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Zhang L, Wang J, Tang Z, Lin Z, Su R, Hu N, Tang Y, Ge G, Fan J, Tong MH, Xue Y, Zhou Y, Cheng H. The nuclear exosome co-factor MTR4 shapes the transcriptome for meiotic initiation. Nat Commun 2025; 16:2605. [PMID: 40097464 PMCID: PMC11914058 DOI: 10.1038/s41467-025-57898-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/05/2025] [Indexed: 03/19/2025] Open
Abstract
Nuclear RNA decay has emerged as a mechanism for post-transcriptional gene regulation in cultured cells. However, whether this process occurs in animals and holds biological relevance remains largely unexplored. Here, we demonstrate that MTR4, the central cofactor of the nuclear RNA exosome, is essential for embryogenesis and spermatogenesis. Embryonic development of Mtr4 knockout mice arrests at 6.5 day. Germ cell-specific knockout of Mtr4 results in male infertility with a specific and severe defect in meiotic initiation. During the pre-meiotic stage, MTR4/exosome represses meiotic genes, which are typically shorter in size and possess fewer introns, through RNA degradation. Concurrently, it ensures the expression of mitotic genes generally exhibiting the opposite features. Consistent with these regulation rules, mature replication-dependent histone mRNAs and polyadenylated retrotransposon RNAs were identified as MTR4/exosome targets in germ cells. In addition, MTR4 regulates alternative splicing of many meiotic genes. Together, our work underscores the importance of nuclear RNA degradation in regulating germline transcriptome, ensuring the appropriate gene expression program for the transition from mitosis to meiosis during spermatogenesis.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jianshu Wang
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Zhidong Tang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
- Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Zhen Lin
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ruibao Su
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Naijing Hu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yao Tang
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China
| | - Gaoxiang Ge
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Jing Fan
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ming-Han Tong
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, Hubei Key Laboratory of Cell Homeostasis, RNA Institute, Wuhan University, Wuhan, China.
| | - Hong Cheng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
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Taniue K, Sugawara A, Zeng C, Han H, Gao X, Shimoura Y, Ozeki AN, Onoguchi-Mizutani R, Seki M, Suzuki Y, Hamada M, Akimitsu N. The MTR4/hnRNPK complex surveils aberrant polyadenylated RNAs with multiple exons. Nat Commun 2024; 15:8684. [PMID: 39419981 PMCID: PMC11487169 DOI: 10.1038/s41467-024-51981-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 08/21/2024] [Indexed: 10/19/2024] Open
Abstract
RNA surveillance systems degrade aberrant RNAs that result from defective transcriptional termination, splicing, and polyadenylation. Defective RNAs in the nucleus are recognized by RNA-binding proteins and MTR4, and are degraded by the RNA exosome complex. Here, we detect aberrant RNAs in MTR4-depleted cells using long-read direct RNA sequencing and 3' sequencing. MTR4 destabilizes intronic polyadenylated transcripts generated by transcriptional read-through over one or more exons, termed 3' eXtended Transcripts (3XTs). MTR4 also associates with hnRNPK, which recognizes 3XTs with multiple exons. Moreover, the aberrant protein translated from KCTD13 3XT is a target of the hnRNPK-MTR4-RNA exosome pathway and forms aberrant condensates, which we name KCTD13 3eXtended Transcript-derived protein (KeXT) bodies. Our results suggest that RNA surveillance in human cells inhibits the formation of condensates of a defective polyadenylated transcript-derived protein.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
- Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Anzu Sugawara
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Chao Zeng
- Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Han Han
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Xinyue Gao
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Yuki Shimoura
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Atsuko Nakanishi Ozeki
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Rena Onoguchi-Mizutani
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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Chen S, Jiang Q, Fan J, Cheng H. Nuclear mRNA export. Acta Biochim Biophys Sin (Shanghai) 2024; 57:84-100. [PMID: 39243141 PMCID: PMC11802349 DOI: 10.3724/abbs.2024145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/17/2024] [Indexed: 09/09/2024] Open
Abstract
In eukaryotic cells, gene expression begins with transcription in the nucleus, followed by the maturation of messenger RNAs (mRNAs). These mRNA molecules are then exported to the cytoplasm through the nuclear pore complex (NPC), a process that serves as a critical regulatory phase of gene expression. The export of mRNA is intricately linked to precursor mRNA (pre-mRNA) processing, ensuring that only properly processed mRNA reaches the cytoplasm. This coordination is essential, as recent studies have revealed that mRNA export factors not only assist in transport but also influence upstream processing steps, adding a layer of complexity to gene regulation. Furthermore, the export process competes with RNA processing and degradation pathways, maintaining a delicate balance vital for accurate gene expression. While these mechanisms are generally conserved across eukaryotes, significant differences exist between yeast and higher eukaryotic cells, particularly due to the more genome complexity of the latter. This review delves into the current research on mRNA export in higher eukaryotic cells, focusing on its role in the broader context of gene expression regulation and highlighting how it interacts with other gene expression processes to ensure precise and efficient gene functionality in complex organisms.
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Affiliation(s)
- Suli Chen
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
| | - Qingyi Jiang
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
| | - Jing Fan
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
- The Key Laboratory of Developmental Genes and Human DiseaseSchool of Life Science and TechnologySoutheast UniversityNanjing210096China
| | - Hong Cheng
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou310024China
- Key Laboratory of RNA InnovationScience and EngineeringShanghai Key Laboratory of Molecular AndrologyShanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200031China
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Chaudhuri A, Paul S, Banerjea M, Das B. Polyadenylated versions of small non-coding RNAs in Saccharomyces cerevisiae are degraded by Rrp6p/Rrp47p independent of the core nuclear exosome. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:155-186. [PMID: 38783922 PMCID: PMC11115967 DOI: 10.15698/mic2024.05.823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 05/25/2024]
Abstract
In Saccharomyces cerevisiae, polyadenylated forms of mature (and not precursor) small non-coding RNAs (sncRNAs) those fail to undergo proper 3'-end maturation are subject to an active degradation by Rrp6p and Rrp47p, which does not require the involvement of core exosome and TRAMP components. In agreement with this finding, Rrp6p/Rrp47p is demonstrated to exist as an exosome-independent complex, which preferentially associates with mature polyadenylated forms of these sncRNAs. Consistent with this observation, a C-terminally truncated version of Rrp6p (Rrp6p-ΔC2) lacking physical association with the core nuclear exosome supports their decay just like its full-length version. Polyadenylation is catalyzed by both the canonical and non-canonical poly(A) polymerases, Pap1p and Trf4p. Analysis of the polyadenylation profiles in WT and rrp6-Δ strains revealed that the majority of the polyadenylation sites correspond to either one to three nucleotides upstream or downstream of their mature ends and their poly(A) tails ranges from 10-15 adenylate residues. Most interestingly, the accumulated polyadenylated snRNAs are functional in the rrp6-Δ strain and are assembled into spliceosomes. Thus, Rrp6p-Rrp47p defines a core nuclear exosome-independent novel RNA turnover system in baker's yeast targeting imperfectly processed polyadenylated sncRNAs that accumulate in the absence of Rrp6p.
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Affiliation(s)
- Anusha Chaudhuri
- Present Position: Zentrum fǜr Molekulare, Medizin, Institut fǜr Kardiovaskuläre Regeneration, Haus 25B, Goethe-Universität, Theodor-Stern-Kai 7, Universitätsklinikum, 60590 Frankfurt am Main, Germany
| | - Soumita Paul
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata – 700 032, West Bengal, India
| | - Mayukh Banerjea
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata – 700 032, West Bengal, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, 188 Raja S.C. Mullick Road, Kolkata – 700 032, West Bengal, India
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Srinivasan S, He X, Mirza S, Mager J. Exosome complex components 1 and 2 are vital for early mammalian development. Gene Expr Patterns 2024; 51:119346. [PMID: 37940010 PMCID: PMC10939940 DOI: 10.1016/j.gep.2023.119346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
Exosome Complex Components 1 and 2 (EXOSC1 and 2) are two proteins in the RNA Exosome complex whose main function is 5' → 3' RNA degradation and processing. The RNA exosome complex is comprised of nine subunits that form two separate components: the S1/KH cap and the PH-core. EXOSC1 and 2 are both part of the S1/KH cap and are involved in binding nascent RNA. As part of a systemic characterization of early lethal alleles produced by the Knockout Mouse Project, we have examined Exosc1 and Exosc2 homozygous null (mutant) embryos to determine developmental and molecular phenotypes of embryos lacking their functions. Our studies reveal that Exosc1 null embryos implant and form an egg cylinder but are developmentally delayed and fail to initiate gastrulation by embryonic day 7.5. In contrast, Exosc2 null embryos are lethal during peri-implantation stages, and while they do form a morphologically normal blastocyst at E3.5, they cannot be recovered at post-implantation stages. We show the absence of stage-specific developmental and altered lineage-specification in both Exosc1 and Exosc2 mutant embryos and conclude that these genes are essential for the successful progression through early mammalian development.
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Affiliation(s)
- Sanjana Srinivasan
- Department of Veterinary and Animal Sciences, University of Massachusetts- Amherst, Amherst, MA, 01002, USA
| | - Xinjian He
- Department of Veterinary and Animal Sciences, University of Massachusetts- Amherst, Amherst, MA, 01002, USA
| | - Sarah Mirza
- Department of Veterinary and Animal Sciences, University of Massachusetts- Amherst, Amherst, MA, 01002, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts- Amherst, Amherst, MA, 01002, USA.
