Nucleus (Austin, Tex.)最新文献

{"title":"Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes.","authors":"Ricardo S Randall,&nbsp;Claire Jourdain,&nbsp;Anna Nowicka,&nbsp;Kateřina Kaduchová,&nbsp;Michaela Kubová,&nbsp;Mohammad A Ayoub,&nbsp;Veit Schubert,&nbsp;Christophe Tatout,&nbsp;Isabelle Colas,&nbsp;Kalyanikrishna,&nbsp;Sophie Desset,&nbsp;Sarah Mermet,&nbsp;Aurélia Boulaflous-Stevens,&nbsp;Ivona Kubalová,&nbsp;Terezie Mandáková,&nbsp;Stefan Heckmann,&nbsp;Martin A Lysak,&nbsp;Martina Panatta,&nbsp;Raffaella Santoro,&nbsp;Daniel Schubert,&nbsp;Ales Pecinka,&nbsp;Devin Routh,&nbsp;Célia Baroux","doi":"10.1080/19491034.2022.2144013","DOIUrl":"https://doi.org/10.1080/19491034.2022.2144013","url":null,"abstract":"<p><p>Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.<b>Abbreviations:</b> 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"13 1","pages":"277-299"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9754023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10469645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion.","authors":"Roman Barth, Haitham A Shaban","doi":"10.1080/19491034.2022.2088988","DOIUrl":"10.1080/19491034.2022.2088988","url":null,"abstract":"<p><p>Gene transcription by RNA polymerase II (RNAPol II) is a tightly regulated process in the genomic, temporal, and spatial context. Recently, we have shown that chromatin exhibits spatially coherently moving regions over the entire nucleus, which is enhanced by transcription. Yet, it remains unclear how the mobility of RNA Pol II molecules is affected by transcription regulation and whether this response depends on the coordinated chromatin movement. We applied our Dense Flow reConstruction and Correlation method to analyze nucleus-wide coherent movements of RNA Pol II in living human cancer cells. We observe a spatially coherent movement of RNA Pol II molecules over <math><mo>≈</mo></math>1 μm, which depends on transcriptional activity. Inducing transcription in quiescent cells decreased the coherent motion of RNA Pol II. We then quantify the spatial correlation length of RNA Pol II in the context of DNA motion. RNA Pol II and chromatin spatially coherent motions respond oppositely to transcriptional activities. Our study holds the potential of studying the chromatin environment in different nuclear processes.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":" ","pages":"194-202"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9225503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40058478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uip4p modulates nuclear pore complex function in <i>Saccharomyces cerevisiae</i>.","authors":"Pallavi Deolal,&nbsp;Imlitoshi Jamir,&nbsp;Krishnaveni Mishra","doi":"10.1080/19491034.2022.2034286","DOIUrl":"https://doi.org/10.1080/19491034.2022.2034286","url":null,"abstract":"<p><p>A double membrane bilayer perforated by nuclear pore complexes (NPCs) governs the shape of the nucleus, the prominent distinguishing organelle of a eukaryotic cell. Despite the absence of lamins in yeasts, the nuclear morphology is stably maintained and shape changes occur in a regulated fashion. In a quest to identify factors that contribute to regulation of nuclear shape and function in <i>Saccharomyces cerevisiae</i>, we used a fluorescence imaging based approach. Here we report the identification of a novel protein, Uip4p, that is required for regulation of nuclear morphology. Loss of Uip4 compromises NPC function and loss of nuclear envelope (NE) integrity. Our localization studies show that Uip4 localizes to the NE and endoplasmic reticulum (ER) network. Furthermore, we demonstrate that the localization and expression of Uip4 is regulated during growth, which is crucial for NPC distribution.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":" ","pages":"79-93"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855845/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39928735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate.","authors":"Charlotte R Pfeifer,&nbsp;Michael P Tobin,&nbsp;Sangkyun Cho,&nbsp;Manasvita Vashisth,&nbsp;Lawrence J Dooling,&nbsp;Lizeth Lopez Vazquez,&nbsp;Emma G Ricci-De Lucca,&nbsp;Keiann T Simon,&nbsp;Dennis E Discher","doi":"10.1080/19491034.2022.2045726","DOIUrl":"https://doi.org/10.1080/19491034.2022.2045726","url":null,"abstract":"<p><p>Nuclear rupture has long been associated with deficits or defects in lamins, with recent results also indicating a role for actomyosin stress, but key physical determinants of rupture remain unclear. Here, lamin-B filaments stably interact with the nuclear membrane at sites of low Gaussian curvature yet dilute at high curvature to favor rupture, whereas lamin-A depletion requires high strain-rates. Live-cell imaging of lamin-B1 gene-edited cancer cells is complemented by fixed-cell imaging of rupture in: iPS-derived progeria patients cells, cells within beating chick embryo hearts, and cancer cells with multi-site rupture after migration through small pores. Data fit a model of stiff filaments that detach from a curved surface.Rupture is modestly suppressed by inhibiting myosin-II and by hypotonic stress, which slow the strain-rates. Lamin-A dilution and rupture probability indeed increase above a threshold rate of nuclear pulling. Curvature-sensing mechanisms of proteins at plasma membranes, including Piezo1, might thus apply at nuclear membranes.<b>Summary statement:</b> High nuclear curvature drives lamina dilution and nuclear envelope rupture even when myosin stress is inhibited. Stiff filaments generally dilute from sites of high Gaussian curvature, providing mathematical fits of experiments.