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Lee SR, Pollard DA, Galati DF, Kelly ML, Miller B, Mong C, Morris MN, Roberts-Nygren K, Kapler GM, Zinkgraf M, Dang HQ, Branham E, Sasser J, Tessier E, Yoshiyama C, Matsumoto M, Turman G. Disruption of a ∼23-24 nucleotide small RNA pathway elevates DNA damage responses in Tetrahymena thermophila. Mol Biol Cell 2021; 32:1335-1346. [PMID: 34010017 PMCID: PMC8694037 DOI: 10.1091/mbc.e20-10-0631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endogenous RNA interference (RNAi) pathways regulate a wide range of cellular processes in diverse eukaryotes, yet in the ciliated eukaryote, Tetrahymena thermophila, the cellular purpose of RNAi pathways that generate ∼23–24 nucleotide (nt) small (s)RNAs has remained unknown. Here, we investigated the phenotypic and gene expression impacts on vegetatively growing cells when genes involved in ∼23–24 nt sRNA biogenesis are disrupted. We observed slower proliferation and increased expression of genes involved in DNA metabolism and chromosome organization and maintenance in sRNA biogenesis mutants RSP1Δ, RDN2Δ, and RDF2Δ. In addition, RSP1Δ and RDN2Δ cells frequently exhibited enlarged chromatin extrusion bodies, which are nonnuclear, DNA-containing structures that may be akin to mammalian micronuclei. Expression of homologous recombination factor Rad51 was specifically elevated in RSP1Δ and RDN2Δ strains, with Rad51 and double-stranded DNA break marker γ-H2A.X localized to discrete macronuclear foci. In addition, an increase in Rad51 and γ-H2A.X foci was also found in knockouts of TWI8, a macronucleus-localized PIWI protein. Together, our findings suggest that an evolutionarily conserved role for RNAi pathways in maintaining genome integrity may be extended even to the early branching eukaryotic lineage that gave rise to Tetrahymena thermophila.
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Affiliation(s)
- Suzanne R Lee
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Daniel A Pollard
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Domenico F Galati
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Megan L Kelly
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Brian Miller
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Christina Mong
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Megan N Morris
- Biology Department, Western Washington University, Bellingham, WA 98225
| | | | - Geoffrey M Kapler
- Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843
| | - Matthew Zinkgraf
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Hung Q Dang
- Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843
| | - Erica Branham
- Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843
| | - Jason Sasser
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Erin Tessier
- Biology Department, Western Washington University, Bellingham, WA 98225
| | | | - Maya Matsumoto
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Gaea Turman
- Biology Department, Western Washington University, Bellingham, WA 98225
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Wang C, Lin H. Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs. Genome Biol 2021; 22:27. [PMID: 33419460 PMCID: PMC7792047 DOI: 10.1186/s13059-020-02221-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022] Open
Abstract
PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathway in regulating the expression of other major classes of RNAs in germ cells. In this review, we summarize how PIWI proteins and piRNAs regulate the expression of many disparate RNAs, describing a highly complex global genomic regulatory relationship at the RNA level through which piRNAs functionally connect all major constituents of the genome in the germline.
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Affiliation(s)
- Chen Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06519, USA.
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Khurana JS, Clay DM, Moreira S, Wang X, Landweber LF. Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha. RNA (NEW YORK, N.Y.) 2018; 24:18-29. [PMID: 29079634 PMCID: PMC5733567 DOI: 10.1261/rna.061333.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 09/10/2017] [Indexed: 06/07/2023]
Abstract
Dicer-dependent small noncoding RNAs play important roles in gene regulation in a wide variety of organisms. Endogenous small interfering RNAs (siRNAs) are part of an ancient pathway of transposon control in plants and animals. The ciliate, Oxytricha trifallax, has approximately 16,000 gene-sized chromosomes in its somatic nucleus. Long noncoding RNAs establish high ploidy levels at the onset of sexual development, but the factors that regulate chromosome copy numbers during cell division and growth have been a mystery. We report a novel function of a class of Dicer (Dcl-1)- and RNA-dependent RNA polymerase (RdRP)-dependent endogenous small RNAs in regulating chromosome copy number and gene dosage in O. trifallax Asexually growing populations express an abundant class of 21-nt sRNAs that map to both coding and noncoding regions of most chromosomes. These sRNAs are bound to chromatin and their levels surprisingly do not correlate with mRNA levels. Instead, the levels of these small RNAs correlate with genomic DNA copy number. Reduced sRNA levels in dcl-1 or rdrp mutants lead to concomitant reduction in chromosome copy number. Furthermore, these cells show no signs of transposon activation, but instead display irregular nuclear architecture and signs of replication stress. In conclusion, Oxytricha Dcl-1 and RdRP-dependent small RNAs that derive from the somatic nucleus contribute to the maintenance of gene dosage, possibly via a role in DNA replication, offering a novel role for these small RNAs in eukaryotes.
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Affiliation(s)
- Jaspreet S Khurana
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Derek M Clay
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Sandrine Moreira
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Laura F Landweber
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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