Molecular Anatomy of the Architectural NEAT1 Noncoding
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Biogenesis of Nuclear Bodies
Downloaded from http://cshperspectives.cshlp.org/ on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Biogenesis of Nuclear Bodies Miroslav Dundr1 and Tom Misteli2 1Department of Cell Biology, Rosalind Franklin University of Medicine and Science, North Chicago, Ilinois 60064 2National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892 Correspondence: [email protected]; [email protected] The nucleus is unique amongst cellular organelles in that it contains a myriad of discrete suborganelles. These nuclear bodies are morphologically and molecularly distinct entities, and they host specific nuclear processes. Although the mode of biogenesis appears to differ widely between individual nuclear bodies, several common design principles are emerging, particularly, the ability of nuclear bodies to form de novo, a role of RNA as a struc- tural element and self-organization as a mode of formation. The controlled biogenesis of nuclear bodies is essential for faithful maintenance of nuclear architecture during the cell cycle and is an important part of cellular responses to intra- and extracellular events. he mammalian cell nucleus contains a mul- seems to act indirectly by regulating the local Ttitude of discrete suborganelles, referred to concentration of its components in the nucleo- as nuclear bodies or nuclear compartments plasm. (reviewed in Dundr and Misteli 2001; Spector In many ways, nuclear bodies are similar 2001; Lamond and Spector 2003; Handwerger to conventional cellular organelles in the cy- and Gall 2006; Zhao et al. 2009). These bodies toplasm. Like cytoplasmic organelles, they con- are an essential part of the nuclear landscape tain a specific set of resident proteins, which as they compartmentalize the nuclear space defines each structure molecularly. -
Nucleus Size and DNA Accessibility Are Linked to the Regulation Of
Grosch et al. BMC Biology (2020) 18:42 https://doi.org/10.1186/s12915-020-00770-y RESEARCH ARTICLE Open Access Nucleus size and DNA accessibility are linked to the regulation of paraspeckle formation in cellular differentiation Markus Grosch1, Sebastian Ittermann1, Ejona Rusha2, Tobias Greisle1, Chaido Ori1,3, Dong-Jiunn Jeffery Truong4, Adam C. O’Neill1, Anna Pertek2, Gil Gregor Westmeyer4 and Micha Drukker1,2* Abstract Background: Many long noncoding RNAs (lncRNAs) have been implicated in general and cell type-specific molecular regulation. Here, we asked what underlies the fundamental basis for the seemingly random appearance of nuclear lncRNA condensates in cells, and we sought compounds that can promote the disintegration of lncRNA condensates in vivo. Results: As a basis for comparing lncRNAs and cellular properties among different cell types, we screened lncRNAs in human pluripotent stem cells (hPSCs) that were differentiated to an atlas of cell lineages. We found that paraspeckles, which form by aggregation of the lncRNA NEAT1, are scaled by the size of the nucleus, and that small DNA-binding molecules promote the disintegration of paraspeckles and other lncRNA condensates. Furthermore, we found that paraspeckles regulate the differentiation of hPSCs. Conclusions: Positive correlation between the size of the nucleus and the number of paraspeckles exist in numerous types of human cells. The tethering and structure of paraspeckles, as well as other lncRNAs, to the genome can be disrupted by small molecules that intercalate in DNA. The structure-function relationship of lncRNAs that regulates stem cell differentiation is likely to be determined by the dynamics of nucleus size and binding site accessibility. -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Long Non-Coding RNA NEAT1 Promotes Proliferation, Migration
Int. J. Med. Sci. 2018, Vol. 15 1227 Ivyspring International Publisher International Journal of Medical Sciences 2018; 15(11): 1227-1234. doi: 10.7150/ijms.25662 Research Paper Long non-coding RNA NEAT1 promotes proliferation, migration and invasion of human osteosarcoma cells Pengcheng Li1, Rui Huang2, Tao Huang1, Shuo Cheng1, Yao Chen1, Zhihang Wang1 1. Department of Orthopedics, The First Affiliated Hospital of China Medical University. Shenyang 110001, Liaoning, P.R. China 2. Department of Clinical Medicine, Da Lian Medical University. Dalian 116000, Liaoning, P.R. China. Corresponding author: Tao Huang, Department of Orthopedics, The First Affiliated Hospital of China Medical University. Shenyang 110001, Liaoning, P.R. China. Email: [email protected] © Ivyspring International