Microtubule stiffening by the doublecortin-domain protein ZYG-8 contributes to mitotic spindle orientation during zygote division in Caenorhabditis elegans.

Code ↔ Paper

3 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 3 matches

[1] § Materials and methods › M12- Simulation using cytosim ↔ src/sim/fibers/dynamic_fiber.h, lines 1–78 · score 0.61 · dynamic instability, minus ends, plus ends, MAPs, Cytosim, tubulin
[2] § Materials and methods › M12- Simulation using cytosim ↔ src/sim/fibers/dynamic_fiber_prop.h, lines 12–130 · score 0.53 · force velocity relationship, stalled, shrinking, microtubules
[3] § Materials and methods › M12- Simulation using cytosim ↔ src/sim/fibers/classic_fiber.h, lines 1–51 · score 0.52 · dynamic instability, classic, plus ends, Cytosim, tubulin, force

Paper

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The authors' code

C/C++ header · 169 lines · 4.7 KB · cecill-2.1 · 1 match

// Cytosim was created by Francois Nedelec. Copyright 2007-2017 EMBL.
#ifndef DYNAMIC_FIBER_H
#define DYNAMIC_FIBER_H
#include "sim.h"
#include "vector.h"
#include "node_list.h"
#include "fiber.h"
class DynamicFiberProp;
/// A Fiber with discrete growth and dynamic instability at the PLUS_END
/**
This implements the microtubule dynamic instability model proposed by
Brun, Rupp et al. with a 'hard-coded' coupling parameter N=2.
Assembly and disassembly follow discrete steps of size `prop->unit_length`.
The model keeps track of the discrete state of the two terminal units of tubulin.
This leads to 4 different states, which are mapped to [STATE_GREEN, STATE_RED].
The growth speed is reduced under antagonistic force by an exponential factor:\n
Measurement of the Force-Velocity Relation for Growing Microtubules\n
Marileen Dogterom and Bernard Yurke\n
Science Vol 278 pp 856-860; 1997\n
http://www.sciencemag.org/content/278/5339/856.abstract
...and this increases the catastrophe rate:\n
Dynamic instability of MTs is regulated by force\n
M.Janson, M. de Dood, M. Dogterom.\n
Journal of Cell Biology Vol 161, Nb 6, 2003\n
Figure 2 C\n
http://www.jcb.org/cgi/doi/10.1083/jcb.200301147
If you use this model, please cite:\n
A theory of microtubule catastrophes and their regulation\n
Brun L, Rupp B, Ward J, Nedelec F\n
PNAS 106 (50) 21173-21178; 2009\n
http://www.pnas.org/content/106/50/21173
The predicted mean time until catastrophe is approximately
growing_rate = growing_speed / unit_length
real ctime = growing_rate / ( 3 * hydrolysis_rate * hydrolysis_rate );
The implemented model includes off-rate in the assembly state, as described in:\n
Random Hydrolysis Controls the Dynamic Instability of Microtubules\n
Ranjith Padinhateeri, Anatoly B Kolomeisky, and David Lacoste\n
Biophys J 102, 1274–1283 (2012)\n
http://dx.doi.org/10.1016/j.bpj.2011.12.059
This is not implemented:
- the MINUS_END is not dynamic,
- rescues are not included.
.
See the @ref DynamicFiberPar.
// @todo DynamicFiber detach_rate should depend on the state of the subunit
// @todo DynamicFiber should keep the entire state vector of the subunits
Note: A Gillespie simulation method is used.
This class is not fully tested (17. Feb 2011).
@ingroup FiberGroup
*/
class DynamicFiber : public Fiber
{
private:
/// assembly during last time-step
real mGrowthP;
real mGrowthM;
/// Gillespie countdown timers for PLUS_END:
real nextGrowthP;
real nextHydrolP;
real nextShrinkP;
/// Gillespie countdown timers for MINUS_END:
real nextGrowthM;
real nextHydrolM;
real nextShrinkM;
/// state of units near the PLUS_END: [0] is terminal, [1] is penultimate unit
unsigned unitP[3];
/// dynamic state of PLUS_END
state_t mStateP;
/// state of units near the MINUS_END
unsigned unitM[3];
/// dynamic state of MINUS_END
state_t mStateM;
/// calculate dynamic state from unit states near PLUS_END
state_t calculateStateP() const;
/// calculate dynamic state from unit states near MINUS_END
state_t calculateStateM() const;
public:
/// the Property of this object
DynamicFiberProp const* prop;
/// constructor
DynamicFiber(DynamicFiberProp const*);
/// destructor
virtual ~DynamicFiber();
//--------------------------------------------------------------------------
/// return assembly/disassembly state of MINUS_END
state_t dynamicStateM() const;
/// return assembly/disassembly state of PLUS_END
state_t dynamicStateP() const;
/// change state of MINUS_END
void setDynamicStateM(state_t s);
/// change state of PLUS_END
void setDynamicStateP(state_t s);
/// length increment at MINUS_END during last time-step
real freshAssemblyM() const { return mGrowthM; }
/// length increment at PLUS_END during last time-step
real freshAssemblyP() const { return mGrowthP; }
//--------------------------------------------------------------------------
/// simulate dynamic instability of PLUS_END
int stepPlusEnd();
/// simulate dynamic instability of MINUS_END
int stepMinusEnd();
/// monte-carlo step
void step();
//--------------------------------------------------------------------------
/// write to Outputter
void write(Outputter&) const;
/// read from Inputter
void read(Inputter&, Simul&, ObjectTag);
};
#endif