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Taniue K, Tanu T, Shimoura Y, Mitsutomi S, Han H, Kakisaka R, Ono Y, Tamamura N, Takahashi K, Wada Y, Mizukami Y, Akimitsu N. RNA Exosome Component EXOSC4 Amplified in Multiple Cancer Types Is Required for the Cancer Cell Survival. Int J Mol Sci 2022; 23:496. [PMID: 35008922 PMCID: PMC8745236 DOI: 10.3390/ijms23010496] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/26/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022] Open
Abstract
The RNA exosome is a multi-subunit ribonuclease complex that is evolutionally conserved and the major cellular machinery for the surveillance, processing, degradation, and turnover of diverse RNAs essential for cell viability. Here we performed integrated genomic and clinicopathological analyses of 27 RNA exosome components across 32 tumor types using The Cancer Genome Atlas PanCancer Atlas Studies' datasets. We discovered that the EXOSC4 gene, which encodes a barrel component of the RNA exosome, was amplified across multiple cancer types. We further found that EXOSC4 alteration is associated with a poor prognosis of pancreatic cancer patients. Moreover, we demonstrated that EXOSC4 is required for the survival of pancreatic cancer cells. EXOSC4 also repressed BIK expression and destabilized SESN2 mRNA by promoting its degradation. Furthermore, knockdown of BIK and SESN2 could partially rescue pancreatic cells from the reduction in cell viability caused by EXOSC4 knockdown. Our study provides evidence for EXOSC4-mediated regulation of BIK and SESN2 mRNA in the survival of pancreatic tumor cells.
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Affiliation(s)
- Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yuki Shimoura
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Shuhei Mitsutomi
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Han Han
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Rika Kakisaka
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo 065-0033, Japan; (R.K.); (Y.O.)
| | - Nobue Tamamura
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Kenji Takahashi
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Youichiro Wada
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
| | - Yusuke Mizukami
- Cancer Genomics and Precision Medicine, Department of Medicine, Asahikawa Medical University, Asahikawa 078-8510, Japan; (N.T.); (K.T.); (Y.M.)
| | - Nobuyoshi Akimitsu
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan; (T.T.); (Y.S.); (S.M.); (H.H.); (Y.W.)
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Tanu T, Taniue K, Imamura K, Onoguchi-Mizutani R, Han H, Jensen TH, Akimitsu N. hnRNPH1-MTR4 complex-mediated regulation of NEAT1v2 stability is critical for IL8 expression. RNA Biol 2021; 18:537-547. [PMID: 34470577 DOI: 10.1080/15476286.2021.1971439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Many long noncoding RNAs (lncRNAs) are localized in the nucleus and play important roles in various biological processes, including cell proliferation, differentiation and antiviral response. Yet, it remains unclear how some nuclear lncRNAs are turned over. Here we show that the heterogeneous nuclear ribonucleoprotein H1 (hnRNPH1) controls expression levels of NEAT1v2, a lncRNA involved in the formation of nuclear paraspeckles. hnRNPH1 associates, in an RNA-independent manner, with the RNA helicase MTR4/MTREX, an essential co-factor of the nuclear ribonucleolytic RNA exosome. hnRNPH1 localizes in nuclear speckles and depletion of hnRNPH1 enhances NEAT1v2-mediated expression of the IL8 mRNA, encoding a cytokine involved in the innate immune response. Taken together, our results indicate that the hnRNPH1-MTR4 linkage regulates IL8 expression through the degradation of NEAT1v2 RNA.
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Affiliation(s)
- Tanzina Tanu
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Kenzui Taniue
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Han Han
- Isotope Science Center, The University of Tokyo, Tokyo, Japan
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
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Cherkasova V, Iben JR, Pridham KJ, Kessler AC, Maraia RJ. The leucine-NH4+ uptake regulator Any1 limits growth as part of a general amino acid control response to loss of La protein by fission yeast. PLoS One 2021; 16:e0253494. [PMID: 34153074 PMCID: PMC8216550 DOI: 10.1371/journal.pone.0253494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022] Open
Abstract
The sla1+ gene of Schizosachharoymces pombe encodes La protein which promotes proper processing of precursor-tRNAs. Deletion of sla1 (sla1Δ) leads to disrupted tRNA processing and sensitivity to target of rapamycin (TOR) inhibition. Consistent with this, media containing NH4+ inhibits leucine uptake and growth of sla1Δ cells. Here, transcriptome analysis reveals that genes upregulated in sla1Δ cells exhibit highly significant overalp with general amino acid control (GAAC) genes in relevant transcriptomes from other studies. Growth in NH4+ media leads to additional induced genes that are part of a core environmental stress response (CESR). The sla1Δ GAAC response adds to evidence linking tRNA homeostasis and broad signaling in S. pombe. We provide evidence that deletion of the Rrp6 subunit of the nuclear exosome selectively dampens a subset of GAAC genes in sla1Δ cells suggesting that nuclear surveillance-mediated signaling occurs in S. pombe. To study the NH4+-effects, we isolated sla1Δ spontaneous revertants (SSR) of the slow growth phenotype and found that GAAC gene expression and rapamycin hypersensitivity were also reversed. Genome sequencing identified a F32V substitution in Any1, a known negative regulator of NH4+-sensitive leucine uptake linked to TOR. We show that 3H-leucine uptake by SSR-any1-F32V cells in NH4+-media is more robust than by sla1Δ cells. Moreover, F32V may alter any1+ function in sla1Δ vs. sla1+ cells in a distinctive way. Thus deletion of La, a tRNA processing factor leads to a GAAC response involving reprogramming of amino acid metabolism, and isolation of the any1-F32V rescuing mutant provides an additional specific link.
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Affiliation(s)
- Vera Cherkasova
- Kelly@DeWitt, Inc, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States of America
| | - James R. Iben
- Molecular Genomics Core, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States of America
| | - Kevin J. Pridham
- Fralin Biomedical Research Institute at Virginia Tech, Roanoke, VA, United States of America
| | - Alan C. Kessler
- Section on Molecular and Cell Biology, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD United States of America
| | - Richard J. Maraia
- Section on Molecular and Cell Biology, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD United States of America
- * E-mail:
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9
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RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules 2021; 11:biom11010076. [PMID: 33430019 PMCID: PMC7826747 DOI: 10.3390/biom11010076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucleoproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. SMUG1 may be required for post-transcriptional regulation and quality control of rRNAs, partly by regulating rRNA and stability.
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10
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Wang Y, Weng C, Chen X, Zhou X, Huang X, Yan Y, Zhu C. CDE-1 suppresses the production of risiRNA by coupling polyuridylation and degradation of rRNA. BMC Biol 2020; 18:115. [PMID: 32887607 PMCID: PMC7472701 DOI: 10.1186/s12915-020-00850-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 08/17/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Modification of RNAs, particularly at the terminals, is critical for various essential cell processes; for example, uridylation is implicated in tumorigenesis, proliferation, stem cell maintenance, and immune defense against viruses and retrotransposons. Ribosomal RNAs can be regulated by antisense ribosomal siRNAs (risiRNAs), which downregulate pre-rRNAs through the nuclear RNAi pathway in Caenorhabditis elegans. However, the biogenesis and regulation of risiRNAs remain obscure. Previously, we showed that 26S rRNAs are uridylated at the 3'-ends by an unknown terminal polyuridylation polymerase before the rRNAs are degraded by a 3' to 5' exoribonuclease SUSI-1(ceDIS3L2). RESULTS Here, we found that CDE-1, one of the three C.elegans polyuridylation polymerases (PUPs), is specifically involved in suppressing risiRNA production. CDE-1 localizes to perinuclear granules in the germline and uridylates Argonaute-associated 22G-RNAs, 26S, and 5.8S rRNAs at the 3'-ends. Immunoprecipitation followed by mass spectrometry (IP-MS) revealed that CDE-1 interacts with SUSI-1(ceDIS3L2). Consistent with these results, both CDE-1 and SUSI-1(ceDIS3L2) are required for the inheritance of RNAi. CONCLUSIONS This work identified a rRNA surveillance machinery of rRNAs that couples terminal polyuridylation and degradation.
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Affiliation(s)
- Yun Wang
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- School of Bioengineering, Huainan Normal University, Huainan, 232038, Anhui, People's Republic of China.
| | - Chenchun Weng
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Xiangyang Chen
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Xufei Zhou
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Xinya Huang
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Yonghong Yan
- National Institute of Biological Sciences, Beijing, 102206, People's Republic of China
| | - Chengming Zhu
- National Science Center for Physical Sciences at Microscale Division of Molecular & Cell Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
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11
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Yu L, Kim J, Jiang L, Feng B, Ying Y, Ji KY, Tang Q, Chen W, Mai T, Dou W, Zhou J, Xiang LY, He YF, Yang D, Li Q, Fu X, Xu Y. MTR4 drives liver tumorigenesis by promoting cancer metabolic switch through alternative splicing. Nat Commun 2020; 11:708. [PMID: 32024842 PMCID: PMC7002374 DOI: 10.1038/s41467-020-14437-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 01/09/2020] [Indexed: 01/10/2023] Open
Abstract
The metabolic switch from oxidative phosphorylation to glycolysis is required for tumorigenesis in order to provide cancer cells with energy and substrates of biosynthesis. Therefore, it is important to elucidate mechanisms controlling the cancer metabolic switch. MTR4 is a RNA helicase associated with a nuclear exosome that plays key roles in RNA processing and surveillance. We demonstrate that MTR4 is frequently overexpressed in hepatocellular carcinoma (HCC) and is an independent diagnostic marker predicting the poor prognosis of HCC patients. MTR4 drives cancer metabolism by ensuring correct alternative splicing of pre-mRNAs of critical glycolytic genes such as GLUT1 and PKM2. c-Myc binds to the promoter of the MTR4 gene and is important for MTR4 expression in HCC cells, indicating that MTR4 is a mediator of the functions of c-Myc in cancer metabolism. These findings reveal important roles of MTR4 in the cancer metabolic switch and present MTR4 as a promising therapeutic target for treating HCC.
