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https://www.readbyqxmd.com/read/30084812/meta-analysis-of-gene-expression-profiles-of-peripheral-blood-cells-in-systemic-lupus-erythematosus
#1
Sang-Cheol Bae, Young Ho Lee
Our purpose was to identify differentially expressed (DE) genes and biological processes associated with gene expression changes in systemic lupus erythematosus (SLE). We performed a meta-analysis using the INMEX program (integrative meta-analysis of expression data) on publicly available microarray Genetic Expression Omnibus (GEO) datasets of peripheral blood mononuclear cells (PBMCs) of SLE patients and healthy controls. We performed Gene Ontology (GO) enrichment analysis by using hypergeometric tests. In total, five comparisons (2 B cells, 2 CD4 T cells, and 1 myeloid cell) from two GEO datasets containing 51 cases and 46 controls were included in the meta-analysis...
July 30, 2018: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/30080298/proliferation-cancer-and-aging-novel-functions-of-the-nucleolar-methyltransferase-fibrillarin
#2
REVIEW
Maria Y Shubina, Yana R Musinova, Eugene V Sheval
Fibrillarin is an essential nucleolar protein that catalyzes the 2'-O-methylation of ribosomal RNAs. Recently, experimental data have begun to accumulate that suggest that fibrillarin can influence various cellular processes, development of pathological processes, and even aging. The exact mechanism by which fibrillarin can influence these processes has not been found, but some experimental data indicate that up- or downregulation of fibrillarin can modify the ribosome structure and, thus, causе an alteration in relative efficiency with which various mRNAs are translated...
August 6, 2018: Cell Biology International
https://www.readbyqxmd.com/read/30064522/the-involvement-of-tau-in-nucleolar-transcription-and-the-stress-response
#3
Mahmoud B Maina, Laura J Bailey, Sherin Wagih, Luca Biasetti, Saskia J Pollack, James P Quinn, Julian R Thorpe, Aidan J Doherty, Louise C Serpell
Tau is known for its pathological role in neurodegenerative diseases, including Alzheimer's disease (AD) and other tauopathies. Tau is found in many subcellular compartments such as the cytosol and the nucleus. Although its normal role in microtubule binding is well established, its nuclear role is still unclear. Here, we reveal that tau localises to the nucleolus in undifferentiated and differentiated neuroblastoma cells (SHSY5Y), where it associates with TIP5, a key player in heterochromatin stability and ribosomal DNA (rDNA) transcriptional repression...
July 31, 2018: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/29943658/nucleolin-modulates-compartmentalization-and-dynamics-of-histone-2b-ecfp-in-the-nucleolus
#4
Ayantika Sen Gupta, Gaurav Joshi, Sumit Pawar, Kundan Sengupta
Eukaryotic cells have 2 to ​3 discrete nucleoli required for ribosome synthesis. Nucleoli are phase separated nuclear sub-organelles. Here we examined the role of nuclear Lamins and nucleolar factors in modulating the compartmentalization and dynamics of histone 2B (H2B-ECFP) in the nucleolus. Live imaging and Fluorescence Recovery After Photobleaching (FRAP) of labelled H2B, showed that the depletion of Lamin B1, Fibrillarin (FBL) or Nucleostemin (GNL3), enhances H2B-ECFP mobility in the nucleolus. Furthermore, Nucleolin knockdown significantly decreases H2B-ECFP compartmentalization in the nucleolus, while H2B-ECFP residence and mobility in the nucleolus was prolonged upon Nucleolin overexpression...
June 26, 2018: Nucleus
https://www.readbyqxmd.com/read/29806702/interaction-of-cacybp-sip-with-npm1-and-its-influence-on-npm1-localization-and-function-in-oxidative-stress
#5
Sara Rosińska, Anna Filipek
Calcyclin (S100A6) binding protein/Siah-1 interacting protein (CacyBP/SIP) is mainly a cytoplasmic protein; however, some literature data suggested its presence in the nucleus. In this work we examined more precisely the nuclear localization and function of CacyBP/SIP. By applying mass spectrometry, we have identified several nuclear proteins, among them is nucleophosmin (NPM1), that may interact with CacyBP/SIP. Subsequent assays revealed that CacyBP/SIP forms complexes with NPM1 in the cell and that the interaction between these two proteins is direct...