dynamic_fiber.h, under cecill-2.1 · at the source

Overview

Authors: Louis Cueff¹, Loïc Schmitt¹, Ewen Huet¹, Sylvain Pastezeur¹, Méline Coquil¹, Talia Savary¹, Anouk Sénard¹, Jacques Pécréaux¹, Hélène Bouvrais¹

ORCID iDs: Louis Cueff, Loïc Schmitt, Ewen Huet, Sylvain Pastezeur, Talia Savary, Anouk Sénard, Jacques Pécréaux, Hélène Bouvrais

CNRS, Univ Rennes, IGDR (Institut de Génétique et Développement de Rennes) – UMR 6290, Rennes, France

Institutions: Centre National de la Recherche Scientifique (France); Institut de génétique et de développement de Rennes (France); Université de Rennes (France)

Journal: PLoS genetics, volume 22, issue 6, article e1012196

Dates: received 21 October 2025; accepted 1 June 2026; published online 29 June 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1371/journal.pgen.1012196 · PMID 42371962 · PMCID PMC13340844 · OpenAlex W4404918954

Open access: gold, a free copy (OpenAlex)

Preprint: doi:10.1101/2024.11.29.624795

Status: code verified

Categories: C. elegans (organism), cellular / molecular (subfield)

Methods: Spectral & time-frequency, Statistics, Machine learning, Preprocessing, Evoked potentials, Connectivity, fMRI & imaging, Smoothing, state filtering, decompositions

MeSH: Caenorhabditis elegans*, Caenorhabditis elegans Proteins*, Microtubule-Associated Proteins*, Microtubules*, Spindle Apparatus*, Zygote*, Animals, Mitosis, Mutation, RNA Interference (* major topic)

Journal subjects: Biology and Life Sciences, Cell Biology, Cellular Structures and Organelles, Cytoskeleton, Microtubules, Developmental Biology, Embryology, Embryos, Centrosomes, Cell Processes, Cell Cycle and Cell Division, Anaphase, Genetics, Epigenetics, RNA interference, Gene expression, Genetic interference, Biochemistry, Nucleic acids, RNA, Research and Analysis Methods, Imaging Techniques, Fluorescence Imaging, Animal Studies, Experimental Organism Systems, Model Organisms, Caenorhabditis Elegans, Animal Models, Organisms, Eukaryota, Animals, Invertebrates, Nematoda, Caenorhabditis, Zoology, Cellular Types, Animal Cells, Germ Cells, OVA, Zygotes

Topic: Microtubule and mitosis dynamics (Cell Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex

Funding: Ligue Contre le Cancer (PhD thesis funding, 3 years, CARID grant, Finistère commitee, Ille et Vilaine & Deux-Sèvres committees, 2019, Côtes d’Armor & Ille-et-Vilaine committees, 2021); Région Bretagne (ARED 2025, PhD thesis funding); Agence Nationale de la Recherche (ANR-22-CE45-001601); Université de Rennes (Défis scientifiques, 2020)

