Stochastic Modeling Yields a Mechanistic Framework for Spindle Attachment Error Correction in Budding Yeast Mitosis.

Abstract:

:Proper segregation of the replicated genome requires that kinetochores form and maintain bioriented, amphitelic attachments to microtubules from opposite spindle poles and eliminate erroneous, syntelic attachments to microtubules from the same spindle pole. Phosphorylation of kinetochore proteins destabilizes low-tension kinetochore-microtubule attachments, yet tension stabilizes bioriented attachments. This conundrum for forming high-tension amphitelic attachments is recognized as the "initiation problem of biorientation (IPBO)." A delay before kinetochore-microtubule detachment solves the IPBO, but it lacks a mechanistic framework. We developed a stochastic mathematical model for kinetochore-microtubule error correction in yeast that reveals: (1) under low chromatin tension, requiring a large number of phosphorylation events at multiple sites to achieve detachment provides the necessary delay; and (2) kinetochore-induced microtubule depolymerization generates tension in amphitelic, but not syntelic, attachments. With these requirements, the model provides a mechanistic framework for the delay before detachment to solve the IPBO and demonstrates the high degree of amphitely observed experimentally for wild-type spindles under optimal conditions.

journal_name

Cell Syst

journal_title

Cell systems

authors

Tubman ES,Biggins S,Odde DJ

doi

10.1016/j.cels.2017.05.003

subject

Has Abstract

pub_date

2017-06-28 00:00:00

pages

645-650.e5

issue

6

eissn

2405-4712

issn

2405-4720

pii

S2405-4712(17)30182-5

journal_volume

4

pub_type

杂志文章
  • Divergent Aging of Isogenic Yeast Cells Revealed through Single-Cell Phenotypic Dynamics.

    abstract::Although genetic mutations that alter organisms' average lifespans have been identified in aging research, our understanding of the dynamic changes during aging remains limited. Here, we integrate single-cell imaging, microfluidics, and computational modeling to investigate phenotypic divergence and cellular heterogen...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.02.002

    authors: Jin M,Li Y,O'Laughlin R,Bittihn P,Pillus L,Tsimring LS,Hasty J,Hao N

    更新日期:2019-03-27 00:00:00

  • Environment Tunes Propagation of Cell-to-Cell Variation in the Human Macrophage Gene Network.

    abstract::Cell-to-cell variation in gene expression and the propagation of such variation (PoV or "noise propagation") from one gene to another in the gene network, as reflected by gene-gene correlation across single cells, are commonly observed in single-cell transcriptomic studies and can shape the phenotypic diversity of cel...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.03.002

    authors: Martins AJ,Narayanan M,Prüstel T,Fixsen B,Park K,Gottschalk RA,Lu Y,Andrews-Pfannkoch C,Lau WW,Wendelsdorf KV,Tsang JS

    更新日期:2017-04-26 00:00:00

  • The Key Parameters that Govern Translation Efficiency.

    abstract::Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA and identify the key parameters that govern the overall rate of protein synthesis,...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.12.003

    authors: Erdmann-Pham DD,Dao Duc K,Song YS

    更新日期:2020-02-26 00:00:00

  • Genotype-Fitness Maps of EGFR-Mutant Lung Adenocarcinoma Chart the Evolutionary Landscape of Resistance for Combination Therapy Optimization.

    abstract::Cancer evolution poses a central obstacle to cure, as resistant clones expand under therapeutic selection pressures. Genome sequencing of relapsed disease can nominate genomic alterations conferring resistance but sample collection lags behind, limiting therapeutic innovation. Genome-wide screens offer a complementary...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.10.002

    authors: Bolan PO,Zviran A,Brenan L,Schiffman JS,Dusaj N,Goodale A,Piccioni F,Johannessen CM,Landau DA

    更新日期:2020-01-22 00:00:00

  • Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation.

