The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling

Histone variants within the H2A family show high divergences in their C-terminal regions. In this work, we have studied how these divergences and in particular, how a part of the H2A COOH-terminus, the docking domain, is implicated in both structural and functional properties of the nucleosome. Using biochemical methods in combination with Atomic Force Microscopy and Electron Cryo-Microscopy, we show that the H2A-docking domain is a key structural feature within the nucleosome. Deletion of this domain or replacement with the incomplete docking domain from the variant H2A.Bbd results in significant structural alterations in the nucleosome, including an increase in overall accessibility to nucleases, un-wrapping of ∼10 bp of DNA from each end of the nucleosome and associated changes in the entry/exit angle of DNA ends. These structural alterations are associated with a reduced ability of the chromatin remodeler RSC to both remodel and mobilize the nucleosomes. Linker histone H1 binding is also abrogated in nucleosomes containing the incomplete docking domain of H2A.Bbd. Our data illustrate the unique role of the H2A-docking domain in coordinating the structural-functional aspects of the nucleosome properties. Moreover, our data suggest that incorporation of a ‘defective’ docking domain may be a primary structural role of H2A.Bbd in chromatin

Etude des fonctions mitotiques du domaine amino-terminal de CENP-A

The histone variant CENP-A is the epigenetic factor responsible for centromere deter- mination. It allows the recruitment of a handful of centromeric proteins, and thus acts as the primary foundation for the kinetochore. It comprises an unstructured amino-terminal domain to which no precise function has yet been assigned, although it is established in some species that the mere presence of that domain is required for proper centromere func- tion and thus successful completion of mitosis. We have established several human cell lines stably expressing GFP-tagged CENP-A constructs, allowing us to perform pseudoge- netic experiments by siRNA-mediated silencing of the endogenous CENP-A. Our results show a dramatic increase of mitotic defects and plurinuclear cells when cells express only the globular domain of CENP-A; this is in accordance with the litterature and confirms the importance of the amino-terminal tail. More importantly, a similar increase of mitotic defects is observed when cells express a full-length, but non-phosphatable, CENP-A. Our results show the involvement of the phosphatable serine 7 of CENP-A in the successful completion of mitosis, and may suggest that the role of the whole amino-terminal tail of CENP-A could be reduced to this single phosphorylation event.Le variant d'histone CENP-A est le facteur responsable de la détermination épigéné- tique du centromère. Il permet le recrutement de nombreuses protéines centromériques, et constitue ainsi la brique fondatrice du kinétochore. Il possède un domaine amino-terminal non structuré dont la fonction précise reste encore à élucider, bien qu'il soit déjà établi chez certaines espèces que ce domaine est requis pour le bon fonctionnement du cen- tromère et conséquemment le bon déroulement de la mitose. Nous avons construit des lignées cellulaires humaines exprimant stablement diverses formes mutantes de CENP-A, qui nous ont permis de réaliser des expériences de pseudogénétique en supprimant l'ex- pression de la protéine CENP-A endogène. Nous observons une augmentation drastique du taux de défauts de ségrégation des chromosomes et de cellules plurinucléées dans des cellules exprimant uniquement le domaine globulaire de CENP-A, ce qui est en accord avec les données de la littérature et confirme l'importance du domaine amino-terminal. Un phénotype similaire est observé dans des cellules exprimant une protéine CENP-A entière mais dont le domaine amino-terminal n'est pas phosphorylable. Nos résultats montrent l'implication de la phosphorylation de la sérine de CENP-A dans le bon déroulement de la mitose, et suggèrent que la fonction mitotique du domaine amino-terminal est centrée sur cette seule phosphorylation

