RESUMO
MOTIVATION: Deciphering nucleosome-nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. RESULTS: We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools. AVAILABILITYAND IMPLEMENTATION: https://github.com/Karimi-Lab/inucs/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Assuntos
Nucleossomos , SoftwareRESUMO
The histone H3 variant CENP-A marks centromeres epigenetically and is essential for mitotic fidelity. Previous crystallographic studies of the CENP-A nucleosome core particle (NCP) reconstituted with a human α-satellite DNA derivative revealed both DNA ends to be highly flexible, a feature important for CENP-A mitotic functions. However, recent cryo-EM studies of CENP-A NCP complexes comprising primarily Widom 601 DNA reported well-ordered DNA ends. Here, we report the cryo-EM structure of the CENP-A 601 NCP determined by Volta phase-plate imaging. The data reveal that one ('left') 601 DNA end is well ordered whereas the other ('right') end is flexible and partly detached from the histone core, suggesting sequence-dependent dynamics of the DNA termini. Indeed, a molecular dynamics simulation of the CENP-A 601 NCP confirmed the distinct dynamics of the two DNA extremities. Reprocessing the image data using two-fold symmetry yielded a cryo-EM map in which both DNA ends appeared well ordered, indicating that such an artefact may inadvertently arise if NCP asymmetry is lost during image processing. These findings enhance our understanding of the dynamic features that discriminate CENP-A from H3 nucleosomes by revealing that DNA end flexibility can be fine-tuned in a sequence-dependent manner.
Assuntos
Proteína Centromérica A/química , DNA/química , Nucleossomos/química , Microscopia Crioeletrônica , Humanos , Simulação de Dinâmica Molecular , Nucleossomos/ultraestruturaRESUMO
Chromatin remodelers are complexes able to both alter histone-DNA interactions and to mobilize nucleosomes. The mechanism of their action and the conformation of remodeled nucleosomes remain a matter of debates. In this work we compared the type and structure of the products of nucleosome remodeling by SWI/SNF and ACF complexes using high-resolution microscopy combined with novel biochemical approaches. We find that SWI/SNF generates a multitude of nucleosome-like metastable particles termed "remosomes". Restriction enzyme accessibility assay, DNase I footprinting and AFM experiments reveal perturbed histone-DNA interactions within these particles. Electron cryo-microscopy shows that remosomes adopt a variety of different structures with variable irregular DNA path, similar to those described upon RSC remodeling. Remosome DNA accessibility to restriction enzymes is also markedly increased. We suggest that the generation of remosomes is a common feature of the SWI/SNF family remodelers. In contrast, the ACF remodeler, belonging to ISWI family, only produces repositioned nucleosomes and no evidence for particles associated with extra DNA, or perturbed DNA paths was found. The remosome generation by the SWI/SNF type of remodelers may represent a novel mechanism involved in processes where nucleosomal DNA accessibility is required, such as DNA repair or transcription regulation.
Assuntos
Montagem e Desmontagem da Cromatina/fisiologia , Proteínas Fúngicas/fisiologia , Complexos Multiproteicos/fisiologia , Nucleossomos/fisiologia , Saccharomyces cerevisiae/metabolismo , Trifosfato de Adenosina/metabolismo , Trifosfato de Adenosina/farmacologia , Animais , Sistema Livre de Células , Montagem e Desmontagem da Cromatina/genética , Proteínas Cromossômicas não Histona/fisiologia , Pegada de DNA , DNA Bacteriano/metabolismo , Desoxirribonucleases de Sítio Específico do Tipo II , Histonas/genética , Histonas/metabolismo , Microscopia de Força Atômica , Nucleossomos/ultraestrutura , Plasmídeos/química , Proteínas de Ligação a RNA/fisiologia , Proteínas Recombinantes/metabolismo , Saccharomyces cerevisiae/ultraestrutura , Xenopus laevis/genéticaRESUMO
OBJECTIVE: The primary objective was to report this rare case and discuss the probable mechanism of thyroid storm following anterior cervical spine surgery for Kochs cervical spine.
RESUMO
The primary objective was to report this rare case and discuss the probable mechanism of thyroid storm following anterior cervical spine surgery for Kochs cervical spine.