May 28, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29736196/identification-of-functional-domain-s-of-fibrillarin-interacted-with-p2-of-rice-stripe-virus
#6
Luping Zheng, Jie He, Zuomei Ding, Chenlong Zhang, Ruoxue Meng
p2 of Rice stripe virus may promote virus systemic infection by interacting with the full length of fibrillarin from Nicotiana benthamiana (NbFib2) in the nucleolus and cajal body (CB). NbFib2 contains three functional domains. We used yeast two-hybrid, colocalization, and bimolecular fluorescence complementation (BiFC) assays to study the interactions between p2 and the three domains of NbFib2, namely, the N-terminal fragment containing a glycine and arginine-rich (GAR) domain, the central RNA-binding domain, and the C-terminal fragment containing an α -helical domain...
2018: Canadian Journal of Infectious Diseases & Medical Microbiology
https://www.readbyqxmd.com/read/29712923/activity-dependent-lona-regulates-translation-by-coordinating-rrna-transcription-and-methylation
#7
Dingfeng Li, Juan Zhang, Ming Wang, Xiaohui Li, Huarui Gong, Huiping Tang, Lin Chen, Lili Wan, Qiang Liu
The ribosome is indispensable for precisely controlling the capacity of protein synthesis. However, how translational machinery is coordinated to meet the translational demands remains elusive. Here, we identify a nucleolar-specific lncRNA (LoNA), its 5' portion binds and sequesters nucleolin to suppress rRNA transcription, and its snoRNA like 3' end recruits and diminishes fibrillarin activity to reduce rRNA methylation. Activity-dependent decrease of LoNA leads to elevated rRNA and ribosome levels, an increased proportion of polysomes, mRNA polysome loading, and protein translation...
April 30, 2018: Nature Communications
https://www.readbyqxmd.com/read/29648937/endothelial-wound-repair-of-the-organ-cultured-porcine-corneas
#8
Ingrida Smeringaiova, Stanislava Reinstein Merjava, Zbynek Stranak, Pavel Studeny, Jan Bednar, Katerina Jirsova
PURPOSE: To assess whether injured porcine endothelium of small and large corneoscleral disc differ in its reparative/regenerative capacity under various conditions of organ culture storage. MATERIAL AND METHODS: 166 paired porcine corneas were trephined to obtain tissues with diameter 12.0 mm and 17.5 mm (with area neighboring endothelial periphery). In tested discs, central endothelium was mechanically wounded. Density of live endothelial cells (LECD), percentage of dead cells (%DC), coefficient of variation and cell hexagonality were assessed in central and paracentral endothelium following 5- or 9-day incubation in medium with 2% or 10% fetal bovine serum...
July 2018: Current Eye Research
https://www.readbyqxmd.com/read/29590189/versatile-approach-for-functional-analysis-of-human-proteins-and-efficient-stable-cell-line-generation-using-flp-mediated-recombination-system
#9
Roman J Szczesny, Katarzyna Kowalska, Kamila Klosowska-Kosicka, Aleksander Chlebowski, Ewelina P Owczarek, Zbigniew Warkocki, Tomasz M Kulinski, Dorota Adamska, Kamila Affek, Agata Jedroszkowiak, Anna V Kotrys, Rafal Tomecki, Pawel S Krawczyk, Lukasz S Borowski, Andrzej Dziembowski
Deciphering a function of a given protein requires investigating various biological aspects. Usually, the protein of interest is expressed with a fusion tag that aids or allows subsequent analyses. Additionally, downregulation or inactivation of the studied gene enables functional studies. Development of the CRISPR/Cas9 methodology opened many possibilities but in many cases it is restricted to non-essential genes. Recombinase-dependent gene integration methods, like the Flp-In system, are very good alternatives...
2018: PloS One
https://www.readbyqxmd.com/read/29477341/fibrillarin-is-essential-for-s-phase-progression-and-neuronal-differentiation-in-zebrafish-dorsal-midbrain-and-retina
#10
Stéphanie Bouffard, Emilie Dambroise, Alessandro Brombin, Sylvain Lempereur, Isabelle Hatin, Matthieu Simion, Raphaël Corre, Franck Bourrat, Jean-Stéphane Joly, Françoise Jamen
Fibrillarin (Fbl) is a highly conserved protein that plays an essential role in ribosome biogenesis and more particularly in the methylation of ribosomal RNAs and rDNA histones. In cellular models, FBL was shown to play an important role in tumorigenesis and stem cell differentiation. We used the zebrafish as an in vivo model to study Fbl function during embryonic development. We show here that the optic tectum and the eye are severely affected by Fbl depletion whereas ventral regions of the brain are less impacted...