Investigating functions of CENP-A N-tail in mitosis

Le variant d'histone CENP-A est le facteur responsable de la détermination épigéné- tique du centromère. Il permet le recrutement de nombreuses protéines centromériques, et constitue ainsi la brique fondatrice du kinétochore. Il possède un domaine amino-terminal non structuré dont la fonction précise reste encore à élucider, bien qu'il soit déjà établi chez certaines espèces que ce domaine est requis pour le bon fonctionnement du cen- tromère et conséquemment le bon déroulement de la mitose. Nous avons construit des lignées cellulaires humaines exprimant stablement diverses formes mutantes de CENP-A, qui nous ont permis de réaliser des expériences de pseudogénétique en supprimant l'ex- pression de la protéine CENP-A endogène. Nous observons une augmentation drastique du taux de défauts de ségrégation des chromosomes et de cellules plurinucléées dans des cellules exprimant uniquement le domaine globulaire de CENP-A, ce qui est en accord avec les données de la littérature et confirme l'importance du domaine amino-terminal. Un phénotype similaire est observé dans des cellules exprimant une protéine CENP-A entière mais dont le domaine amino-terminal n'est pas phosphorylable. Nos résultats montrent l'implication de la phosphorylation de la sérine de CENP-A dans le bon déroulement de la mitose, et suggèrent que la fonction mitotique du domaine amino-terminal est centrée sur cette seule phosphorylation.The histone variant CENP-A is the epigenetic factor responsible for centromere deter- mination. It allows the recruitment of a handful of centromeric proteins, and thus acts as the primary foundation for the kinetochore. It comprises an unstructured amino-terminal domain to which no precise function has yet been assigned, although it is established in some species that the mere presence of that domain is required for proper centromere func- tion and thus successful completion of mitosis. We have established several human cell lines stably expressing GFP-tagged CENP-A constructs, allowing us to perform pseudoge- netic experiments by siRNA-mediated silencing of the endogenous CENP-A. Our results show a dramatic increase of mitotic defects and plurinuclear cells when cells express only the globular domain of CENP-A; this is in accordance with the litterature and confirms the importance of the amino-terminal tail. More importantly, a similar increase of mitotic defects is observed when cells express a full-length, but non-phosphatable, CENP-A. Our results show the involvement of the phosphatable serine 7 of CENP-A in the successful completion of mitosis, and may suggest that the role of the whole amino-terminal tail of CENP-A could be reduced to this single phosphorylation event

SSSOM-Java

An implementation of the SSSOM specification for Java. It provides a Java library to manipulate mapping sets and a ROBOT plugin with two commands to extract mappings from cross-references in a OWL ontology and to inject mappings-derived axioms into an ontology. Version 0.5.0 fixes a couple of bugs in the TSV parser and the ROBOT injector, makes the TSV writer fully predictable, and adds a new interface to easily visit all slots in a mapping or mapping set

SSSOM-Java

<p>An implementation of the <a href="https://mapping-commons.github.io/sssom/spec/">SSSOM specification</a> for Java. It provides a Java library and a command-line tool to manipulate mapping sets, and a <a href="http://robot.obolibrary.org/">ROBOT</a> plugin with two commands to extract mappings from cross-references in a OWL ontology and to inject mappings-derived axioms into an ontology.</p> <p>Version 0.7.3 adds support for <em>Extended Prefix Maps</em> (allowing to “reconciliate” IRIs in a mapping set against an EPM) as well as several new options to <em>sssom-cli</em> to better control both the transform prefix map and the output prefix map, as well as the output metadata.</p&gt

