Nucleus (Austin, Tex.)最新文献

{"title":"MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid-liquid phase separation and restricted by DNA methylation.","authors":"Hui Zhang,&nbsp;Hector Romero,&nbsp;Annika Schmidt,&nbsp;Katalina Gagova,&nbsp;Weihua Qin,&nbsp;Bianca Bertulat,&nbsp;Anne Lehmkuhl,&nbsp;Manuela Milden,&nbsp;Malte Eck,&nbsp;Tobias Meckel,&nbsp;Heinrich Leonhardt,&nbsp;M Cristina Cardoso","doi":"10.1080/19491034.2021.2024691","DOIUrl":"https://doi.org/10.1080/19491034.2021.2024691","url":null,"abstract":"<p><p>Heterochromatin is the highly compacted form of chromatin with various condensation levels hallmarked by high DNA methylation. MeCP2 is mostly known as a DNA methylation reader but has also been reported as a heterochromatin organizer. Here, we combine liquid-liquid phase separation (LLPS) analysis and single-molecule tracking with quantification of local MeCP2 concentrations <i>in vitro</i> and <i>in vivo</i> to explore the mechanism of MeCP2-driven heterochromatin organization and dynamics. We show that MeCP2 alone forms liquid-like spherical droplets via multivalent electrostatic interactions and with isotropic mobility. Crowded environments and DNA promote MeCP2 LLPS and slow down MeCP2 mobility. DNA methylation, however, restricts the growth of heterochromatin compartments correlating with immobilization of MeCP2. Furthermore, MeCP2 self-interaction is required for LLPS and is disrupted by Rett syndrome mutations. In summary, we are able to model the heterochromatin compartmentalization as well as MeCP2 concentration and heterogeneous motion in the minimal <i>in vitro</i> system.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/18/0d/KNCL_13_2024691.PMC8855868.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39916427","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":"Spelling out the roles of individual nucleoporins in nuclear export of mRNA.","authors":"Mark Tingey, Yichen Li, Wenlan Yu, Albert Young, Weidong Yang","doi":"10.1080/19491034.2022.2076965","DOIUrl":"10.1080/19491034.2022.2076965","url":null,"abstract":"<p><p>The Nuclear Pore Complex (NPC) represents a critical passage through the nuclear envelope for nuclear import and export that impacts nearly every cellular process at some level. Recent technological advances in the form of Auxin Inducible Degron (AID) strategies and Single-Point Edge-Excitation sub-Diffraction (SPEED) microscopy have enabled us to provide new insight into the distinct functions and roles of nuclear basket nucleoporins (Nups) upon nuclear docking and export for mRNAs. In this paper, we provide a review of our recent findings as well as an assessment of new techniques, updated models, and future perspectives in the studies of mRNA's nuclear export.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9132428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9415494","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":"A-type lamins involvement in transport and implications in cancer?","authors":"Nicholas R Scott,&nbsp;Sapun H Parekh","doi":"10.1080/19491034.2022.2118418","DOIUrl":"https://doi.org/10.1080/19491034.2022.2118418","url":null,"abstract":"<p><p>Nuclear lamins and transport are intrinsically linked, but their relationship is yet to be fully unraveled. A multitude of complex, coupled interactions between lamins and nucleoporins (Nups), which mediate active transport into and out of the nucleus, combined with well documented dysregulation of lamins in many cancers, suggests that lamins and nuclear transport may play a pivotal role in carcinogenesis and the preservation of cancer. Changes of function related to lamin/Nup activity can principally lead to DNA damage, further increasing the genetic diversity within a tumor, which could lead to the reduction the effectiveness of antineoplastic treatments. This review discusses and synthesizes different connections of lamins to nuclear transport and offers a number of outlook questions, the answers to which could reveal a new perspective on the connection of lamins to molecular transport of cancer therapeutics, in addition to their established role in nuclear mechanics.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/64/d6/KNCL_13_2118418.PMC9481127.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40361709","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":"Autophagy regulates rRNA synthesis.","authors":"Yinfeng Xu,&nbsp;Wei Wan","doi":"10.1080/19491034.2022.2114661","DOIUrl":"https://doi.org/10.1080/19491034.2022.2114661","url":null,"abstract":"<p><p>Autophagy has emerged as a key regulator of cell metabolism. Recently, we have demonstrated that autophagy is involved in RNA metabolism by regulating ribosomal RNA (rRNA) synthesis. We found that autophagy-deficient cells display much higher 47S precursor rRNA level, which is caused by the accumulation of SQSTM1/p62 (sequestosome 1) but not other autophagy receptors. Mechanistically, SQSTM1 accumulation potentiates the activation of MTOR (mechanistic target of rapamycin kinase) complex 1 (MTORC1) signaling, which facilitates the assembly of RNA polymerase I pre-initiation complex at ribosomal DNA (rDNA) promoter regions and leads to the activation of rDNA transcription. Finally, we showed that SQSTM1 accumulation is responsible for the increase in protein synthesis, cell growth and cell proliferation in autophagy-deficient cells. Taken together, our findings reveal a regulatory role of autophagy and autophagy receptor SQSTM1 in rRNA synthesis and may provide novel mechanisms for the hyperactivated rDNA transcription in autophagy-related human diseases.<b>Abbreviations:</b> 5-FUrd: 5-fluorouridine; LAP: MAP1LC3/LC3-associated phagocytosis; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; PIC: pre-initiation complex; POLR1: RNA polymerase I; POLR1A: RNA polymerase I subunit A; rDNA: ribosomal DNA; RRN3: RRN3 homolog, RNA polymerase I transcription factor; rRNA: ribosomal RNA; SQSTM1/p62: sequestosome 1; TP53INP2: tumor protein p53 inducible nuclear protein 2; UBTF: upstream binding transcription factor.</p>","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9415535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9180216","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":"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":null,"pages":null},"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":"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":null,"pages":null},"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":"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":null,"pages":null},"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":"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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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}