May 1, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29284691/adenosine-to-inosine-editing-of-microrna-487b-alters-target-gene-selection-after-ischemia-and-promotes-neovascularization
#11
Reginald V C T van der Kwast, Eva van Ingen, Laura Parma, Hendrika A B Peters, Paul H A Quax, A Yaël Nossent
RATIONALE: Adenosine-to-inosine editing of microRNAs has the potential to cause a shift in target site selection. 2'-O-ribose-methylation of adenosine residues, however, has been shown to inhibit adenosine-to-inosine editing. OBJECTIVE: To investigate whether angiomiR miR487b is subject to adenosine-to-inosine editing or 2'-O-ribose-methylation during neovascularization. METHODS AND RESULTS: Complementary DNA was prepared from C57BL/6-mice subjected to hindlimb ischemia...
February 2, 2018: Circulation Research
https://www.readbyqxmd.com/read/29190286/nucleolar-sub-compartments-in-motion-during-rrna-synthesis-inhibition-contraction-of-nucleolar-condensed-chromatin-and-gathering-of-fibrillar-centers-are-concomitant
#12
Pavel Tchelidze, Aassif Benassarou, Hervé Kaplan, Marie-Françoise O'Donohue, Laurent Lucas, Christine Terryn, Levan Rusishvili, Giorgi Mosidze, Nathalie Lalun, Dominique Ploton
The nucleolus produces the large polycistronic transcript (47S precursor) containing the 18S, 5.8S and 28S rRNA sequences and hosts most of the nuclear steps of pre-rRNA processing. Among numerous components it contains condensed chromatin and active rRNA genes which adopt a more accessible conformation. For this reason, it is a paradigm of chromosome territory organization. Active rRNA genes are clustered within several fibrillar centers (FCs), in which they are maintained in an open configuration by Upstream Binding Factor (UBF) molecules...
2017: PloS One
https://www.readbyqxmd.com/read/29163603/novel-ribonuclease-activity-differs-between-fibrillarins-from-arabidopsis-thaliana
#13
Ulises Rodriguez-Corona, Alejandro Pereira-Santana, Margarita Sobol, Luis C Rodriguez-Zapata, Pavel Hozak, Enrique Castano
Fibrillarin is one of the most important nucleolar proteins that have been shown as essential for life. Fibrillarin localizes primarily at the periphery between fibrillar center and dense fibrillar component as well as in Cajal bodies. In most plants there are at least two different genes for fibrillarin. In Arabidopsis thaliana both genes show high level of expression in transcriptionally active cells. Here, we focus on two important differences between A. thaliana fibrillarins. First and most relevant is the enzymatic activity by AtFib2...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29158377/evidence-for-rrna-2-o-methylation-plasticity-control-of-intrinsic-translational-capabilities-of-human-ribosomes
#14
Jenny Erales, Virginie Marchand, Baptiste Panthu, Sandra Gillot, Stéphane Belin, Sandra E Ghayad, Maxime Garcia, Florian Laforêts, Virginie Marcel, Agnès Baudin-Baillieu, Pierre Bertin, Yohann Couté, Annie Adrait, Mélanie Meyer, Gabriel Therizols, Marat Yusupov, Olivier Namy, Théophile Ohlmann, Yuri Motorin, Frédéric Catez, Jean-Jacques Diaz
Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells...
December 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28994181/age-associated-dysregulation-of-protein-metabolism-in-the-mammalian-oocyte
#15
Francesca E Duncan, Susmita Jasti, Ariel Paulson, John M Kelsh, Barbara Fegley, Jennifer L Gerton
Reproductive aging is characterized by a marked decline in oocyte quality that contributes to infertility, miscarriages, and birth defects. This decline is multifactorial, and the underlying mechanisms are under active investigation. Here, we performed RNA-Seq on individual growing follicles from reproductively young and old mice to identify age-dependent functions in oocytes. This unbiased approach revealed genes involved in cellular processes known to change with age, including mitochondrial function and meiotic chromosome segregation, but also uncovered previously unappreciated categories of genes related to proteostasis and organelles required for protein metabolism...