Etude des fonctions mitotiques du domaine amino-terminal de CENP-A

The histone variant CENP-A is the epigenetic factor responsible for centromere deter- mination. It allows the recruitment of a handful of centromeric proteins, and thus acts as the primary foundation for the kinetochore. It comprises an unstructured amino-terminal domain to which no precise function has yet been assigned, although it is established in some species that the mere presence of that domain is required for proper centromere func- tion and thus successful completion of mitosis. We have established several human cell lines stably expressing GFP-tagged CENP-A constructs, allowing us to perform pseudoge- netic experiments by siRNA-mediated silencing of the endogenous CENP-A. Our results show a dramatic increase of mitotic defects and plurinuclear cells when cells express only the globular domain of CENP-A; this is in accordance with the litterature and confirms the importance of the amino-terminal tail. More importantly, a similar increase of mitotic defects is observed when cells express a full-length, but non-phosphatable, CENP-A. Our results show the involvement of the phosphatable serine 7 of CENP-A in the successful completion of mitosis, and may suggest that the role of the whole amino-terminal tail of CENP-A could be reduced to this single phosphorylation event.Le variant d'histone CENP-A est le facteur responsable de la détermination épigéné- tique du centromère. Il permet le recrutement de nombreuses protéines centromériques, et constitue ainsi la brique fondatrice du kinétochore. Il possède un domaine amino-terminal non structuré dont la fonction précise reste encore à élucider, bien qu'il soit déjà établi chez certaines espèces que ce domaine est requis pour le bon fonctionnement du cen- tromère et conséquemment le bon déroulement de la mitose. Nous avons construit des lignées cellulaires humaines exprimant stablement diverses formes mutantes de CENP-A, qui nous ont permis de réaliser des expériences de pseudogénétique en supprimant l'ex- pression de la protéine CENP-A endogène. Nous observons une augmentation drastique du taux de défauts de ségrégation des chromosomes et de cellules plurinucléées dans des cellules exprimant uniquement le domaine globulaire de CENP-A, ce qui est en accord avec les données de la littérature et confirme l'importance du domaine amino-terminal. Un phénotype similaire est observé dans des cellules exprimant une protéine CENP-A entière mais dont le domaine amino-terminal n'est pas phosphorylable. Nos résultats montrent l'implication de la phosphorylation de la sérine de CENP-A dans le bon déroulement de la mitose, et suggèrent que la fonction mitotique du domaine amino-terminal est centrée sur cette seule phosphorylation

KGCL-Java

<p>Changes since KGCL-Java 0.2.0:</p> <ul> <li>Support for edge deletion (<code>delete edge</code> command).</li> <li>Support for node move operations (<code>move</code>, <code>deepen</code>, <code>shallow</code> commands).</li> <li>Support for predicate change (<code>change relationship</code> command).</li> </ul>Should you wish to cite this software, please do so using the following metadata

SSSOM-Java

<p>An implementation of the <a href="https://mapping-commons.github.io/sssom/spec/">SSSOM specification</a> for Java. It provides a Java library and a command-line tool to manipulate mapping sets, and a <a href="http://robot.obolibrary.org/">ROBOT</a> plugin with two commands to extract mappings from cross-references in a OWL ontology and to inject mappings-derived axioms into an ontology.</p><p>Version 0.6.2 updates the ROBOT plugin's <i>inject</i> command to allow the production of annotated axioms and updates the command-line tool <i>sssom-cli</i> to allow specifying individual SSSOM/T rules directly on the command line.</p&gt

KGCL-Java

<p>KGCL-Java is an implementation of the <a href="https://github.com/INCATools/kgcl">Knowledge Graph Change Language </a><a href="https://github.com/INCATools/kgcl">(KGCL)</a> specification for the Java language. It provides a Java library to manipulate KGCL changes and a <a href="http://robot.obolibrary.org/">ROBOT</a> pluggable command to parse and apply KGCL changes to a OWL ontology.</p> <p>Version 0.3.0 adds support for more change operations: <em>delete edge</em>, <em>move</em>, <em>deepen</em>, <em>shallow</em>, and <em>change relationship</em>.</p&gt

SSSOM-Java

<p>An implementation of the <a href="https://mapping-commons.github.io/sssom/spec/">SSSOM specification</a> for Java. It provides a Java library and a command-line tool to manipulate mapping sets, and a <a href="http://robot.obolibrary.org/">ROBOT</a> plugin with two commands to extract mappings from cross-references in a OWL ontology and to inject mappings-derived axioms into an ontology.</p> <p>Version 0.7.4 fixes the SSSOM/TSV writer to ensure that YAML and TSV strings are properly escaped when needed. It also adds <em>experimental</em> support for reading and writing non-standard metadata.</p&gt