Publisher. This is an open access article distributed under the terms of the Creative Commons Attribution (CC BY-NC) license (https://creativecommons.org/licenses/by-nc/4.0/). See http://ivyspring.com/terms for full terms and conditions. Received: 2018.02.22; Accepted: 2018.05.27; Published: 2018.07.30 Abstract Aim: Long non-coding RNAs (LncRNAs) have been identified to play a crucial role in tumorigenesis and the progression of many types of tumors. However, the clinical significance and biological function of lncRNA nuclear-enriched abundant transcript 1(NEAT1) in human osteosarcoma remains unknown. Here, we investigated the role of NEAT1 in human osteosarcoma cell lines and clinical tumor samples. Methods: In this study, expression of NEAT1 was analyzed in 19 osteosarcoma tissues and paired adjacent non-tumor tissues by using quantitative real-time PCR. Additionally, knockdown of NEAT1 expression using Lentivirus-mediated siRNA was performed in order to explore the biological function of NEAT1 on osteosarcoma cell proliferation and metastasis through MTT, colony formation assay and transwell assay. -
The Sub-Nuclear Localization of RNA-Binding Proteins in KSHV-Infected Cells
cells Article The Sub-Nuclear Localization of RNA-Binding Proteins in KSHV-Infected Cells Ella Alkalay, Chen Gam Ze Letova Refael, Irit Shoval, Noa Kinor, Ronit Sarid and Yaron Shav-Tal * The Mina & Everard Goodman Faculty of Life Sciences and The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel; [email protected] (E.A.); [email protected] (C.G.Z.L.R.); [email protected] (I.S.); [email protected] (N.K.); [email protected] (R.S.) * Correspondence: [email protected] Received: 14 August 2020; Accepted: 21 August 2020; Published: 25 August 2020 Abstract: RNA-binding proteins, particularly splicing factors, localize to sub-nuclear domains termed nuclear speckles. During certain viral infections, as the nucleus fills up with replicating virus compartments, host cell chromatin distribution changes, ending up condensed at the nuclear periphery. In this study we wished to determine the fate of nucleoplasmic RNA-binding proteins and nuclear speckles during the lytic cycle of the Kaposi’s sarcoma associated herpesvirus (KSHV). We found that nuclear speckles became fewer and dramatically larger, localizing at the nuclear periphery, adjacent to the marginalized chromatin. Enlarged nuclear speckles contained splicing factors, whereas other proteins were nucleoplasmically dispersed. Polyadenylated RNA, typically found in nuclear speckles under regular conditions, was also found in foci separated from nuclear speckles in infected cells. Poly(A) foci did not contain lncRNAs known to colocalize with nuclear speckles but contained the poly(A)-binding protein PABPN1. Examination of the localization of spliced viral RNAs revealed that some spliced transcripts could be detected within the nuclear speckles. -
Lncrna NEAT1 in Paraspeckles: a Structural Scaffold for Cellular DNA Damage Response Systems?
non-coding RNA Review LncRNA NEAT1 in Paraspeckles: A Structural Scaffold for Cellular DNA Damage Response Systems? Elisa Taiana 1,2,* , Domenica Ronchetti 1,2 , Katia Todoerti 2, Lucia Nobili 1 , Pierfrancesco Tassone 3, Nicola Amodio 3 and Antonino Neri 1,2,* 1 Department of Oncology and Hemato-oncology, University of Milan, 20122 Milan, Italy; [email protected] (D.R.); [email protected] (L.N.) 2 Hematology, Fondazione Cà Granda IRCCS Policlinico, 20122 Milan, Italy; [email protected] 3 Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy; [email protected] (P.T.); [email protected] (N.A.) * Correspondence: [email protected] (E.T.); [email protected] (A.N.); Tel.: +39-02-5032-0420 (E.T. & A.N.) Received: 5 June 2020; Accepted: 28 June 2020; Published: 1 July 2020 Abstract: Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) reported to be frequently deregulated in various types of cancers and neurodegenerative processes. NEAT1 is an indispensable structural component of paraspeckles (PSs), which are dynamic and membraneless nuclear bodies that affect different cellular functions, including stress response. Furthermore, increasing evidence supports the crucial role of NEAT1 and essential structural proteins of PSs (PSPs) in the regulation of the DNA damage repair (DDR) system. This review aims to provide an overview of the current knowledge on the involvement of NEAT1 and PSPs in DDR, which might strengthen the rationale underlying future NEAT1-based therapeutic options in tumor and neurodegenerative diseases. Keywords: lncRNA; NEAT1; paraspeckle; DNA damage repair; cancer; neurodegenerative disease 1. -