    abstract::Signaling proteins display remarkable cell-to-cell heterogeneity in their dynamic responses to stimuli, but the consequences of this heterogeneity remain largely unknown. For instance, the contribution of the dynamics of the innate immune transcription factor nuclear factor κB (NF-κB) to gene expression output is disp...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.03.010

    authors: Lane K,Van Valen D,DeFelice MM,Macklin DN,Kudo T,Jaimovich A,Carr A,Meyer T,Pe'er D,Boutet SC,Covert MW

    更新日期:2017-04-26 00:00:00

  • Principles of Systems Biology, No. 31.

    abstract::This month: selected work from the 2018 RECOMB meeting, organized by Ecole Polytechnique and held last April in Paris. ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2018.08.005

    authors: Cho H,Berger B,Peng J,Galitzine C,Vitek O,Beltran PMJ,Cristea IM,Görtler F,Solbrig S,Wettig T,Oefner PJ,Spang R,Altenbuchinger M,Basso RS,Hochbaum D,Vandin F,Silverbush D,Cristea S,Yanovich G,Geiger T,Beerenwinkel

    更新日期:2018-08-22 00:00:00

  • The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

    abstract::The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data,...

    journal_title:Cell systems

    pub_type: 杂志文章,评审

    doi:10.1016/j.cels.2017.11.001

    authors: Keenan AB,Jenkins SL,Jagodnik KM,Koplev S,He E,Torre D,Wang Z,Dohlman AB,Silverstein MC,Lachmann A,Kuleshov MV,Ma'ayan A,Stathias V,Terryn R,Cooper D,Forlin M,Koleti A,Vidovic D,Chung C,Schürer SC,Vasiliauskas J,

    更新日期:2018-01-24 00:00:00

  • Mapping Complex Traits in a Diversity Outbred F1 Mouse Population Identifies Germline Modifiers of Metastasis in Human Prostate Cancer.

    abstract::It is unclear how standing genetic variation affects the prognosis of prostate cancer patients. To provide one controlled answer to this problem, we crossed a dominant, penetrant mouse model of prostate cancer to Diversity Outbred mice, a collection of animals that carries over 40 million SNPs. Integration of disease ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2016.10.018

    authors: Winter JM,Gildea DE,Andreas JP,Gatti DM,Williams KA,Lee M,Hu Y,Zhang S,NISC Comparative Sequencing Program.,Mullikin JC,Wolfsberg TG,McDonnell SK,Fogarty ZC,Larson MC,French AJ,Schaid DJ,Thibodeau SN,Churchill GA,Craw

    更新日期:2017-01-25 00:00:00

  • Orientation of Turing-like Patterns by Morphogen Gradients and Tissue Anisotropies.

    abstract::Patterning of periodic stripes during development requires mechanisms to control both stripe spacing and orientation. A number of models can explain how stripe spacing is controlled, including molecular mechanisms, such as Turing's reaction-diffusion model, as well as cell-based and mechanical mechanisms. However, how...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2015.12.001

    authors: Hiscock TW,Megason SG

    更新日期:2015-12-23 00:00:00

  • Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma.

    abstract::Adenocarcinoma accounts for more than 40% of lung malignancy, and microscopic pathology evaluation is indispensable for its diagnosis. However, how histopathology findings relate to molecular abnormalities remains largely unknown. Here, we obtained H&E-stained whole-slide histopathology images, pathology reports, RNA ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.10.014

    authors: Yu KH,Berry GJ,Rubin DL,Ré C,Altman RB,Snyder M

    更新日期:2017-12-27 00:00:00

  • SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species.

    abstract::Single-cell RNA-seq has emerged as a powerful tool in diverse applications, from determining the cell-type composition of tissues to uncovering regulators of developmental programs. A near-universal step in the analysis of single-cell RNA-seq data is to hypothesize the identity of each cell. Often, this is achieved by...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.06.004

    authors: Tan Y,Cahan P

    更新日期:2019-08-28 00:00:00

  • The Effects of Stochasticity at the Single-Cell Level and Cell Size Control on the Population Growth.

    abstract::Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the experimentally observed correlations between mother-daughter generation times that...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.08.015

    authors: Lin J,Amir A

    更新日期:2017-10-25 00:00:00

  • How Do Chaperones Protect a Cell's Proteins from Oxidative Damage?