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Affiliation(s)
- Lili Yu
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China.
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Jinchul Kim
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0322, USA
| | - Lei Jiang
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Bingbing Feng
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Yue Ying
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Kai-Yuan Ji
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
| | - Qingshuang Tang
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Wancheng Chen
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Taoyi Mai
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
| | - Wenlong Dou
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Jianlong Zhou
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Le-Yang Xiang
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Yang-Fan He
- Department of Pathology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, China
| | - Dinghua Yang
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Qingjiao Li
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China
| | - Xuemei Fu
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China.
- Shenzhen Children's Hospital, 7019 Yitian Road, Shenzhen, 518026, China.
| | - Yang Xu
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, 518033, China.
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China.
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0322, USA.
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12
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Zigáčková D, Rájecká V, Vaňáčová Š. Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays. Methods Mol Biol 2020; 2062:237-253. [PMID: 31768980 DOI: 10.1007/978-1-4939-9822-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The RNA exosome processes a wide variety of RNA and mediates RNA maturation, quality control and decay. In marked contrast to its high processivity in vivo, the purified exosome exhibits only weak activity on RNA substrates in vitro. Its activity is regulated by several auxiliary proteins, and protein complexes. In budding yeast, the activity of exosome is enhanced by the polyadenylation complex referred to as TRAMP. TRAMP oligoadenylates precursors and aberrant forms of RNAs to promote their trimming or complete degradation by exosomes. This chapter provides protocols for the purification of TRAMP and exosome complexes from yeast and the in vitro evaluation of exosome activation by the TRAMP complex. The protocols can be used for different purposes, such as the assessment of the role of individual subunits, protein domains or particular mutations in TRAMP-exosome RNA processing in vitro.
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Affiliation(s)
- Dagmar Zigáčková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Veronika Rájecká
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Štěpánka Vaňáčová
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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13
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Adriaens C, Rambow F, Bervoets G, Silla T, Mito M, Chiba T, Asahara H, Hirose T, Nakagawa S, Jensen TH, Marine JC. The long noncoding RNA NEAT1_1 is seemingly dispensable for normal tissue homeostasis and cancer cell growth. RNA (NEW YORK, N.Y.) 2019; 25:1681-1695. [PMID: 31551298 PMCID: PMC6859857 DOI: 10.1261/rna.071456.119] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/30/2019] [Indexed: 05/27/2023]
Abstract
NEAT1 is one of the most studied lncRNAs, in part because its silencing in mice causes defects in mammary gland development and corpus luteum formation and protects them from skin cancer development. Moreover, depleting NEAT1 in established cancer cell lines reduces growth and sensitizes cells to DNA damaging agents. However, NEAT1 produces two isoforms and because the short isoform, NEAT1_1, completely overlaps the 5' part of the long NEAT1_2 isoform; the respective contributions of each of the isoforms to these phenotypes has remained unclear. Whereas NEAT1_1 is highly expressed in most tissues, NEAT1_2 is the central architectural component of paraspeckles, which are nuclear bodies that assemble in specific tissues and cells exposed to various forms of stress. Using dual RNA-FISH to detect both NEAT1_1 outside of the paraspeckles and NEAT1_2/NEAT1 inside this nuclear body, we report herein that NEAT1_1 levels are dynamically regulated during the cell cycle and targeted for degradation by the nuclear RNA exosome. Unexpectedly, however, cancer cells engineered to lack NEAT1_1, but not NEAT1_2, do not exhibit cell cycle defects. Moreover, Neat1_1-specific knockout mice do not exhibit the phenotypes observed in Neat1-deficient mice. We propose that NEAT1 functions are mainly, if not exclusively, attributable to NEAT1_2 and, by extension, to paraspeckles.
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Affiliation(s)
- Carmen Adriaens
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
| | - Greet Bervoets
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
| | - Toomas Silla
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, 351-0198 Saitama, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 113-8510 Tokyo, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University, 113-8510 Tokyo, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, 060-0808 Sapporo, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, 060-0812 Sapporo, Japan
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, 3000 Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Oncology Department, KU Leuven, 3000 Leuven, Belgium
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14
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Lange H, Ndecky SYA, Gomez-Diaz C, Pflieger D, Butel N, Zumsteg J, Kuhn L, Piermaria C, Chicher J, Christie M, Karaaslan ES, Lang PLM, Weigel D, Vaucheret H, Hammann P, Gagliardi D. RST1 and RIPR connect the cytosolic RNA exosome to the Ski complex in Arabidopsis. Nat Commun 2019; 10:3871. [PMID: 31455787 PMCID: PMC6711988 DOI: 10.1038/s41467-019-11807-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/05/2019] [Indexed: 02/01/2023] Open
Abstract
The RNA exosome is a key 3’−5’ exoribonuclease with an evolutionarily conserved structure and function. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM-repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate RNA quality control siRNAs (rqc-siRNAs) produced by the post-transcriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. The small RNA populations observed in rst1 and ripr mutants are also detected in mutants lacking the RRP45B/CER7 core exosome subunit. Thus, molecular and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known Ski subunits. RST1 is not restricted to plants, as homologues with a similar domain architecture but unknown function exist in animals, including humans. Cytosolic RNA degradation by the RNA exosome requires the Ski complex. Here the authors show that the proteins RST1 and RIPR assist the RNA exosome and the Ski complex in RNA degradation, thereby preventing the production of secondary siRNAs from endogenous mRNAs.
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Affiliation(s)
- Heike Lange
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Simon Y A Ndecky
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Carlos Gomez-Diaz
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Nicolas Butel
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Julie Zumsteg
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Christina Piermaria
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Johana Chicher
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Michael Christie
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Ezgi S Karaaslan
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hervé Vaucheret
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Philippe Hammann
- Plateforme protéomique Strasbourg Esplanade FR1589 du CNRS, Université de Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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15
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Lee D, Park D, Park JH, Kim JH, Shin C. Poly(A)-specific ribonuclease sculpts the 3' ends of microRNAs. RNA (NEW YORK, N.Y.) 2019; 25:388-405. [PMID: 30591540 PMCID: PMC6380276 DOI: 10.1261/rna.069633.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/21/2018] [Indexed: 05/08/2023]
Abstract
The 3' ends of metazoan microRNAs (miRNAs) are initially defined by the RNase III enzymes during maturation, but subsequently experience extensive modifications by several enzymatic activities. For example, terminal nucleotidyltransferases (TENTs) elongate miRNAs by adding one or a few nucleotides to their 3' ends, which occasionally leads to differential regulation of miRNA stability or function. However, the catalytic entities that shorten miRNAs and the molecular consequences of such shortening are less well understood, especially in vertebrates. Here, we report that poly(A)-specific ribonuclease (PARN) sculpts the 3' ends of miRNAs in human cells. By generating PARN knockout cells and characterizing their miRNAome, we demonstrate that PARN digests the 3' extensions of miRNAs that are derived from the genome or attached by TENTs, thereby effectively reducing the length of miRNAs. Surprisingly, PARN-mediated shortening has little impact on miRNA stability, suggesting that this process likely operates to finalize miRNA maturation, rather than to initiate miRNA decay. PARN-mediated shortening is pervasive across most miRNAs and appears to be a conserved mechanism contributing to the 3' end formation of vertebrate miRNAs. Our findings add miRNAs to the expanding list of noncoding RNAs whose 3' end formation depends on PARN.
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Affiliation(s)
- Dooyoung Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Daechan Park
- Department of Biological Sciences, Ajou University, Suwon 16499, Republic of Korea
| | - June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Jong Heon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Republic of Korea
- Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Republic of Korea
| | - Chanseok Shin
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
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16
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Droll D, Wei G, Guo G, Fan Y, Baumgarten S, Zhou Y, Xiao Y, Scherf A, Zhang Q. Disruption of the RNA exosome reveals the hidden face of the malaria parasite transcriptome. RNA Biol 2018; 15:1206-1214. [PMID: 30235972 PMCID: PMC7000224 DOI: 10.1080/15476286.2018.1517014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Antisense transcription emerges as a key regulator of important biological processes in the human malaria parasite Plasmodium falciparum. RNA-processing factors, however, remain poorly characterized in this pathogen. Here, we purified the multiprotein RNA exosome complex of malaria parasites by affinity chromatography, using HA-tagged PfRrp4 and PfDis3 as the ligands. Seven distinct core exosome subunits (PfRrp41, PfMtr3, PfRrp42, PfRrp45, PfRrp4, PfRrp40, PfCsl4) and two exoribonuclease proteins PfRrp6 and PfDis3 are identified by mass spectrometry. Western blot analysis detects Dis3 and Rrp4 predominantly in the cytoplasmic fraction during asexual blood stage development. An inducible gene knock out of the PfDis3 subunit reveals the upregulation of structural and coding RNA, but the vast majority belongs to antisense RNA. Furthermore, we detect numerous types of cryptic unstable transcripts (CUTs) linked to virulence gene families including antisense RNA in the rif gene family. Our work highlights the limitations of steady-state RNA analysis to predict transcriptional activity and link the RNA surveillance machinery directly with post-transcriptional control and gene expression in malaria parasites.