Citations: cited by 1 paper (Europe PMC); 204 references in the paper

Abstract

In the Caenorhabditis elegans zygote, mutations in zyg-8DCLK1, the sole Doublecortin-family member, disrupt mitotic spindle positioning, as seen by immunofluorescence. Doublecortin proteins bind microtubules and are thought to stabilise or rigidify them. In the zygote, ZYG-8 only modestly affects microtubule growth and nucleation. We thus investigated whether these moderate dynamic perturbations alone could explain the spindle mispositioning observed in zyg-8 mutants. Using three complementary genetic perturbations—RNAi-mediated depletion of ZYG-8, its overexpression, and the thermosensitive zyg-8(or484ts) mutant (that disrupts microtubule binding)—we observed altered spindle pole oscillations and changes in microtubule cortical-contact behaviour, indicative of impaired cortical forces. Importantly, these phenotypes could not be fully explained by previously reported alterations in microtubule dynamics, suggesting an additional mechanism. Our findings indicate that ZYG-8 increases microtubule rigidity: ZYG-8 depletion or mutation led to more frequent microtubule bending and higher curvature and tortuosity. Simulations confirmed that reduced rigidity prolongs cortical contact lifetimes, an effect we experimentally observed in zyg-8(RNAi) embryos. Using custom biophysical assays, we showed that microtubule softening in zyg-8(RNAi) embryos and zyg-8 mutants reduced the efficiency of centring forces, leading to exaggerated spindle-pole oscillations. In mutants, the largest oscillations caused spindle poles to move closer to the cell periphery, preventing re-centring and resulting in spindle mispositioning and misorientation during late anaphase. Importantly, reducing cortical pulling forces rescued orientation defects, highlighting the importance of balanced pulling-pushing forces for proper spindle positioning. We propose that sufficient microtubule rigidity is essential for generating effective cortical pushing forces, potentially in synergy with other microtubule properties, which contribute to centring mechanisms that ensure accurate spindle orientation in late mitosis. Given that DCLK1 is frequently deregulated in human cancers and that accurate spindle positioning is essential for maintaining cell proliferation-differentiation balance, these findings may have implications for understanding how disruptions in microtubule mechanics contribute to carcinogenesis.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 3 matches between paragraphs and lines of code.

Zenodo 14246919

License: cecill-2.1

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Size: 1 file

Software Heritage: not checked

Found in: the text, “M12- Simulation using cytosim”

Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Matplotlib (2 files), NumPy (1 file)

Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)

27 September 2026: the link answers (HTTP 200)

514 files

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At the source: doi.org/10.5281/zenodo.14246919

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Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 9 authors, 10 MeSH terms, 4 funders, 198 references.

Cite

This paper

Cueff, L., Schmitt, L., Huet, E., Pastezeur, S., Coquil, M., Savary, T., Sénard, A., Pécréaux, J., & Bouvrais, H. (2026). Microtubule stiffening by the doublecortin-domain protein ZYG-8 contributes to mitotic spindle orientation during zygote division in Caenorhabditis elegans. PLoS genetics, 22(6), e1012196. https://doi.org/10.1371/journal.pgen.1012196

BibTeX

@article{cueff2026microtubule, author = {Cueff, Louis and Schmitt, Loïc and Huet, Ewen and Pastezeur, Sylvain and Coquil, Méline and Savary, Talia and Sénard, Anouk and Pécréaux, Jacques and Bouvrais, Hélène}, title = {{Microtubule stiffening by the doublecortin-domain protein ZYG-8 contributes to mitotic spindle orientation during zygote division in Caenorhabditis elegans}}, journal = {PLoS genetics}, year = {2026}, month = jun, volume = {22}, number = {6}, pages = {e1012196}, publisher = {PLOS}, issn = {1553-7390}, doi = {10.1371/journal.pgen.1012196}, url = {https://doi.org/10.1371/journal.pgen.1012196}, pmid = {42371962}, pmcid = {PMC13340844} }

RIS

TY - JOUR AU - Cueff, Louis AU - Schmitt, Loïc AU - Huet, Ewen AU - Pastezeur, Sylvain AU - Coquil, Méline AU - Savary, Talia AU - Sénard, Anouk AU - Pécréaux, Jacques AU - Bouvrais, Hélène TI - Microtubule stiffening by the doublecortin-domain protein ZYG-8 contributes to mitotic spindle orientation during zygote division in Caenorhabditis elegans T2 - PLoS genetics J2 - PLoS Genet PY - 2026 DA - 2026/06/29 VL - 22 IS - 6 SP - e1012196 SN - 1553-7390 PB - PLOS DO - 10.1371/journal.pgen.1012196 UR - https://doi.org/10.1371/journal.pgen.1012196 LA - en ER -

CSL-JSON

{ "id": "10.1371/journal.pgen.1012196", "type": "article-journal", "title": "Microtubule stiffening by the doublecortin-domain protein ZYG-8 contributes to mitotic spindle orientation during zygote division in Caenorhabditis elegans", "container-title": "PLoS genetics", "author": [ { "family": "Cueff", "given": "Louis" }, { "family": "Schmitt", "given": "Loïc" }, { "family": "Huet", "given": "Ewen" }, { "family": "Pastezeur", "given": "Sylvain" }, { "family": "Coquil", "given": "Méline" }, { "family": "Savary", "given": "Talia" }, { "family": "Sénard", "given": "Anouk" }, { "family": "Pécréaux", "given": "Jacques" }, { "family": "Bouvrais", "given": "Hélène" } ], "container-title-short": "PLoS Genet", "volume": "22", "issue": "6", "page": "e1012196", "DOI": "10.1371/journal.pgen.1012196", "PMID": "42371962", "PMCID": "PMC13340844", "ISSN": "1553-7390", "publisher": "PLOS", "URL": "https://doi.org/10.1371/journal.pgen.1012196", "language": "en", "issued": { "date-parts": [ [ 2026, 6, 29 ] ] } }

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