Three-Dimensional Thermodynamic Simulation of Condensin as a DNA-Based Translocase.

Josh Lawrimore, Yunyan He, Gregory M Forest, Kerry Bloom

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

Statistical mechanics of chromosomes: in vivo and in silico approaches reveal high-level organization and structure arise exclusively through mechanical feedback between loop extruders and chromatin substrate properties.Nucleic acids research · 2020
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Josh LawrimoreDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Yunyan HeDepartment of Mathematics and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Gregory M ForestDepartment of Mathematics and Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.

Kerry BloomDepartment of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. kerry_bloom@unc.edu.

Funding

Structure and Function of a Eukaryotic CentromereR37GM032238 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI BLOOM, KERRY S, YEH, ELAINE YING · 2011 to 2020

$5.2M

NIGMS NIH HHS R37 GM032238

6 · The paper itself

Abstract

Chromatin dynamics and organization can be altered by condensin complexes. In turn, the molecular behavior of a condensin complex changes based on the tension of the substrate to which condensin is bound. This interplay between chromatin organization and condensin behavior demonstrates the need for tools that allows condensin complexes to be observed on a variety of chromatin organizations. We provide a method for simulating condensin complexes on a dynamic polymer substrate using the polymer dynamics simulator ChromoShake and the condensin simulator RotoStep. These simulations can be converted into simulated fluorescent images that are able to be directly compared to experimental images of condensin and fluorescently labeled chromatin. Our pipeline enables users to explore how changes in condensin behavior alters chromatin dynamics and vice versa while providing simulated image datasets that can be directly compared to experimental observations.

Indexed as

Adenosine TriphosphatasesChromatinDNADNA-Binding ProteinsMolecular Dynamics SimulationMultiprotein ComplexesPolymersThermodynamicsAdenosine TriphosphatasesChromatincondensin complexesDNADNA-Binding ProteinsMultiprotein ComplexesPolymersChromatinChromoShakeComputational image analysisCondensinMicroscope Simulator 2Polymer dynamics simulatorRotoStepSimulated fluorescent images

Identifiers

PMID31147925

DOI10.1007/978-1-4939-9520-2_21

PMCPMC6904244

What OpenQuestion holds

Textmetadata

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Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.