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Affiliation(s)
- Dorothea Droll
- a Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs , Institut Pasteur , Paris , France.,b CNRS, ERL 9195 , Paris , France.,c INSERM, Unit U1201 , Paris , France
| | - Guiying Wei
- d Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital , Tongji University School of Medicine , Shanghai , China
| | - Gangqiang Guo
- d Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital , Tongji University School of Medicine , Shanghai , China
| | - Yanting Fan
- d Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital , Tongji University School of Medicine , Shanghai , China
| | - Sebastian Baumgarten
- a Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs , Institut Pasteur , Paris , France.,b CNRS, ERL 9195 , Paris , France.,c INSERM, Unit U1201 , Paris , France
| | - Yiqing Zhou
- e CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , China
| | - Youli Xiao
- e CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , China
| | - Artur Scherf
- a Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs , Institut Pasteur , Paris , France.,b CNRS, ERL 9195 , Paris , France.,c INSERM, Unit U1201 , Paris , France
| | - Qingfeng Zhang
- d Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital , Tongji University School of Medicine , Shanghai , China
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17
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Erroneous ribosomal RNAs promote the generation of antisense ribosomal siRNA. Proc Natl Acad Sci U S A 2018; 115:10082-10087. [PMID: 30224484 DOI: 10.1073/pnas.1800974115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Ribosome biogenesis is a multistep process, during which mistakes can occur at any step of pre-rRNA processing, modification, and ribosome assembly. Misprocessed rRNAs are usually detected and degraded by surveillance machineries. Recently, we identified a class of antisense ribosomal siRNAs (risiRNAs) that down-regulate pre-rRNAs through the nuclear RNAi pathway. To further understand the biological roles of risiRNAs, we conducted both forward and reverse genetic screens to search for more suppressor of siRNA (susi) mutants. We isolated a number of genes that are broadly conserved from yeast to humans and are involved in pre-rRNA modification and processing. Among them, SUSI-2(ceRRP8) is homologous to human RRP8 and engages in m1A methylation of the 26S rRNA. C27F2.4(ceBUD23) is an m7G-methyltransferase of the 18S rRNA. E02H1.1(ceDIMT1L) is a predicted m6(2)Am6(2)A-methyltransferase of the 18S rRNA. Mutation of these genes led to a deficiency in modification of rRNAs and elicited accumulation of risiRNAs, which further triggered the cytoplasmic-to-nuclear and cytoplasmic-to-nucleolar translocations of the Argonaute protein NRDE-3. The rRNA processing deficiency also resulted in accumulation of risiRNAs. We also isolated SUSI-3(RIOK-1), which is similar to human RIOK1, that cleaves the 20S rRNA to 18S. We further utilized RNAi and CRISPR-Cas9 technologies to perform candidate-based reverse genetic screens and identified additional pre-rRNA processing factors that suppressed risiRNA production. Therefore, we concluded that erroneous rRNAs can trigger risiRNA generation and subsequently, turn on the nuclear RNAi-mediated gene silencing pathway to inhibit pre-rRNA expression, which may provide a quality control mechanism to maintain homeostasis of rRNAs.
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18
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Singh P, Saha U, Paira S, Das B. Nuclear mRNA Surveillance Mechanisms: Function and Links to Human Disease. J Mol Biol 2018; 430:1993-2013. [PMID: 29758258 DOI: 10.1016/j.jmb.2018.05.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/30/2018] [Accepted: 05/07/2018] [Indexed: 01/05/2023]
Abstract
Production of export-competent mRNAs involves transcription and a series of dynamic processing and modification events of pre-messenger RNAs in the nucleus. Mutations in the genes encoding the transcription and mRNP processing machinery and the complexities involved in the biogenesis events lead to the formation of aberrant messages. These faulty transcripts are promptly eliminated by the nuclear RNA exosome and its cofactors to safeguard the cells and organisms from genetic catastrophe. Mutations in the components of the core nuclear exosome and its cofactors lead to the tissue-specific dysfunction of exosomal activities, which are linked to diverse human diseases and disorders. In this article, we examine the structure and function of both the yeast and human RNA exosome complex and its cofactors, discuss the nature of the various altered amino acid residues implicated in these diseases with the speculative mechanisms of the mutation-induced disorders and project the frontier and prospective avenues of the future research in this field.
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Affiliation(s)
- Pragyan Singh
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Upasana Saha
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Sunirmal Paira
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India
| | - Biswadip Das
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata, India.
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19
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H3K4 Methylation Dependent and Independent Chromatin Regulation by JHD2 and SET1 in Budding Yeast. G3-GENES GENOMES GENETICS 2018; 8:1829-1839. [PMID: 29599176 PMCID: PMC5940172 DOI: 10.1534/g3.118.200151] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Set1 and Jhd2 regulate the methylation state of histone H3 lysine-4 (H3K4me) through their opposing methyltransferase and demethylase activities in the budding yeast Saccharomyces cerevisiae. H3K4me associates with actively transcribed genes and, like both SET1 and JHD2 themselves, is known to regulate gene expression diversely. It remains unclear, however, if Set1 and Jhd2 act solely through H3K4me. Relevantly, Set1 methylates lysine residues in the kinetochore protein Dam1 while genetic studies of the S. pombe SET1 ortholog suggest the existence of non-H3K4 Set1 targets relevant to gene regulation. We interrogated genetic interactions of JHD2 and SET1 with essential genes involved in varied aspects of the transcription cycle. Our findings implicate JHD2 in genetic inhibition of the histone chaperone complexes Spt16-Pob3 (FACT) and Spt6-Spn1. This targeted screen also revealed that JHD2 inhibits the Nrd1-Nab3-Sen1 (NNS) transcription termination complex. We find that while Jhd2’s impact on these transcription regulatory complexes likely acts via H3K4me, Set1 governs the roles of FACT and NNS through opposing H3K4-dependent and -independent functions. We also identify diametrically opposing consequences for mutation of H3K4 to alanine or arginine, illuminating that caution must be taken in interpreting histone mutation studies. Unlike FACT and NNS, detailed genetic studies suggest an H3K4me-centric mode of Spt6-Spn1 regulation by JHD2 and SET1. Chromatin immunoprecipitation and transcript quantification experiments show that Jhd2 opposes the positioning of a Spt6-deposited nucleosome near the transcription start site of SER3, a Spt6-Spn1 regulated gene, leading to hyper-induction of SER3. In addition to confirming and extending an emerging role for Jhd2 in the control of nucleosome occupancy near transcription start sites, our findings suggest some of the chromatin regulatory functions of Set1 are independent of H3K4 methylation.
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20
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Morales Y, Olsen KJ, Bulcher JM, Johnson SJ. Structure of frequency-interacting RNA helicase from Neurospora crassa reveals high flexibility in a domain critical for circadian rhythm and RNA surveillance. PLoS One 2018; 13:e0196642. [PMID: 29718972 PMCID: PMC5931499 DOI: 10.1371/journal.pone.0196642] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 04/17/2018] [Indexed: 11/18/2022] Open
Abstract
The FRH (frequency-interacting RNA helicase) protein is the Neurospora crassa homolog of yeast Mtr4, an essential RNA helicase that plays a central role in RNA metabolism as an activator of the nuclear RNA exosome. FRH is also a required component of the circadian clock, mediating protein interactions that result in the rhythmic repression of gene expression. Here we show that FRH unwinds RNA substrates in vitro with a kinetic profile similar to Mtr4, indicating that while FRH has acquired additional functionality, its core helicase function remains intact. In contrast with the earlier FRH structures, a new crystal form of FRH results in an ATP binding site that is undisturbed by crystal contacts and adopts a conformation consistent with nucleotide binding and hydrolysis. Strikingly, this new FRH structure adopts an arch domain conformation that is dramatically altered from previous structures. Comparison of the existing FRH structures reveals conserved hinge points that appear to facilitate arch motion. Regions in the arch have been previously shown to mediate a variety of protein-protein interactions critical for RNA surveillance and circadian clock functions. The conformational changes highlighted in the FRH structures provide a platform for investigating the relationship between arch dynamics and Mtr4/FRH function.
