Nucleus (Austin, Tex.)最新文献_第8页

Modeling the 3D genome of plants. 植物三维基因组建模

Nucleus (Austin, Tex.) Pub Date : 2021-12-01 DOI: 10.1080/19491034.2021.1927503

Marco Di Stefano, Hans-Wilhelm Nützmann

引用次数: 0

HP1β carries an acidic linker domain and requires H3K9me3 for phase separation. HP1β携带酸性连接结构域，需要H3K9me3进行相分离。

Nucleus (Austin, Tex.) Pub Date : 2021-12-01 DOI: 10.1080/19491034.2021.1889858

Weihua Qin, Andreas Stengl, Enes Ugur, Susanne Leidescher, Joel Ryan, M Cristina Cardoso, Heinrich Leonhardt

{"title":"HP1β carries an acidic linker domain and requires H3K9me3 for phase separation.","authors":"Weihua Qin, Andreas Stengl, Enes Ugur, Susanne Leidescher, Joel Ryan, M Cristina Cardoso, Heinrich Leonhardt","doi":"10.1080/19491034.2021.1889858","DOIUrl":"https://doi.org/10.1080/19491034.2021.1889858","url":null,"abstract":"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 separationin vitro and failed to accumulate at heterochromatin in vivo. 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 in vivo.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":" ","pages":"44-57"},"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}

引用次数: 8

In vitro assembly of nuclear envelope in tobacco cultured cells. 烟草培养细胞核包膜的体外组装。

Nucleus (Austin, Tex.) Pub Date : 2021-12-01 DOI: 10.1080/19491034.2021.1930681

Kentaro Tamura, Haruko Ueda, Ikuko Hara-Nishimura

引用次数: 0

Nuclear envelope mechanobiology: linking the nuclear structure and function. 核包膜机械生物学：将核结构与功能联系起来。

Nucleus (Austin, Tex.) Pub Date : 2021-12-01 DOI: 10.1080/19491034.2021.1962610

Matthew Goelzer, Julianna Goelzer, Matthew L Ferguson, Corey P Neu, Gunes Uzer

引用次数: 0

4DNvestigator: time series genomic data analysis toolbox. 研究者:时间序列基因组数据分析工具箱。

Nucleus (Austin, Tex.) Pub Date : 2021-12-01 DOI: 10.1080/19491034.2021.1910437

Stephen Lindsly, Can Chen, Sijia Liu, Scott Ronquist, Samuel Dilworth, Michael Perlman, Indika Rajapakse

引用次数: 10

Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0. 利用nucleusj2.0对核组织进行自动三维生物成像分析。

Nucleus (Austin, Tex.) Pub Date : 2020-12-01 DOI: 10.1080/19491034.2020.1845012

Tristan Dubos, Axel Poulet, Céline Gonthier-Gueret, Guillaume Mougeot, Emmanuel Vanrobays, Yanru Li, Sylvie Tutois, Emilie Pery, Frédéric Chausse, Aline V Probst, Christophe Tatout, Sophie Desset

{"title":"Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2.0.","authors":"Tristan Dubos, Axel Poulet, Céline Gonthier-Gueret, Guillaume Mougeot, Emmanuel Vanrobays, Yanru Li, Sylvie Tutois, Emilie Pery, Frédéric Chausse, Aline V Probst, Christophe Tatout, Sophie Desset","doi":"10.1080/19491034.2020.1845012","DOIUrl":"https://doi.org/10.1080/19491034.2020.1845012","url":null,"abstract":"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 https://www.brookes.ac.uk/indepth/images/ . 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 in situ 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.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"11 1","pages":"315-329"},"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}

引用次数: 13

Are the processes of DNA replication and DNA repair reading a common structural chromatin unit? DNA复制和DNA修复是一个共同的染色质结构单元吗?

Nucleus (Austin, Tex.) Pub Date : 2020-12-01 DOI: 10.1080/19491034.2020.1744415

Stefania Mamberti, M Cristina Cardoso

{"title":"Are the processes of DNA replication and DNA repair reading a common structural chromatin unit?","authors":"Stefania Mamberti, M Cristina Cardoso","doi":"10.1080/19491034.2020.1744415","DOIUrl":"https://doi.org/10.1080/19491034.2020.1744415","url":null,"abstract":"Decades of investigation on genomic DNA have brought us deeper insights into its organization within the nucleus and its metabolic mechanisms. This was fueled by the parallel development of experimental techniques and has stimulated model building to simulate genome conformation in agreement with the experimental data. Here, we will discuss our recent discoveries on the chromatin units of DNA replication and DNA damage response. We will highlight their remarkable structural similarities and how both revealed themselves as clusters of nanofocal structures each on the hundred thousand base pair size range corresponding well with chromatin loop sizes. We propose that the function of these two global genomic processes is determined by the loop level organization of chromatin structure with structure dictating function.Abbreviations: 3D-SIM: 3D-structured illumination microscopy; 3C: chromosome conformation capture; DDR: DNA damage response; FISH: fluorescent in situ hybridization; Hi-C: high conformation capture; HiP-HoP: highly predictive heteromorphic polymer model; IOD: inter-origin distance; LAD: lamina associated domain; STED: stimulated emission depletion microscopy; STORM: stochastic optical reconstruction microscopy; SBS: strings and binders switch model; TAD: topologically associated domain.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"11 1","pages":"66-82"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2020.1744415","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37821767","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}

