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 ResearchMeSH KeywordsAlgorithmsAnimalsChromatinComputational BiologyHumansImage Processing, Computer-AssistedConceptsTopologically 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 techniquesEffect 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
Loops 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