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Affiliation(s)
- Yalemi Morales
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, United States of America
| | - Keith J. Olsen
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, United States of America
| | - Jacqueline M. Bulcher
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, United States of America
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, United States of America
- * E-mail:
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21
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Bourgeois P, Esteve C, Chaix C, Béroud C, Lévy N, Fabre A, Badens C. Tricho-Hepato-Enteric Syndrome mutation update: Mutations spectrum of TTC37 and SKIV2L, clinical analysis and future prospects. Hum Mutat 2018. [PMID: 29527791 DOI: 10.1002/humu.23418] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tricho-Hepato-Enteric syndrome (THES) is a very rare autosomal recessive syndromic enteropathy caused by mutations of either TTC37 or SKIV2L genes. Very little is known of these two gene products in mammals nor of the pathophysiology of the disease. Since the identification of the genes, we have set up the molecular diagnostic of THES in routine, gathering a large cohort with clinical and molecular data. Here, we report the phenotype and genotype analysis of this cohort together with an extensive literature review of THES cases worldwide, that is, 96 individuals harboring mutations in one gene or the other. We set up locus-specific databases for both genes and reviewed the type of mutation as well as their localization in the proteins. No hot spot is evidenced for any type of mutation. The phenotypic analysis was first made on the whole cohort but is limited due to heterogeneity in clinical descriptions. We then examined the lab diagnostic cohort in detail for clinical manifestations. For the first time, we are able to suggest that patients lacking SKIV2L seem more severely affected than those lacking TTC37, in terms of liver damage and prenatal growth impairment.
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Affiliation(s)
- Patrice Bourgeois
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France.,GMGF, Aix Marseille Univ, Marseille, France
| | | | - Charlène Chaix
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France
| | - Christophe Béroud
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France.,GMGF, Aix Marseille Univ, Marseille, France
| | - Nicolas Lévy
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France.,GMGF, Aix Marseille Univ, Marseille, France
| | | | - Alexandre Fabre
- GMGF, Aix Marseille Univ, Marseille, France.,Multidisciplinary Pediatric Service - La Timone Children's Hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France
| | - Catherine Badens
- Molecular genetics Laboratory, Medical genetics and Cell biology Department, La Timone children's hospital, Assistance-Publique des Hôpitaux de Marseille (APHM), Marseille, France.,GMGF, Aix Marseille Univ, Marseille, France
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22
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Zhou Z, Dang Y, Zhou M, Yuan H, Liu Y. Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation. eLife 2018; 7:33569. [PMID: 29547124 PMCID: PMC5869017 DOI: 10.7554/elife.33569] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022] Open
Abstract
Codon usage biases are found in all genomes and influence protein expression levels. The codon usage effect on protein expression was thought to be mainly due to its impact on translation. Here, we show that transcription termination is an important driving force for codon usage bias in eukaryotes. Using Neurospora crassa as a model organism, we demonstrated that introduction of rare codons results in premature transcription termination (PTT) within open reading frames and abolishment of full-length mRNA. PTT is a wide-spread phenomenon in Neurospora, and there is a strong negative correlation between codon usage bias and PTT events. Rare codons lead to the formation of putative poly(A) signals and PTT. A similar role for codon usage bias was also observed in mouse cells. Together, these results suggest that codon usage biases co-evolve with the transcription termination machinery to suppress premature termination of transcription and thus allow for optimal gene expression.
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Affiliation(s)
- Zhipeng Zhou
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Yunkun Dang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.,Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Haiyan Yuan
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, United States
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23
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Chikne V, Gupta SK, Doniger T, K SR, Cohen-Chalamish S, Waldman Ben-Asher H, Kolet L, Yahia NH, Unger R, Ullu E, Kolev NG, Tschudi C, Michaeli S. The Canonical Poly (A) Polymerase PAP1 Polyadenylates Non-Coding RNAs and Is Essential for snoRNA Biogenesis in Trypanosoma brucei. J Mol Biol 2017; 429:3301-3318. [PMID: 28456523 DOI: 10.1016/j.jmb.2017.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 04/14/2017] [Accepted: 04/23/2017] [Indexed: 10/19/2022]
Abstract
The parasite Trypanosoma brucei is the causative agent of African sleeping sickness and is known for its unique RNA processing mechanisms that are common to all the kinetoplastidea including Leishmania and Trypanosoma cruzi. Trypanosomes possess two canonical RNA poly (A) polymerases (PAPs) termed PAP1 and PAP2. PAP1 is encoded by one of the only two genes harboring cis-spliced introns in this organism, and its function is currently unknown. In trypanosomes, all mRNAs, and non-coding RNAs such as small nucleolar RNAs (snoRNAs) and long non-coding RNAs (lncRNAs), undergo trans-splicing and polyadenylation. Here, we show that the function of PAP1, which is located in the nucleus, is to polyadenylate non-coding RNAs, which undergo trans-splicing and polyadenylation. Major substrates of PAP1 are the snoRNAs and lncRNAs. Under the silencing of either PAP1 or PAP2, the level of snoRNAs is reduced. The dual polyadenylation of snoRNA intermediates is carried out by both PAP2 and PAP1 and requires the factors essential for the polyadenylation of mRNAs. The dual polyadenylation of the precursor snoRNAs by PAPs may function to recruit the machinery essential for snoRNA processing.
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Affiliation(s)
- Vaibhav Chikne
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sachin Kumar Gupta
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Shanmugha Rajan K
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Hiba Waldman Ben-Asher
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Liat Kolet
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Nasreen Hag Yahia
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Elisabetta Ullu
- Department of Epidemiology and Microbial Diseases, Yale School of Public Health, New Haven, CT 06536, USA
| | - Nikolay G Kolev
- Department of Epidemiology and Microbial Diseases, Yale School of Public Health, New Haven, CT 06536, USA
| | - Christian Tschudi
- Department of Internal Medicine, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536-0812, USA; Cell Biology, Yale University Medical School, 295 Congress Avenue, New Haven, CT 06536-0812, USA
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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24
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Conti G, Zavallo D, Venturuzzi AL, Rodriguez MC, Crespi M, Asurmendi S. TMV induces RNA decay pathways to modulate gene silencing and disease symptoms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:73-84. [PMID: 27599263 DOI: 10.1111/tpj.13323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/23/2016] [Accepted: 08/31/2016] [Indexed: 06/06/2023]
Abstract
RNA decay pathways comprise a combination of RNA degradation mechanisms that are implicated in gene expression, development and defense responses in eukaryotes. These mechanisms are known as the RNA Quality Control or RQC pathways. In plants, another important RNA degradation mechanism is the post-transcriptional gene silencing (PTGS) mediated by small RNAs (siRNAs). Notably, the RQC pathway antagonizes PTGS by preventing the entry of dysfunctional mRNAs into the silencing pathway to avoid global degradation of mRNA by siRNAs. Viral transcripts must evade RNA degrading mechanisms, thus viruses encode PTGS suppressor proteins to counteract viral RNA silencing. Here, we demonstrate that tobacco plants infected with TMV and transgenic lines expressing TMV MP and CP (coat protein) proteins (which are not linked to the suppression of silencing) display increased transcriptional levels of RNA decay genes. These plants also showed accumulation of cytoplasmic RNA granules with altered structure, increased rates of RNA decay for transgenes and defective transgene PTGS amplification. Furthermore, knockdown of RRP41 or RRP43 RNA exosome components led to lower levels of TMV accumulation with milder symptoms after infection, several developmental defects and miRNA deregulation. Thus, we propose that TMV proteins induce RNA decay pathways (in particular exosome components) to impair antiviral PTGS and this defensive mechanism would constitute an additional counter-defense strategy that lead to disease symptoms.
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Affiliation(s)
- Gabriela Conti
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Hurlingham, Argentina
| | - Diego Zavallo
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
| | - Andrea L Venturuzzi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Hurlingham, Argentina
| | | | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, IPS2, CNRS, INRA, University Paris-Sud, Orsay, France
| | - Sebastian Asurmendi
- Instituto de Biotecnología, CICVyA, INTA, Hurlingham, Argentina
- CONICET, Hurlingham, Argentina
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25
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Yu X, Willmann MR, Anderson SJ, Gregory BD. Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis. THE PLANT CELL 2016; 28:2385-2397. [PMID: 27758893 PMCID: PMC5134982 DOI: 10.1105/tpc.16.00456] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/02/2016] [Accepted: 10/07/2016] [Indexed: 05/19/2023]
Abstract
RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5' end to the 3' end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of cotranslational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that cotranslational RNA decay is XRN4 dependent. Additionally, studies in plants lacking CAP BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap binding complex, reveal a role for this protein in cotranslational decay. In total, our results demonstrate the global prevalence and features of cotranslational RNA decay in a plant transcriptome.
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Affiliation(s)
- Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Matthew R Willmann
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Stephen J Anderson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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26
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Abstract
Spliceosomal snRNPs are complex particles that proceed through a fascinating maturation pathway. Several steps of this pathway are closely linked to nuclear non-membrane structures called Cajal bodies. In this review, I summarize the last 20 y of research in this field. I primarily focus on snRNP biogenesis, specifically on the steps that involve Cajal bodies. I also evaluate the contribution of the Cajal body in snRNP quality control and discuss the role of snRNPs in Cajal body formation.
