Ivan Surovtsev
Research Scientist in Cell BiologyCards
About
Research
Publications
2024
Identifying 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, 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, 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 Research