December 2017: Aging Cell
https://www.readbyqxmd.com/read/28981686/the-nuclear-mitotic-apparatus-protein-numa-controls-rdna-transcription-and-mediates-the-nucleolar-stress-response-in-a-p53-independent-manner
#16
Swaathi Jayaraman, Shirisha Chittiboyina, Yunfeng Bai, Patricia C Abad, Pierre-Alexandre Vidi, Cynthia V Stauffacher, Sophie A Lelièvre
The nuclear mitotic apparatus protein, NuMA, is involved in major cellular events such as DNA damage response, apoptosis and p53-mediated growth-arrest, all of which are under the control of the nucleolus upon stress. Proteomic investigation has identified NuMA among hundreds of nucleolar proteins. Yet, the precise link between NuMA and nucleolar function remains undetermined. We confirm that NuMA is present in the nucleolus and reveal redistribution of NuMA upon actinomycin D or doxorubicin-induced nucleolar stress...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28904332/identification-of-sites-of-2-o-methylation-vulnerability-in-human-ribosomal-rnas-by-systematic-mapping
#17
Sunny Sharma, Virginie Marchand, Yuri Motorin, Denis L J Lafontaine
Ribosomal RNA modifications are important in optimizing ribosome function. Sugar 2'-O-methylation performed by fibrillarin-associated box C/D antisense guide snoRNAs impacts all steps of translation, playing a role in disease etiology (cancer). As it renders adjacent phosphodiester bonds resistant to alkaline treatment, 2'-O-methylation can be monitored qualitatively and quantitatively by applying next-generation sequencing to fragments of randomly cleaved RNA. We remapped all sites of 2'-O-methylation in human rRNAs in two isogenic diploid cell lines, one producing and one not producing the antitumor protein p53...
September 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28872759/hijacking-of-the-nucleolar-protein-fibrillarin-by-tgb1-is-required-for-cell-to-cell-movement-of-barley-stripe-mosaic-virus
#18
Zhenggang Li, Yongliang Zhang, Zhihao Jiang, Xuejiao Jin, Kun Zhang, Xianbing Wang, Chenggui Han, Jialin Yu, Dawei Li
Barley stripe mosaic virus (BSMV) Triple Gene Block1 (TGB1) is a multifunctional movement protein with RNA-binding, ATPase and helicase activities which mainly localizes to the plasmodesmata (PD) in infected cells. Here, we show that TGB1 localizes to the nucleus and the nucleolus, as well as the cytoplasm, and that TGB1 nuclear-cytoplasmic trafficking is required for BSMV cell-to-cell movement. Prediction analyses and laser scanning confocal microscopy (LSCM) experiments verified that TGB1 possesses a nucleolar localization signal (NoLS) (amino acids 95-104) and a nuclear localization signal (NLS) (amino acids 227-238)...
May 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28853436/small-nucleoli-are-a-cellular-hallmark-of-longevity
#19
Varnesh Tiku, Chirag Jain, Yotam Raz, Shuhei Nakamura, Bree Heestand, Wei Liu, Martin Späth, H Eka D Suchiman, Roman-Ulrich Müller, P Eline Slagboom, Linda Partridge, Adam Antebi
Animal lifespan is regulated by conserved metabolic signalling pathways and specific transcription factors, but whether these pathways affect common downstream mechanisms remains largely elusive. Here we show that NCL-1/TRIM2/Brat tumour suppressor extends lifespan and limits nucleolar size in the major C. elegans longevity pathways, as part of a convergent mechanism focused on the nucleolus. Long-lived animals representing distinct longevity pathways exhibit small nucleoli, and decreased expression of rRNA, ribosomal proteins, and the nucleolar protein fibrillarin, dependent on NCL-1...
August 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28814507/systematic-gene-tagging-using-crispr-cas9-in-human-stem-cells-to-illuminate-cell-organization
#20
Brock Roberts, Amanda Haupt, Andrew Tucker, Tanya Grancharova, Joy Arakaki, Margaret A Fuqua, Angelique Nelson, Caroline Hookway, Susan A Ludmann, Irina A Mueller, Ruian Yang, Rick Horwitz, Susanne M Rafelski, Ruwanthi N Gunawardane
We present a CRISPR/Cas9 genome-editing strategy to systematically tag endogenous proteins with fluorescent tags in human induced pluripotent stem cells (hiPSC). To date, we have generated multiple hiPSC lines with monoallelic green fluorescent protein tags labeling 10 proteins representing major cellular structures. The tagged proteins include alpha tubulin, beta actin, desmoplakin, fibrillarin, nuclear lamin B1, nonmuscle myosin heavy chain IIB, paxillin, Sec61 beta, tight junction protein ZO1, and Tom20...
October 15, 2017: Molecular Biology of the Cell
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