    abstract::The accumulation of protein damage in aging organisms is thought to contribute to many aging-related diseases. Yet the properties determining which proteins are most susceptible remain poorly understood. Are certain conformations more vulnerable? Which chaperones are the main guardians? We address these questions with...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2018.05.001

    authors: Santra M,Dill KA,de Graff AMR

    更新日期:2018-06-27 00:00:00

  • Studying Autism in Context.

    abstract::Studying autism genes in the context of the protein complexes to which they belong illustrates the potential of network-centric approaches for understanding complex genetic disease. ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2015.11.004

    authors: Das J,Meyer MJ,Yu H

    更新日期:2015-11-25 00:00:00

  • Entropy-scaling search of massive biological data.

    abstract::Many data sets exhibit well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here we introduce a framework for similarity search based on characterizing a data set's entropy and fractal dimension. We prove that searching scales in tim...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2015.08.004

    authors: Yu YW,Daniels NM,Danko DC,Berger B

    更新日期:2015-08-26 00:00:00

  • Guiding the Refinement of Biochemical Knowledgebases with Ensembles of Metabolic Networks and Machine Learning.

    abstract::Mechanistic models explicitly represent hypothesized biological knowledge. As such, they offer more generalizability than data-driven models. However, identifying model curation efforts that improve performance for mechanistic models is nontrivial. Here, we develop a solution to this problem for genome-scale metabolic...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.11.006

    authors: Medlock GL,Papin JA

    更新日期:2020-01-22 00:00:00

  • Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution.

    abstract::The human interactome is instrumental in the systems-level study of the cell and the contextualization of disease-associated gene perturbations. However, reference organismal interactomes do not capture the cell-type-specific context in which proteins and modules preferentially act. Here, we introduce SCINET, a comput...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.10.007

    authors: Mohammadi S,Davila-Velderrain J,Kellis M

    更新日期:2019-12-18 00:00:00

  • Computational Recipes in Enzymology.

    abstract::How do rich biological behaviors arise from bi-molecular collisions? ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2015.09.006

    authors: Rust MJ

    更新日期:2015-09-23 00:00:00

  • Synthetic 5' UTRs Can Either Up- or Downregulate Expression upon RNA-Binding Protein Binding.

    abstract::The construction of complex gene-regulatory networks requires both inhibitory and upregulatory modules. However, the vast majority of RNA-based regulatory "parts" are inhibitory. Using a synthetic biology approach combined with SHAPE-seq, we explored the regulatory effect of RNA-binding protein (RBP)-RNA interactions ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.04.007

    authors: Katz N,Cohen R,Solomon O,Kaufmann B,Atar O,Yakhini Z,Goldberg S,Amit R

    更新日期:2019-07-24 00:00:00

  • Master regulators of infiltrate recruitment in autoimmune disease identified through network-based molecular deconvolution.

    abstract::Network-based molecular modeling of physiological behaviors has proven invaluable in the study of complex diseases such as cancer, but these approaches remain largely untested in contexts involving interacting tissues such as autoimmunity. Here, using Alopecia Areata (AA) as a model, we have adapted regulatory network...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2015.11.001

    authors: Chen JC,Cerise JE,Jabbari A,Clynes R,Christiano AM

    更新日期:2015-11-25 00:00:00

  • Hunting for Cis-Regulatory Elements in Proteins.

    abstract::A new bioinformatics tool predicts natively disordered protein control elements that function in cis, opening the door to more systematic studies of this biomedically important class of protein modules. ...

    journal_title:Cell systems

    pub_type: 评论,杂志文章

    doi:10.1016/j.cels.2016.02.011

    authors: Gibson TJ,Kumar M

    更新日期:2016-02-24 00:00:00

  • Orchestration of DNA Damage Checkpoint Dynamics across the Human Cell Cycle.