引用次数: 6

LINC-complex mediated positioning of the vegetative nucleus is involved in calcium and ROS signaling in Arabidopsis pollen tubes. 拟南芥花粉管中linc复合物介导的营养核定位参与钙和ROS信号传导。

Nucleus (Austin, Tex.) Pub Date : 2020-12-01 DOI: 10.1080/19491034.2020.1783783

Morgan Moser, Andrew Kirkpatrick, Norman Reid Groves, Iris Meier

{"title":"LINC-complex mediated positioning of the vegetative nucleus is involved in calcium and ROS signaling in Arabidopsis pollen tubes.","authors":"Morgan Moser, Andrew Kirkpatrick, Norman Reid Groves, Iris Meier","doi":"10.1080/19491034.2020.1783783","DOIUrl":"https://doi.org/10.1080/19491034.2020.1783783","url":null,"abstract":"Nuclear movement and positioning play a role in developmental processes throughout life. Nuclear movement and positioning are mediated primarily by linker of nucleoskeleton and cytoskeleton (LINC) complexes. LINC complexes are comprised of the inner nuclear membrane SUN proteins and the outer nuclear membrane (ONM) KASH proteins. In Arabidopsis pollen tubes, the vegetative nucleus (VN) maintains a fixed distance from the pollen tube tip during growth, and the VN precedes the sperm cells (SCs). In pollen tubes of wit12 and wifi, mutants deficient in the ONM component of a plant LINC complex, the SCs precede the VN during pollen tube growth and the fixed VN distance from the tip is lost. Subsequently, pollen tubes frequently fail to burst upon reception. In this study, we sought to determine if the pollen tube reception defect observed in wit12 and wifi is due to decreased sensitivity to reactive oxygen species (ROS). Here, we show that wit12 and wifi are hyposensitive to exogenous H2O2, and that this hyposensitivity is correlated with decreased proximity of the VN to the pollen tube tip. Additionally, we report the first instance of nuclear Ca2+ peaks in growing pollen tubes, which are disrupted in the wit12 mutant. In the wit12 mutant, nuclear Ca2+ peaks are reduced in response to exogenous ROS, but these peaks are not correlated with pollen tube burst. This study finds that VN proximity to the pollen tube tip is required for both response to exogenous ROS, as well as internal nuclear Ca2+ fluctuations.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"11 1","pages":"149-163"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2020.1783783","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38125161","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}

引用次数: 11

CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism. CTCF 作为凝聚素介导的环挤压的边界因子：多步骤机制的证据。

Nucleus (Austin, Tex.) Pub Date : 2020-12-01 DOI: 10.1080/19491034.2020.1782024

Anders S Hansen

引用次数: 45

Lamin microaggregates lead to altered mechanotransmission in progerin-expressing cells. 纤层蛋白微聚集体导致表达早衰蛋白的细胞机械传递的改变。

Nucleus (Austin, Tex.) Pub Date : 2020-12-01 DOI: 10.1080/19491034.2020.1802906

Brooke E Danielsson, Katie V Tieu, Kranthidhar Bathula, Travis J Armiger, Pragna S Vellala, Rebecca E Taylor, Kris Noel Dahl, Daniel E Conway

{"title":"Lamin microaggregates lead to altered mechanotransmission in progerin-expressing cells.","authors":"Brooke E Danielsson, Katie V Tieu, Kranthidhar Bathula, Travis J Armiger, Pragna S Vellala, Rebecca E Taylor, Kris Noel Dahl, Daniel E Conway","doi":"10.1080/19491034.2020.1802906","DOIUrl":"https://doi.org/10.1080/19491034.2020.1802906","url":null,"abstract":"The nuclear lamina is a meshwork of intermediate filament proteins, and lamin A is the primary mechanical protein. An altered splicing of lamin A, known as progerin, causes the disease Hutchinson-Gilford progeria syndrome. Progerin-expressing cells have altered nuclear shapes and stiffened nuclear lamina with microaggregates of progerin. Here, progerin microaggregate inclusions in the lamina are shown to lead to cellular and multicellular dysfunction. We show with Comsol simulations that stiffened inclusions causes redistribution of normally homogeneous forces, and this redistribution is dependent on the stiffness difference and relatively independent of inclusion size. We also show mechanotransmission changes associated with progerin expression in cells under confinement and cells under external forces. Endothelial cells expressing progerin do not align properly with patterning. Fibroblasts expressing progerin do not align properly to applied cyclic force. Combined, these studies show that altered nuclear lamina mechanics and microstructure impacts cytoskeletal force transmission through the cell.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"11 1","pages":"194-204"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/19491034.2020.1802906","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38290727","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}

引用次数: 3