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Affiliation(s)
- David Staněk
- a Institute of Molecular Genetics, Czech Academy of Sciences , Prague , Czech Republic
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27
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Vohhodina J, Harkin DP, Savage KI. Dual roles of DNA repair enzymes in RNA biology/post-transcriptional control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:604-19. [PMID: 27126972 DOI: 10.1002/wrna.1353] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/12/2022]
Abstract
Despite consistent research into the molecular principles of the DNA damage repair pathway for almost two decades, it has only recently been found that RNA metabolism is very tightly related to this pathway, and the two ancient biochemical mechanisms act in alliance to maintain cellular genomic integrity. The close links between these pathways are well exemplified by examining the base excision repair pathway, which is now well known for dual roles of many of its members in DNA repair and RNA surveillance, including APE1, SMUG1, and PARP1. With additional links between these pathways steadily emerging, this review aims to provide a summary of the emerging roles for DNA repair proteins in the post-transcriptional regulation of RNAs. WIREs RNA 2016, 7:604-619. doi: 10.1002/wrna.1353 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jekaterina Vohhodina
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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28
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Zhang X, He X, Liu C, Liu J, Hu Q, Pan T, Duan X, Liu B, Zhang Y, Chen J, Ma X, Zhang X, Luo H, Zhang H. IL-4 Inhibits the Biogenesis of an Epigenetically Suppressive PIWI-Interacting RNA To Upregulate CD1a Molecules on Monocytes/Dendritic Cells. THE JOURNAL OF IMMUNOLOGY 2016; 196:1591-603. [PMID: 26755820 DOI: 10.4049/jimmunol.1500805] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022]
Abstract
The discovery of PIWI-interacting RNAs (piRNAs) revealed the complexity of the RNA world. Although piRNAs were first deemed to be germline specific, substantial evidence shows their various roles in somatic cells; however, their function in highly differentiated immune cells remains elusive. In this study, by initially screening with a small RNA deep-sequencing analysis, we found that a piRNA, tRNA-Glu-derived piRNA [td-piR(Glu)], was expressed much more abundantly in human monocytes than in dendritic cells. By regulating the polymerase III activity, IL-4 potently decreased the biogenesis of tRNA-Glu and, subsequently, td-piR(Glu). Further, we revealed that the td-piR(Glu)/PIWIL4 complex recruited SETDB1, SUV39H1, and heterochromatin protein 1β to the CD1A promoter region and facilitated H3K9 methylation. As a result, the transcription of CD1A was significantly inhibited. Collectively, we demonstrated that a piRNA acted as the signal molecule for a cytokine to regulate the expression of an important membrane protein for lipid Ag presentation.
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Affiliation(s)
- Xue Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xin He
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Chao Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jun Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Qifei Hu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Ting Pan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiaobing Duan
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Bingfeng Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Yiwen Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jingliang Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xingru Ma
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xu Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Haihua Luo
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; and Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
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29
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Lv H, Zhu Y, Qiu Y, Niu L, Teng M, Li X. Structural analysis of Dis3l2, an exosome-independent exonuclease from Schizosaccharomyces pombe. ACTA ACUST UNITED AC 2015; 71:1284-94. [PMID: 26057668 DOI: 10.1107/s1399004715005805] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/23/2015] [Indexed: 01/04/2023]
Abstract
After deadenylation and decapping, cytoplasmic mRNA can be digested in two opposite directions: in the 5'-3' direction by Xrn1 or in the 3'-5' direction by the exosome complex. Recently, a novel 3'-5' RNA-decay pathway involving Dis3l2 has been described that differs from degradation by Xrn1 and the exosome. The product of the Schizosaccharomyces pombe gene SPAC2C4.07c was identified as a homologue of human Dis3l2. In this work, the 2.8 Å resolution X-ray crystal structure of S. pombe Dis3l2 (SpDis3l2) is reported, the conformation of which is obviously different from that in the homologous mouse Dis3l2-RNA complex. Fluorescence polarization assay experiments showed that RNB and S1 are the primary RNA-binding domains and that the CSDs (CSD1 and CSD2) play an indispensable role in the RNA-binding process of SpDis3l2. Taking the structure comparison and mutagenic experiments together, it can be inferred that the RNA-recognition pattern of SpDis3l2 resembles that of its mouse homologue rather than that of the Escherichia coli RNase II-RNA complex. Furthermore, a drastic conformation change could occur following the binding of the RNA substrate to SpDis3l2.
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Affiliation(s)
- Hui Lv
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yuwei Zhu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Yu Qiu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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30
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Weißbach S, Langer C, Puppe B, Nedeva T, Bach E, Kull M, Bargou R, Einsele H, Rosenwald A, Knop S, Leich E. The molecular spectrum and clinical impact of DIS3 mutations in multiple myeloma. Br J Haematol 2014; 169:57-70. [PMID: 25521164 DOI: 10.1111/bjh.13256] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/04/2014] [Indexed: 01/09/2023]
Abstract
Multiple myeloma (MM) is a plasma cell neoplasm that presents with a major biological and clinical heterogeneity. We here investigated the spectrum of clonal and subclonal mutations of DIS3, an active part of the exosome complex, that may play a role in the development or progression of MM. The whole coding sequence of DIS3 was subjected to deep sequencing in 81 uniformly-treated MM patients and 12 MM cell lines and the overall occurrence of DIS3 mutations as well as the presence of DIS3 mutations in minor and major subclones were correlated with cytogenetic alterations and clinical parameters. Our study identified DIS3 mutations in 9/81 patients that were associated with 13q14 deletions and IGH translocations on the cytogenetic level. Specifically, we detected seven novel somatic DIS3 single nucleotide variants (SNVs) and defined three hot spot mutations within the RNB domain. Lastly, we found a trend towards a shorter median overall survival for patients with DIS3 mutations, and patients carrying DIS3 mutations in minor subclones of their tumours showed a significantly worse response to therapy compared to patients with DIS3 mutations in the major subclone.
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Affiliation(s)
- Susann Weißbach
- Institute of Pathology, University of Würzburg, Comprehensive Cancer Center Mainfranken (CCC MF), Würzburg, Germany
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Taylor LL, Jackson RN, Rexhepaj M, King AK, Lott LK, van Hoof A, Johnson SJ. The Mtr4 ratchet helix and arch domain both function to promote RNA unwinding. Nucleic Acids Res 2014; 42:13861-72. [PMID: 25414331 PMCID: PMC4267639 DOI: 10.1093/nar/gku1208] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Mtr4 is a conserved Ski2-like RNA helicase and a subunit of the TRAMP complex that activates exosome-mediated 3′-5′ turnover in nuclear RNA surveillance and processing pathways. Prominent features of the Mtr4 structure include a four-domain ring-like helicase core and a large arch domain that spans the core. The ‘ratchet helix’ is positioned to interact with RNA substrates as they move through the helicase. However, the contribution of the ratchet helix in Mtr4 activity is poorly understood. Here we show that strict conservation along the ratchet helix is particularly extensive for Ski2-like RNA helicases compared to related helicases. Mutation of residues along the ratchet helix alters in vitro activity in Mtr4 and TRAMP and causes slow growth phenotypes in vivo. We also identify a residue on the ratchet helix that influences Mtr4 affinity for polyadenylated substrates. Previous work indicated that deletion of the arch domain has minimal effect on Mtr4 unwinding activity. We now show that combining the arch deletion with ratchet helix mutations abolishes helicase activity and produces a lethal in vivo phenotype. These studies demonstrate that the ratchet helix modulates helicase activity and suggest that the arch domain plays a previously unrecognized role in unwinding substrates.
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Affiliation(s)
- Lacy L Taylor
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Ryan N Jackson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Megi Rexhepaj
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Alejandra Klauer King
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Lindsey K Lott
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center-Houston, Houston, TX 77030, USA
| | - Sean J Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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McIver SC, Kang YA, DeVilbiss AW, O'Driscoll CA, Ouellette JN, Pope NJ, Camprecios G, Chang CJ, Yang D, Bouhassira EE, Ghaffari S, Bresnick EH. The exosome complex establishes a barricade to erythroid maturation. Blood 2014; 124:2285-97. [PMID: 25115889 PMCID: PMC4183988 DOI: 10.1182/blood-2014-04-571083] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/25/2014] [Indexed: 12/28/2022] Open
Abstract
Complex genetic networks control hematopoietic stem cell differentiation into progenitors that give rise to billions of erythrocytes daily. Previously, we described a role for the master regulator of erythropoiesis, GATA-1, in inducing genes encoding components of the autophagy machinery. In this context, the Forkhead transcription factor, Foxo3, amplified GATA-1-mediated transcriptional activation. To determine the scope of the GATA-1/Foxo3 cooperativity, and to develop functional insights, we analyzed the GATA-1/Foxo3-dependent transcriptome in erythroid cells. GATA-1/Foxo3 repressed expression of Exosc8, a pivotal component of the exosome complex, which mediates RNA surveillance and epigenetic regulation. Strikingly, downregulating Exosc8, or additional exosome complex components, in primary erythroid precursor cells induced erythroid cell maturation. Our results demonstrate a new mode of controlling erythropoiesis in which multiple components of the exosome complex are endogenous suppressors of the erythroid developmental program.