    abstract::Although molecular mechanisms that prompt cell-cycle arrest in response to DNA damage have been elucidated, the systems-level properties of DNA damage checkpoints are not understood. Here, using time-lapse microscopy and simulations that model the cell cycle as a series of Poisson processes, we characterize DNA damage...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.09.015

    authors: Chao HX,Poovey CE,Privette AA,Grant GD,Chao HY,Cook JG,Purvis JE

    更新日期:2017-11-22 00:00:00

  • Evaluation of Kuroda et al.: Insight into Yeast Isobutanol Tolerance with Advances Still Needed.

    abstract::One snapshot of the peer review process for "Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast" (Kuroda et al., 2019). ...

    journal_title:Cell systems

    pub_type: 评论,杂志文章

    doi:10.1016/j.cels.2020.01.005

    authors: Hittinger CT

    更新日期:2020-02-26 00:00:00

  • Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.

    abstract::Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth migh...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2015.07.012

    authors: Durand NC,Robinson JT,Shamim MS,Machol I,Mesirov JP,Lander ES,Aiden EL

    更新日期:2016-07-01 00:00:00

  • Quantitative Translation of Dog-to-Human Aging by Conserved Remodeling of the DNA Methylome.

    abstract::All mammals progress through similar physiological stages throughout life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects underlying genomic events is unclear. Here, we map the common methylation changes experienced by mammalian genomes as they age, foc...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2020.06.006

    authors: Wang T,Ma J,Hogan AN,Fong S,Licon K,Tsui B,Kreisberg JF,Adams PD,Carvunis AR,Bannasch DL,Ostrander EA,Ideker T

    更新日期:2020-08-26 00:00:00

  • tRNA Methylation Is a Global Determinant of Bacterial Multi-drug Resistance.

    abstract::Gram-negative bacteria are intrinsically resistant to drugs because of their double-membrane envelope structure that acts as a permeability barrier and as an anchor for efflux pumps. Antibiotics are blocked and expelled from cells and cannot reach high-enough intracellular concentrations to exert a therapeutic effect....

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.03.008

    authors: Masuda I,Matsubara R,Christian T,Rojas ER,Yadavalli SS,Zhang L,Goulian M,Foster LJ,Huang KC,Hou YM

    更新日期:2019-04-24 00:00:00

  • Gene Expression Knockdown by Modulating Synthetic Small RNA Expression in Escherichia coli.

    abstract::Escherichia coli gene expression knockdown using synthetic small RNA (sRNA) can be fine-tuned by altering sRNA sequences to modulate target mRNA-binding ability, but this requires thorough checking for off-target effects. Here, we present an sRNA gene expression knockdown system fine-tuned by using different promoters...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.08.016

    authors: Noh M,Yoo SM,Kim WJ,Lee SY

    更新日期:2017-10-25 00:00:00

  • Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.

    abstract::Accurately translating genotype to phenotype requires accounting for the functional impact of genetic variation at many biological scales. Here we present a strategy for genotype-phenotype reasoning based on existing knowledge of cellular subsystems. These subsystems and their hierarchical organization are defined by ...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2016.02.003

    authors: Yu MK,Kramer M,Dutkowski J,Srivas R,Licon K,Kreisberg J,Ng CT,Krogan N,Sharan R,Ideker T

    更新日期:2016-02-24 00:00:00

  • Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate.

    abstract::Systematic assessment of tyrosine kinase-substrate relationships is fundamental to a better understanding of cellular signaling and its profound alterations in human diseases such as cancer. In human cells, such assessments are confounded by complex signaling networks, feedback loops, conditional activity, and intra-k...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2017.08.001

    authors: Corwin T,Woodsmith J,Apelt F,Fontaine JF,Meierhofer D,Helmuth J,Grossmann A,Andrade-Navarro MA,Ballif BA,Stelzl U

    更新日期:2017-08-23 00:00:00

  • exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

    abstract::Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occa...

    journal_title:Cell systems

    pub_type: 杂志文章

    doi:10.1016/j.cels.2019.03.004

    authors: Rozowsky J,Kitchen RR,Park JJ,Galeev TR,Diao J,Warrell J,Thistlethwaite W,Subramanian SL,Milosavljevic A,Gerstein M

    更新日期:2019-04-24 00:00:00