Nucleus (Austin, Tex.)最新文献

{"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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}

{"title":"Modeling the 3D genome of plants.","authors":"Marco Di Stefano, Hans-Wilhelm Nützmann","doi":"10.1080/19491034.2021.1927503","DOIUrl":"10.1080/19491034.2021.1927503","url":null,"abstract":"<p><p>Chromosomes are the carriers of inheritable traits and define cell function and development. This is not only based on the linear DNA sequence of chromosomes but also on the additional molecular information they are associated with, including the transcription machinery, histone modifications, and their three-dimensional folding. The synergistic application of experimental approaches and computer simulations has helped to unveil how these organizational layers of the genome interplay in various organisms. However, such multidisciplinary approaches are still rarely explored in the plant kingdom. Here, we provide an overview of our current knowledge on plant 3D genome organization and review recent efforts to integrate cutting-edge experiments from microscopy and next-generation sequencing approaches with theoretical models. Building on these recent approaches, we propose possible avenues to extend the application of theoretical modeling in the characterization of the 3D genome organization in plants.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8168717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39036374","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":"HP1β carries an acidic linker domain and requires H3K9me3 for phase separation.","authors":"Weihua Qin,&nbsp;Andreas Stengl,&nbsp;Enes Ugur,&nbsp;Susanne Leidescher,&nbsp;Joel Ryan,&nbsp;M Cristina Cardoso,&nbsp;Heinrich Leonhardt","doi":"10.1080/19491034.2021.1889858","DOIUrl":"https://doi.org/10.1080/19491034.2021.1889858","url":null,"abstract":"<p><p>Liquid-liquid phase separation (LLPS) mediated formation of membraneless organelles has been proposed to coordinate biological processes in space and time. Previously, the formation of phase-separated droplets was described as a unique property of HP1α. Here, we demonstrate that the positive net charge of the intrinsically disordered hinge region (IDR-H) of HP1 proteins is critical for phase separation and that the exchange of four acidic amino acids is sufficient to confer LLPS properties to HP1β. Surprisingly, the addition of mono-nucleosomes promoted H3K9me3-dependent LLPS of HP1β which could be specifically disrupted with methylated but not acetylated H3K9 peptides. HP1β mutants defective in H3K9me3 binding were less efficient in phase separation<i>in vitro </i>and failed to accumulate at heterochromatin <i>in vivo</i>. We propose that multivalent interactions of HP1β with H3K9me3-modified nucleosomes via its chromodomain and dimerization via its chromoshadow domain enable phase separation and contribute to the formation of heterochromatin compartments <i>in vivo</i>.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2021.1889858","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25427755","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":"<i>In vitro</i> assembly of nuclear envelope in tobacco cultured cells.","authors":"Kentaro Tamura, Haruko Ueda, Ikuko Hara-Nishimura","doi":"10.1080/19491034.2021.1930681","DOIUrl":"10.1080/19491034.2021.1930681","url":null,"abstract":"<p><p>The coordinated regulation of the nucelar envelope (NE) reassembly during cell division is an essential event. However, there is little information on the molecular components involved in NE assembly in plant cells. Here we developed an <i>in vitro</i> assay of NE assembly using tobacco BY-2 cultured cells. To start the NE assembly reaction, the demembranated nuclei and the S12 fraction (cytosol and microsomes) were mixed in the presence of GTP and ATP nucleotides. Time-course analysis indicated that tubule structures were extended from the microsomal vesicles that accumulated on the demembranated nuclei, and finally sealed the NE. Immunofluorescence confirmed that the assembled membrane contains a component of nuclear pore complex. The efficiency of the NE assembly is significantly inhibited by GTPγS that suppresses membrane fusion. This <i>in-vitro assay</i> system may elucidate the role of specific proteins and provide important insights into the molecular machinery of NE assembly in plant cells.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2021.1930681","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39014852","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":"Nuclear envelope mechanobiology: linking the nuclear structure and function.","authors":"Matthew Goelzer, Julianna Goelzer, Matthew L Ferguson, Corey P Neu, Gunes Uzer","doi":"10.1080/19491034.2021.1962610","DOIUrl":"10.1080/19491034.2021.1962610","url":null,"abstract":"<p><p>The nucleus, central to cellular activity, relies on both direct mechanical input as well as its molecular transducers to sense external stimuli and respond by regulating intra-nuclear chromatin organization that determines cell function and fate. In mesenchymal stem cells of musculoskeletal tissues, changes in nuclear structures are emerging as a key modulator of their differentiation and proliferation programs. In this review we will first introduce the structural elements of the nucleoskeleton and discuss the current literature on how nuclear structure and signaling are altered in relation to environmental and tissue level mechanical cues. We will focus on state-of-the-art techniques to apply mechanical force and methods to measure nuclear mechanics in conjunction with DNA, RNA, and protein visualization in living cells. Ultimately, combining real-time nuclear deformations and chromatin dynamics can be a powerful tool to study mechanisms of how forces affect the dynamics of genome function.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8432354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10732493","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":"4DNvestigator: time series genomic data analysis toolbox.","authors":"Stephen Lindsly,&nbsp;Can Chen,&nbsp;Sijia Liu,&nbsp;Scott Ronquist,&nbsp;Samuel Dilworth,&nbsp;Michael Perlman,&nbsp;Indika Rajapakse","doi":"10.1080/19491034.2021.1910437","DOIUrl":"https://doi.org/10.1080/19491034.2021.1910437","url":null,"abstract":"<p><p>Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the '4DNvestigator', a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2021.1910437","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10641278","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":"Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0.","authors":"Tristan Dubos,&nbsp;Axel Poulet,&nbsp;Céline Gonthier-Gueret,&nbsp;Guillaume Mougeot,&nbsp;Emmanuel Vanrobays,&nbsp;Yanru Li,&nbsp;Sylvie Tutois,&nbsp;Emilie Pery,&nbsp;Frédéric Chausse,&nbsp;Aline V Probst,&nbsp;Christophe Tatout,&nbsp;Sophie Desset","doi":"10.1080/19491034.2020.1845012","DOIUrl":"https://doi.org/10.1080/19491034.2020.1845012","url":null,"abstract":"<p><p>NucleusJ 1.0, an ImageJ plugin, is a useful tool to analyze nuclear morphology and chromatin organization in plant and animal cells. NucleusJ 2.0 is a new release of NucleusJ, in which image processing is achieved more quickly using a command-lineuser interface. Starting with large collection of 3D nuclei, segmentation can be performed by the previously developed Otsu-modified method or by a new 3D gift-wrapping method, taking better account of nuclear indentations and unstained nucleoli. These two complementary methods are compared for their accuracy by using three types of datasets available to the community at <u>https://www.brookes.ac.uk/indepth/images/</u> . Finally, NucleusJ 2.0 was evaluated using original plant genetic material by assessing its efficiency on nuclei stained with DNA dyes or after 3D-DNA Fluorescence <i>in situ</i> hybridization. With these improvements, NucleusJ 2.0 permits the generation of large user-curated datasets that will be useful for software benchmarking or to train convolution neural networks.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2020.1845012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38570296","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}