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"13 1","pages":"129-143"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8928808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10740729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pericentromeric repetitive ncRNA regulates chromatin interaction and inflammatory gene expression.","authors":"Kenichi Miyata,&nbsp;Akiko Takahashi","doi":"10.1080/19491034.2022.2034269","DOIUrl":"https://doi.org/10.1080/19491034.2022.2034269","url":null,"abstract":"<p><p>Cellular senescence provokes a dramatic alteration of chromatin organization and gene expression profile of proinflammatory factors, thereby contributing to various age-related pathologies via the senescence-associated secretory phenotype (SASP). Chromatin organization and global gene expression are maintained through the CCCTC-binding factor (CTCF). However, the molecular mechanism underlying CTCF regulation and its association with SASP gene expression remains to be fully elucidated. A recent study by our team showed that noncoding RNA (ncRNA) derived from normally silenced pericentromeric repetitive sequences directly impair the DNA binding of CTCF. This CTCF disturbance increases the accessibility of chromatin at the loci of SASP genes and caused the transcription of inflammatory factors. This mechanism may promote malignant transformation.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":" ","pages":"74-78"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8855862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39632604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Filament assembly of the <i>C. elegans</i> lamin in the absence of helix 1A.","authors":"Rebecca de Leeuw,&nbsp;Rafael Kronenberg-Tenga,&nbsp;Matthias Eibauer,&nbsp;Ohad Medalia","doi":"10.1080/19491034.2022.2032917","DOIUrl":"https://doi.org/10.1080/19491034.2022.2032917","url":null,"abstract":"<p><p>Lamins are the major constituent of the nuclear lamina, a protein meshwork underlying the inner nuclear membrane. Nuclear lamins are type V intermediate filaments that assemble into ~3.5 nm thick filaments. To date, only the conditions for the <i>in vitro</i> assembly of <i>Caenorhabditis elegans</i> lamin (<i>Ce</i>-lamin) are known. Here, we investigated the assembly of <i>Ce</i>-lamin filaments by cryo-electron microscopy and tomography. We show that <i>Ce</i>-lamin is composed of ~3.5 nm protofilaments that further interact <i>in vitro</i> and are often seen as 6-8 nm thick filaments. We show that the assembly of lamin filaments is undisturbed by the removal of flexible domains, <i>that is,</i> the intrinsically unstructured head and tail domains. In contrast, much of the coiled-coil domains are scaffold elements that are essential for filament assembly. Moreover, our results suggest that <i>Ce</i>-lamin helix 1A has a minor scaffolding role but is important to the lateral assembly regulation of lamin protofilaments.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":" ","pages":"49-57"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8824219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39773087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution and diversification of the nuclear envelope.","authors":"Norma E Padilla-Mejia, Alexandr A Makarov, Lael D Barlow, Erin R Butterfield, Mark C Field","doi":"10.1080/19491034.2021.1874135","DOIUrl":"10.1080/19491034.2021.1874135","url":null,"abstract":"<p><p>Eukaryotic cells arose ~1.5 billion years ago, with the endomembrane system a central feature, facilitating evolution of intracellular compartments. Endomembranes include the nuclear envelope (NE) dividing the cytoplasm and nucleoplasm. The NE possesses universal features: a double lipid bilayer membrane, nuclear pore complexes (NPCs), and continuity with the endoplasmic reticulum, indicating common evolutionary origin. However, levels of specialization between lineages remains unclear, despite distinct mechanisms underpinning various nuclear activities. Several distinct modes of molecular evolution facilitate organellar diversification and  to understand which apply to the NE, we exploited proteomic datasets of purified nuclear envelopes from model systems for comparative analysis. We find enrichment of core nuclear functions amongst the widely conserved proteins to be less numerous than lineage-specific cohorts, but enriched in core nuclear functions. This, together with consideration of additional evidence, suggests that, despite a common origin, the NE has evolved as a highly diverse organelle with significant lineage-specific functionality.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":" ","pages":"21-41"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38811891","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial for the SEB 2020 special issue 'dynamic organisation of the nucleus across kingdoms'.","authors":"David E Evans","doi":"10.1080/19491034.2021.1883294","DOIUrl":"https://doi.org/10.1080/19491034.2021.1883294","url":null,"abstract":"This special issue is a collection of papers submitted by authors invited to participate in the 2020 Society for Experimental Biology meeting on the theme of 'Dynamic Organisation of the Nucleus Across Kingdoms', co-organized by Roland Foisner, Philippe Colas, David Evans and Katja Graumann. The conference presentations were postponed to 2021 (https://www.sebiology. org/events/event/seb-antwerp-2021) due to the impact of Covid-19, but these collected papers written in the summer and autumn of 2020 present the cross-kingdom insights and novel findings that were central to the aim of the meeting. The meeting is the 3rd in a series [1, 2] intended to