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Affiliation(s)
- Skye C McIver
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Yoon-A Kang
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Andrew W DeVilbiss
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Chelsea A O'Driscoll
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Jonathan N Ouellette
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Nathaniel J Pope
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Genis Camprecios
- Department of Developmental and Regenerative Biology, Mt. Sinai School of Medicine, New York, NY
| | - Chan-Jung Chang
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY; and
| | - David Yang
- Department of Pathology, University of Wisconsin School of Medicine and Public Health, Madison WI
| | - Eric E Bouhassira
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY; and
| | - Saghi Ghaffari
- Department of Developmental and Regenerative Biology, Mt. Sinai School of Medicine, New York, NY
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI
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Parikh AP, Curtis RE, Kuhn I, Becker-Weimann S, Bissell M, Xing EP, Wu W. Network analysis of breast cancer progression and reversal using a tree-evolving network algorithm. PLoS Comput Biol 2014; 10:e1003713. [PMID: 25057922 PMCID: PMC4109850 DOI: 10.1371/journal.pcbi.1003713] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 04/10/2014] [Indexed: 11/19/2022] Open
Abstract
The HMT3522 progression series of human breast cells have been used to discover how tissue architecture, microenvironment and signaling molecules affect breast cell growth and behaviors. However, much remains to be elucidated about malignant and phenotypic reversion behaviors of the HMT3522-T4-2 cells of this series. We employed a "pan-cell-state" strategy, and analyzed jointly microarray profiles obtained from different state-specific cell populations from this progression and reversion model of the breast cells using a tree-lineage multi-network inference algorithm, Treegl. We found that different breast cell states contain distinct gene networks. The network specific to non-malignant HMT3522-S1 cells is dominated by genes involved in normal processes, whereas the T4-2-specific network is enriched with cancer-related genes. The networks specific to various conditions of the reverted T4-2 cells are enriched with pathways suggestive of compensatory effects, consistent with clinical data showing patient resistance to anticancer drugs. We validated the findings using an external dataset, and showed that aberrant expression values of certain hubs in the identified networks are associated with poor clinical outcomes. Thus, analysis of various reversion conditions (including non-reverted) of HMT3522 cells using Treegl can be a good model system to study drug effects on breast cancer.
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Affiliation(s)
- Ankur P. Parikh
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Ross E. Curtis
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Irene Kuhn
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Sabine Becker-Weimann
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Mina Bissell
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Eric P. Xing
- Machine Learning Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (EPX); (WW)
| | - Wei Wu
- Lane Center for Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (EPX); (WW)
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Bacikova V, Pasulka J, Kubicek K, Stefl R. Structure and semi-sequence-specific RNA binding of Nrd1. Nucleic Acids Res 2014; 42:8024-38. [PMID: 24860164 PMCID: PMC4081072 DOI: 10.1093/nar/gku446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, the Nrd1-dependent termination and processing pathways play an important role in surveillance and processing of non-coding ribonucleic acids (RNAs). The termination and subsequent processing is dependent on the Nrd1 complex consisting of two RNA-binding proteins Nrd1 and Nab3 and Sen1 helicase. It is established that Nrd1 and Nab3 cooperatively recognize specific termination elements within nascent RNA, GUA[A/G] and UCUU[G], respectively. Interestingly, some transcripts do not require GUA[A/G] motif for transcription termination in vivo and binding in vitro, suggesting the existence of alternative Nrd1-binding motifs. Here we studied the structure and RNA-binding properties of Nrd1 using nuclear magnetic resonance (NMR), fluorescence anisotropy and phenotypic analyses in vivo. We determined the solution structure of a two-domain RNA-binding fragment of Nrd1, formed by an RNA-recognition motif and helix–loop bundle. NMR and fluorescence data show that not only GUA[A/G] but also several other G-rich and AU-rich motifs are able to bind Nrd1 with affinity in a low micromolar range. The broad substrate specificity is achieved by adaptable interaction surfaces of the RNA-recognition motif and helix–loop bundle domains that sandwich the RNA substrates. Our findings have implication for the role of Nrd1 in termination and processing of many non-coding RNAs arising from bidirectional pervasive transcription.
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Affiliation(s)
- Veronika Bacikova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Josef Pasulka
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 62500, Czech Republic
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Inada T, Makino S. Novel roles of the multi-functional CCR4-NOT complex in post-transcriptional regulation. Front Genet 2014; 5:135. [PMID: 24904636 PMCID: PMC4033010 DOI: 10.3389/fgene.2014.00135] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/25/2014] [Indexed: 11/30/2022] Open
Abstract
The CCR4-NOT complex is a highly conserved specific gene silencer that also serves more general post-transcriptional functions. Specific regulatory proteins including the miRNA-induced silencing complex and its associated proteins, bind to 3’-UTR elements of mRNA and recruit the CCR4-NOT complex thereby promoting poly(A) shortening and repressing translation and/or mRNA degradation. Recent studies have shown that the CCR4-NOT complex that is tethered to mRNA by such regulator(s) represses translation and facilitates mRNA decay independent of a poly(A) tail and its shortening. In addition to deadenylase activity, the CCR4-NOT complex also has an E3 ubiquitin ligase activity and is involved in a novel protein quality control system, i.e., co-translational proteasomal-degradation of aberrant proteins. In this review, we describe recent progress in elucidation of novel roles of the multi-functional complex CCR4-NOT in post-transcriptional regulation.
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Affiliation(s)
- Toshifumi Inada
- Laboratory of Gene Regulation, Graduate School of Pharmaceutical Sciences, Tohoku University Sendai, Japan
| | - Shiho Makino
- Laboratory of Gene Regulation, Graduate School of Pharmaceutical Sciences, Tohoku University Sendai, Japan
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36
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Liu H, Luo M, Wen JK. mRNA stability in the nucleus. J Zhejiang Univ Sci B 2014; 15:444-54. [PMID: 24793762 PMCID: PMC4076601 DOI: 10.1631/jzus.b1400088] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 04/11/2014] [Indexed: 01/15/2023]
Abstract
Eukaryotic gene expression is controlled by different levels of biological events, such as transcription factors regulating the timing and strength of transcripts production, alteration of transcription rate by RNA processing, and mRNA stability during RNA processing and translation. RNAs, especially mRNAs, are relatively vulnerable molecules in living cells for ribonucleases (RNases). The maintenance of quality and quantity of transcripts is a key issue for many biological processes. Extensive studies draw the conclusion that the stability of RNAs is dedicated-regulated, occurring co- and post-transcriptionally, and translation-coupled as well, either in the nucleus or cytoplasm. Recently, RNA stability in the nucleus has aroused much research interest, especially the stability of newly-made transcripts. In this article, we summarize recent progresses on mRNA stability in the nucleus, especially focusing on quality control of newly-made RNA by RNA polymerase II in eukaryotes.
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Affiliation(s)
- Han Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Min Luo
- Chongqing Institute of Tuberculosis Prevention and Treatment, Chongqing 400050, China
| | - Ji-kai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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37
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Jobert L, Nilsen H. Regulatory mechanisms of RNA function: emerging roles of DNA repair enzymes. Cell Mol Life Sci 2014; 71:2451-65. [PMID: 24496644 PMCID: PMC4055861 DOI: 10.1007/s00018-014-1562-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/05/2014] [Accepted: 01/10/2014] [Indexed: 12/13/2022]
Abstract
The acquisition of an appropriate set of chemical modifications is required in order to establish correct structure of RNA molecules, and essential for their function. Modification of RNA bases affects RNA maturation, RNA processing, RNA quality control, and protein translation. Some RNA modifications are directly involved in the regulation of these processes. RNA epigenetics is emerging as a mechanism to achieve dynamic regulation of RNA function. Other modifications may prevent or be a signal for degradation. All types of RNA species are subject to processing or degradation, and numerous cellular mechanisms are involved. Unexpectedly, several studies during the last decade have established a connection between DNA and RNA surveillance mechanisms in eukaryotes. Several proteins that respond to DNA damage, either to process or to signal the presence of damaged DNA, have been shown to participate in RNA quality control, turnover or processing. Some enzymes that repair DNA damage may also process modified RNA substrates. In this review, we give an overview of the DNA repair proteins that function in RNA metabolism. We also discuss the roles of two base excision repair enzymes, SMUG1 and APE1, in RNA quality control.
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Affiliation(s)
- Laure Jobert
- Division of Medicine, Department of Clinical Molecular Biology, Akershus University Hospital, Nordbyhagen, 1478 Lørenskog, Norway
| | - Hilde Nilsen
- Division of Medicine, Department of Clinical Molecular Biology, Akershus University Hospital, Nordbyhagen, 1478 Lørenskog, Norway
- Department of Clinical Molecular Biology, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Blindern, P.O.Box 1171, 0318 Oslo, Norway
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Halbach F, Reichelt P, Rode M, Conti E. The yeast ski complex: crystal structure and RNA channeling to the exosome complex. Cell 2013; 154:814-26. [PMID: 23953113 DOI: 10.1016/j.cell.2013.07.017] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 05/13/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference. Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry. The crystal structure of an S. cerevisiae 370 kDa core complex shows that Ski3 forms an array of 33 TPR motifs organized in N-terminal and C-terminal arms. The C-terminal arm of Ski3 and the two Ski8 subunits position the helicase core of Ski2 centrally within the complex, enhancing RNA binding. The Ski3 N-terminal arm and the Ski2 insertion domain allosterically modulate the ATPase and helicase activities of the complex. Biochemical data suggest that the Ski complex can thread RNAs directly to the exosome, coupling the helicase and the exoribonuclease through a continuous RNA channel. Finally, we identify a Ski8-binding motif common to Ski3 and Spo11, rationalizing the moonlighting properties of Ski8 in mRNA decay and meiosis.
