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      The rDNA Loci—Intersections of Replication, Transcription, and Repair Pathways

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          Abstract

          Genes encoding ribosomal RNA (rDNA) are essential for cell survival and are particularly sensitive to factors leading to genomic instability. Their repetitive character makes them prone to inappropriate recombinational events arising from collision of transcriptional and replication machineries, resulting in unstable rDNA copy numbers. In this review, we summarize current knowledge on the structure and organization of rDNA, its role in sensing changes in the genome, and its linkage to aging. We also review recent findings on the main factors involved in chromatin assembly and DNA repair in the maintenance of rDNA stability in the model plants Arabidopsis thaliana and the moss Physcomitrella patens, providing a view across the plant evolutionary tree.

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          The Nucleolus under Stress

          Séverine Boulon, Belinda J. Westman, Saskia Hutten … (2010)
          Cells typically respond quickly to stress, altering their metabolism to compensate. In mammalian cells, stress signaling usually leads to either cell-cycle arrest or apoptosis, depending on the severity of the insult and the ability of the cell to recover. Stress also often leads to reorganization of nuclear architecture, reflecting the simultaneous inhibition of major nuclear pathways (e.g., replication and transcription) and activation of specific stress responses (e.g., DNA repair). In this review, we focus on how two nuclear organelles, the nucleolus and the Cajal body, respond to stress. The nucleolus senses stress and is a central hub for coordinating the stress response. We review nucleolar function in the stress-induced regulation of p53 and the specific changes in nucleolar morphology and composition that occur upon stress. Crosstalk between nucleoli and CBs is also discussed in the context of stress responses.
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            The economics of ribosome biosynthesis in yeast.

            Jonathan R Warner (1999)
            In a rapidly growing yeast cell, 60% of total transcription is devoted to ribosomal RNA, and 50% of RNA polymerase II transcription and 90% of mRNA splicing are devoted to ribosomal proteins (RPs). Coordinate regulation of the approximately 150 rRNA genes and 137 RP genes that make such prodigious use of resources is essential for the economy of the cell. This is entrusted to a number of signal transduction pathways that can abruptly induce or silence the ribosomal genes, leading to major implications for the expression of other genes as well.
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              R-Loops as Cellular Regulators and Genomic Threats

              Madzia Crossley, Michael Bocek, Karlene A. Cimprich (2019)
              During transcription, the nascent RNA strand can base pair with its template DNA, displacing the non-template strand as ssDNA and forming a structure called an R-loop. R-loops are common across many domains of life and cause DNA damage in certain contexts. In this review, we summarize recent results implicating R-loops as important regulators of cellular processes such as transcription termination, gene regulation, and DNA repair. We also highlight recent work suggesting that R-loops can be problematic to cells as blocks to efficient transcription and replication that trigger the DNA damage response. Finally, we discuss how R-loops may contribute to cancer, neurodegeneration, and inflammatory diseases and compare the available next-generation sequencing-based approaches to map R-loops genome wide.
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                Author and article information

                Contributors
                Vassiliki Stamatopoulou: Role: Academic Editor
                Journal
                Journal ID (nlm-ta): Int J Mol Sci
                Journal ID (iso-abbrev): Int J Mol Sci
                Journal ID (publisher-id): ijms
                Title: International Journal of Molecular Sciences
                Publisher: MDPI
                ISSN (Electronic): 1422-0067
                Publication date (Electronic): 28 January 2021
                Publication date Collection: February 2021
                Volume: 22
                Issue: 3
                Electronic Location Identifier: 1302
                Affiliations
                [1 ]Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, CZ-61137 Brno, Czech Republic; ivanka.goff@ 123456gmail.com
                [2 ]Chromatin Molecular Complexes, Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-62500 Brno, Czech Republic
                [3 ]Department of Cell Biology and Radiobiology, Institute of Biophysics of the Czech Academy of Sciences, CZ-61265 Brno, Czech Republic
                Author notes
                [* ]Correspondence: fajkus@ 123456sci.muni.cz
                Author information
                https://orcid.org/0000-0003-3977-8090
                https://orcid.org/0000-0002-3112-1716
                Article
                Publisher ID: ijms-22-01302
                DOI: 10.3390/ijms22031302
                PMC ID: 7865372
                PubMed ID: 33525595
                SO-VID: e99cecbc-54ed-4716-9375-1eca13513a54
                Copyright © © 2021 by the authors.
                License:

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                Date received : 05 January 2021
                Date accepted : 25 January 2021
                Categories
                Subject: Review

                ScienceOpen disciplines: Molecular biology
                Keywords: rdna organization,genome stability,rrna genes,ribosome,caf-1,rad51,rtel1
                Data availability:
                ScienceOpen disciplines: Molecular biology
                Keywords: rdna organization, genome stability, rrna genes, ribosome, caf-1, rad51, rtel1

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