highlight the immense value of sharing knowledge of the nucleus across kingdoms. Here we present a combination of review and original results and methods providing new insights into the field in a landmark year. Understanding the origins of the structural components of the nucleus underpins many of our efforts to advance understanding of mechanisms and function. This collection of papers provides significant insights – both across kingdoms [3] and in detailed reviews of the current state of knowledge in higher plants [4, 5]. One of the fascinations of studying the dynamic structure of the nucleus is the way in which a range of conserved functions are carried out by such a diversity of lineage-specific components. While a small number of highly conserved proteins point back to their presence in the Last Eukaryotic Common Ancestor, many show a surprising diversification and even functionally conserved proteins show a wide range of structural characteristics. Indeed, from this collection of papers, the reader can only wonder whether the statement of PadillaMeija et al. [3] that ‘findings suggest a rather surprising level of divergence associated with a structure that, in a very real sense, defines the eukaryotic cell’ is, in fact, an understatement. While recognizing the limitations imposed by the challenges of defining the nuclear proteome, Padilla-Meija and coworkers [3] provide detailed comparative insights into its evolution using carefully selected data from protozoans to mammals. Through a comparative analysis of previously described datasets from model systems and by expansion of this data, for instance, by searching using queries from Trypanosoma brucei, they provide a valuable coverage of nuclear constituents, structure and function, providing insights and a data set of great value for further exploration. Nuclear Envelope Associated (NEA) proteins provide particular challenges. Some are also found in other cellular locations, others are synthesized at the NE; others are multifunctional, with only a small part of their activity at the NE and many have only been characterized in one model organism while their functions in others are uncertain. There is much to be done! Two other papers in the collection expand the overview of Padilla-Meija to consider advances in knowledge of the plant nuclear prot","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":" ","pages":"42-43"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2021.1883294","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25333017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physical constraints in polymer modeling of chromatin associations with the nuclear periphery at kilobase scale.","authors":"Annaël Brunet,&nbsp;Nicolas Destainville,&nbsp;Philippe Collas","doi":"10.1080/19491034.2020.1868105","DOIUrl":"https://doi.org/10.1080/19491034.2020.1868105","url":null,"abstract":"<p><p>Interactions of chromatin with the nuclear lamina imposes a radial genome distribution important for nuclear functions. How physical properties of chromatin affect these interactions is unclear. We used polymer simulations to model how physical parameters of chromatin affect its interaction with the lamina. Impact of polymer stiffness is greater than stretching on its configurations at the lamina; these are manifested as trains describing extended interactions, and loops describing desorbed regions . Conferring an attraction potential leads to persistent interaction and adsorption-desorption regimes manifested by fluctuations between trains and loops. These are modulated by polymer stiffness and stretching, with a dominant impact of stiffness on resulting structural configurations. We infer that flexible euchromatin is more prone to stochastic interactions with lamins than rigid heterochromatin characterizing constitutive LADs. Our models provide insights on the physical properties of chromatin as a polymer which affect the dynamics and patterns of interactions with the nuclear lamina.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":" ","pages":"6-20"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2020.1868105","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38811655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stochastic gene expression and chromosome interactions in protecting the human active X from silencing by <i>XIST</i>.","authors":"Barbara R Migeon","doi":"10.1080/19491034.2020.1850981","DOIUrl":"https://doi.org/10.1080/19491034.2020.1850981","url":null,"abstract":"<p><p>Mammals use X chromosome inactivation to compensate for the sex difference in numbers of X chromosomes. A relatively unexplored question is how the active X is protected from inactivation by its own XIST gene, the long non-coding RNA, which initiates silence of the inactive X.  Previous studies of autosomal duplications show that human chromosome 19 plays a critical role in protecting the active X. I proposed that it genetically interacts with the X chromosome to repress XIST function on the future active X.  Here, I show that the type of  chromosome 19 duplication influences the outcome of the interaction: the presence of three chromosome 19s is tolerated whereas duplications affecting only one chromosome 19 are not. The different outcomes have mechanistic implications for how chromosome 19 interacts with the future active X, pointing to a role for stochastic gene expression and possibly physical interaction.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":" ","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2020.1850981","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38619639","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}