cycle progressionChromosome dynamicsFork passageChromosome segregationPleiotropic defectsChromosomal biasCaulobacter crescentusAsymmetric localizationReplication forksCellular functionsCycle regulationGenomic techniquesQuantitative cell imagingCell divisionGapRCycle progressionCell cycleDNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos
Surovtsev IV, Campos M, Jacobs-Wagner C. DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: e7268-e7276. PMID: 27799522, PMCID: PMC5135302, DOI: 10.1073/pnas.1616118113.Peer-Reviewed Original ResearchConceptsParA ATPase activityParA gradientCellular physiologyATP bindingBinds DNAIntracellular patterningChromosomal lociATP hydrolysisIntracellular transportInside cellsMultiple copiesMultiple cargoesDNA fluctuationsATPase activityIntracellular patternMacromolecular componentsCargoDNAPatterningMinimal systemBindingSignature patternsParBCargo dynamicsCells
2015
Oufti: an integrated software package for high‐accuracy, high‐throughput quantitative microscopy analysis
Paintdakhi A, Parry B, Campos M, Irnov I, Elf J, Surovtsev I, Jacobs-Wagner C. Oufti: an integrated software package for high‐accuracy, high‐throughput quantitative microscopy analysis. Molecular Microbiology 2015, 99: 767-777. PMID: 26538279, PMCID: PMC4752901, DOI: 10.1111/mmi.13264.Peer-Reviewed Original ResearchConceptsSingle-cell studiesOpen-source software packageGraphical user interfaceComplex subcellular organizationSoftware packageImage analysisUser interfaceMassive datasetsCellular functionsSubcellular organizationBacterial researchHigh-throughput analysisTouching cellsMicrobial cellsSubpixel precisionInteractive modulesComputational skillsComputational solutionPost-processing analysisPhenotypic variabilityFluorescence signalQuantitative microscopy analysisCell morphologyAutomated MeasurementConfluent samples
2014
A Constant Size Extension Drives Bacterial Cell Size Homeostasis
Campos M, Surovtsev IV, Kato S, Paintdakhi A, Beltran B, Ebmeier SE, Jacobs-Wagner C. A Constant Size Extension Drives Bacterial Cell Size Homeostasis. Cell 2014, 159: 1433-1446. PMID: 25480302, PMCID: PMC4258233, DOI: 10.1016/j.cell.2014.11.022.Peer-Reviewed Original ResearchConceptsCell size homeostasisCell size controlSize homeostasisSingle-cell microscopyCell cycle controlCaulobacter crescentusAsymmetric divisionHomeostasis mechanismsBacteria Escherichia coliCell cycleEscherichia coliDifferent growth ratesCell growthCell lengthSize controlCell sizeHomeostasisBacteriaSize thresholdGrowth rateDivisionDirect experimental evidenceCrescentusSize paradigmColiEvidence for a DNA-relay mechanism in ParABS-mediated chromosome segregation
Lim HC, Surovtsev IV, Beltran BG, Huang F, Bewersdorf J, Jacobs-Wagner C. Evidence for a DNA-relay mechanism in ParABS-mediated chromosome segregation. ELife 2014, 3: e02758. PMID: 24859756, PMCID: PMC4067530, DOI: 10.7554/elife.02758.Peer-Reviewed Original ResearchConceptsChromosome segregationPartition complexParA-like proteinBacterial chromosome segregationDNA-binding activityParABS systemCytoplasmic cargoCaulobacter crescentusDNA regionsBiochemical approachesIntracellular transportTranslocation forceCellular parametersChromosomesTransient tethersCrescentusParABSMajor roleSegregationComplexesMechanismProteinTranslocationConservationBacteriaCellular Metabolism Fluidizes the Glassy Bacterial Cytoplasm
Parry B, Surovtsev I, Cabeen M, O'Hern C, Dufresne E, Jacobs-Wagner C. Cellular Metabolism Fluidizes the Glassy Bacterial Cytoplasm. Biophysical Journal 2014, 106: 313a. DOI: 10.1016/j.bpj.2013.11.1814.Peer-Reviewed Original Research
2013
The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity
Parry BR, Surovtsev IV, Cabeen MT, O’Hern C, Dufresne ER, Jacobs-Wagner C. The Bacterial Cytoplasm Has Glass-like Properties and Is Fluidized by Metabolic Activity. Cell 2013, 156: 183-194. PMID: 24361104, PMCID: PMC3956598, DOI: 10.1016/j.cell.2013.11.028.Peer-Reviewed Original Research
2010
Spatial organization of the flow of genetic information in bacteria
Montero Llopis P, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T, Jacobs-Wagner C. Spatial organization of the flow of genetic information in bacteria. Nature 2010, 466: 77-81. PMID: 20562858, PMCID: PMC2896451, DOI: 10.1038/nature09152.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsCaulobacter crescentusChaperoninsChromosomes, BacterialDiffusionDNA, BacterialEndoribonucleasesEscherichia coliGene Expression Regulation, BacterialIn Situ Hybridization, FluorescenceLac OperonProtein BiosynthesisRibosomesRNA StabilityRNA TransportRNA, BacterialRNA, MessengerTranscription, GeneticConceptsSites of transcriptionC. crescentusCaulobacter crescentusEukaryotic cellsCellular physiologyMRNA decayMature mRNAMRNA processesRNase EMRNA substratesMRNA localizationGenetic informationGene expressionBacterial cellsEscherichia coliQuantitative fluorescenceCrescentusSitu hybridizationSpatial organizationMRNABacteriaLimited dispersionCellsTranscriptionTranslation