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Shatskikh AS, Fefelova EA, Klenov MS. Functions of RNAi Pathways in Ribosomal RNA Regulation. Noncoding RNA 2024; 10:19. [PMID: 38668377 PMCID: PMC11054153 DOI: 10.3390/ncrna10020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.
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Affiliation(s)
- Aleksei S. Shatskikh
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia;
| | - Elena A. Fefelova
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Mikhail S. Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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Tchurikov NA, Alembekov IR, Klushevskaya ES, Kretova AN, Keremet AM, Sidorova AE, Meilakh PB, Chechetkin VR, Kravatskaya GI, Kravatsky YV. Genes Possessing the Most Frequent DNA DSBs Are Highly Associated with Development and Cancers, and Essentially Overlap with the rDNA-Contacting Genes. Int J Mol Sci 2022; 23:ijms23137201. [PMID: 35806206 PMCID: PMC9266645 DOI: 10.3390/ijms23137201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/15/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
Double-strand DNA breakes (DSBs) are the most deleterious and widespread examples of DNA damage. They inevitably originate from endogenous mechanisms in the course of transcription, replication, and recombination, as well as from different exogenous factors. If not properly repaired, DSBs result in cell death or diseases. Genome-wide analysis of DSBs has revealed the numerous endogenous DSBs in human chromosomes. However, until now, it has not been clear what kind of genes are preferentially subjected to breakage. We performed a genetic and epigenetic analysis of the most frequent DSBs in HEK293T cells. Here, we show that they predominantly occur in the active genes controlling differentiation, development, and morphogenesis. These genes are highly associated with cancers and other diseases. About one-third of the genes possessing frequent DSBs correspond to rDNA-contacting genes. Our data suggest that a specific set of active genes controlling morphogenesis are the main targets of DNA breakage in human cells, although there is a specific set of silent genes controlling metabolism that also are enriched in DSBs. We detected this enrichment by different activators and repressors of transcription at DSB target sites, as well breakage at promoters. We propose that both active transcription and silencing of genes give a propensity for DNA breakage. These results have implications for medicine and gene therapy.
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Affiliation(s)
- Nickolai A. Tchurikov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Correspondence:
| | - Ildar R. Alembekov
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Elena S. Klushevskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Antonina N. Kretova
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Ann M. Keremet
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Anastasia E. Sidorova
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Polina B. Meilakh
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Vladimir R. Chechetkin
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Galina I. Kravatskaya
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
| | - Yuri V. Kravatsky
- Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia; (I.R.A.); (E.S.K.); (A.N.K.); (A.M.K.); (A.E.S.); (P.B.M.); (V.R.C.); (G.I.K.); (Y.V.K.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, Russia
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