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Affiliation(s)
- Felix Halbach
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried/Munich, Germany
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Morris MR, Astuti D, Maher ER. Perlman syndrome: overgrowth, Wilms tumor predisposition and DIS3L2. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:106-13. [PMID: 23613427 DOI: 10.1002/ajmg.c.31358] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Perlman syndrome is a rare autosomal recessively inherited congenital overgrowth syndrome characterized by polyhydramnios, macrosomia, characteristic facial dysmorphology, renal dysplasia and nephroblastomatosis and multiple congenital anomalies. Perlman syndrome is associated with high neonatal mortality and, survivors have developmental delay and a high risk of Wilms tumor. Recently a Perlman syndrome locus was mapped to chromosome 2q37 and homozygous or compound heterozygous mutations were characterized in DIS3L2. The DIS3L2 gene product has ribonuclease activity and homology to the DIS3 component of the RNA exosome. It has been postulated that the clinical features of Perlman syndrome result from disordered RNA metabolism and, though the precise targets of DIS3L2 have yet to be characterized, in cellular models DIS3L2 knockdown is associated with abnormalities of cell growth and division.
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Zhuang Y, Zhang H, Lin S. Polyadenylation of 18S rRNA in algae(1). JOURNAL OF PHYCOLOGY 2013; 49:570-579. [PMID: 27007045 DOI: 10.1111/jpy.12068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 12/23/2012] [Indexed: 06/05/2023]
Abstract
Polyadenylation is best known for occurring to mRNA of eukaryotes transcribed by RNA polymerase II to stabilize mRNA molecules and promote their translation. rRNAs transcribed by RNA polymerase I or III are typically believed not to be polyadenylated. However, there is increasing evidence that polyadenylation occurs to nucleus-encoded rRNAs as part of the RNA degradation pathway. To examine whether the same polyadenylation-assisted degradation pathway occurs in algae, we surveyed representative species of algae including diatoms, chlorophytes, dinoflagellates and pelagophytes using oligo (dT)-primed reversed transcription PCR (RT-PCR). In all the algal species examined, truncated 18S rRNA or its precursor molecules with homo- or hetero-polymeric poly(A) tails were detected. Mining existing algal expressed sequence tag (EST) data revealed polyadenylated truncated 18S rRNA in four additional phyla of algae. rRNA polyadenylation occurred at various internal positions along the 18S rRNA and its precursor sequences. Moreover, putative homologs of noncanonical poly(A) polymerase (ncPAP) Trf4p, which is responsible for polyadenylating nuclear-encoded RNA and targeting it for degradation, were detected from the genomes and transcriptomes of five phyla of algae. Our results suggest that polyadenylation-assisted RNA degradation mechanism widely exists in algae, particularly for the nucleus-encoded rRNA and its precursors.
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Affiliation(s)
- Yunyun Zhuang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
- Marine Biodiversity and Global Change Research Center and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
- Marine Biodiversity and Global Change Research Center and State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361005, China
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Sugiyama T, Wanatabe N, Kitahata E, Tani T, Sugioka-Sugiyama R. Red5 and three nuclear pore components are essential for efficient suppression of specific mRNAs during vegetative growth of fission yeast. Nucleic Acids Res 2013; 41:6674-86. [PMID: 23658229 PMCID: PMC3711435 DOI: 10.1093/nar/gkt363] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Zinc-finger domains are found in many nucleic acid-binding proteins in both prokaryotes and eukaryotes. Proteins carrying zinc-finger domains have important roles in various nuclear transactions, including transcription, mRNA processing and mRNA export; however, for many individual zinc-finger proteins in eukaryotes, the exact function of the protein is not fully understood. Here, we report that Red5 is involved in efficient suppression of specific mRNAs during vegetative growth of Schizosaccharomyces pombe. Red5, which contains five C3H1-type zinc-finger domains, localizes to the nucleus where it forms discrete dots. A red5 point mutation, red5-2, results in the upregulation of specific meiotic mRNAs in vegetative mutant red5-2 cells; northern blot data indicated that these meiotic mRNAs in red5-2 cells have elongated poly(A) tails. RNA-fluorescence in situ hybridization results demonstrate that poly(A)+ RNA species accumulate in the nucleolar regions of red5-deficient cells. Moreover, Red5 genetically interacts with several mRNA export factors. Unexpectedly, three components of the nuclear pore complex also suppress a specific set of meiotic mRNAs. These results indicate that Red5 function is important to meiotic mRNA degradation; they also suggest possible connections among selective mRNA decay, mRNA export and the nuclear pore complex in vegetative fission yeast.
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42
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Vilfan ID, Tsai YC, Clark TA, Wegener J, Dai Q, Yi C, Pan T, Turner SW, Korlach J. Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology 2013; 11:8. [PMID: 23552456 PMCID: PMC3623877 DOI: 10.1186/1477-3155-11-8] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 01/25/2013] [Indexed: 01/05/2023] Open
Abstract
Background Zero-mode waveguides (ZMWs) are photonic nanostructures that create highly confined optical observation volumes, thereby allowing single-molecule-resolved biophysical studies at relatively high concentrations of fluorescent molecules. This principle has been successfully applied in single-molecule, real-time (SMRT®) DNA sequencing for the detection of DNA sequences and DNA base modifications. In contrast, RNA sequencing methods cannot provide sequence and RNA base modifications concurrently as they rely on complementary DNA (cDNA) synthesis by reverse transcription followed by sequencing of cDNA. Thus, information on RNA modifications is lost during the process of cDNA synthesis. Results Here we describe an application of SMRT technology to follow the activity of reverse transcriptase enzymes synthesizing cDNA on thousands of single RNA templates simultaneously in real time with single nucleotide turnover resolution using arrays of ZMWs. This method thereby obtains information from the RNA template directly. The analysis of the kinetics of the reverse transcriptase can be used to identify RNA base modifications, shown by example for N6-methyladenine (m6A) in oligonucleotides and in a specific mRNA extracted from total cellular mRNA. Furthermore, the real-time reverse transcriptase dynamics informs about RNA secondary structure and its rearrangements, as demonstrated on a ribosomal RNA and an mRNA template. Conclusions Our results highlight the feasibility of studying RNA modifications and RNA structural rearrangements in ZMWs in real time. In addition, they suggest that technology can be developed for direct RNA sequencing provided that the reverse transcriptase is optimized to resolve homonucleotide stretches in RNA.
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Abstract
Most RNAs in eukaryotic cells are produced as precursors that undergo processing at the 3' and/or 5' end to generate the mature transcript. In addition, many transcripts are degraded not only as part of normal recycling, but also when recognized as aberrant by the RNA surveillance machinery. The exosome, a conserved multiprotein complex containing two nucleases, is involved in both the 3' processing and the turnover of many RNAs in the cell. A series of factors, including the TRAMP (Trf4-Air2-Mtr4 polyadenylation) complex, Mpp6 and Rrp47, help to define the targets to be processed and/or degraded and assist in exosome function. The majority of the data on the exosome and RNA maturation/decay have been derived from work performed in the yeast Saccharomyces cerevisiae. In the present paper, we provide an overview of the exosome and its role in RNA processing/degradation and discuss important new insights into exosome composition and function in human cells.
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Abstract
In order to control and/or enhance the specificity and activity of nuclear surveillance and degradation, exosomes cooperate with the polyadenylation complex called TRAMP. Two forms of TRAMP operate in budding yeast, TRAMP4 and TRAMP5. They oligoadenylate defective or precursor forms of RNAs and promote trimming or complete degradation by exosomes. TRAMPs target a wide variety of nuclear transcripts. The known substrates include the noncoding RNAs originating from pervasive transcription from diverse parts of the yeast genome. Although TRAMP and exosomes can be triggered to a subset of their targets via the RNA-binding complex Nrd1, it is still not completely understood how TRAMP recognizes other aberrant RNAs. The existence of TRAMP-like complexes in other organisms indicates the importance of nuclear surveillance for general cell biology. In this chapter, we review the current understanding of TRAMP function and substrate repertoire. We discuss the advances in TRAMP biochemistry with respect to its catalytic activities and RNA recognition. Finally, we speculate about the possible mechanisms by which TRAMP activates exosomes.
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Affiliation(s)
- Peter Holub
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Stepanka Vanacova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
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Lee G, Bratkowski MA, Ding F, Ke A, Ha T. Elastic coupling between RNA degradation and unwinding by an exoribonuclease. Science 2012; 336:1726-9. [PMID: 22745434 DOI: 10.1126/science.1216848] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Rrp44 (Dis3) is a key catalytic subunit of the yeast exosome complex and can processively digest structured RNA one nucleotide at a time in the 3' to 5' direction. Its motor function is powered by the energy released from the hydrolytic nuclease reaction instead of adenosine triphosphate hydrolysis as in conventional helicases. Single-molecule fluorescence analysis revealed that instead of unwinding RNA in single base pair steps, Rrp44 accumulates the energy released by multiple single nucleotide step hydrolysis reactions until about four base pairs are unwound in a burst. Kinetic analyses showed that RNA unwinding, not cleavage or strand release, determines the overall RNA degradation rate and that the unwinding step size is determined by the nonlinear elasticity of the Rrp44/RNA complex, but not by duplex stability.
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Affiliation(s)
- Gwangrog Lee
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
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Nag A, Steitz JA. Tri-snRNP-associated proteins interact with subunits of the TRAMP and nuclear exosome complexes, linking RNA decay and pre-mRNA splicing. RNA Biol 2012; 9:334-42. [PMID: 22336707 PMCID: PMC3384585 DOI: 10.4161/rna.19431] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Nuclear RNA decay factors are involved in many different pathways including rRNA processing, snRNA and snoRNA biogenesis, pre-mRNA processing, and the rapid decay of cryptic intergenic transcripts. In contrast to its yeast counterpart, the mammalian nuclear decay machinery is largely uncharacterized. Here we report interactions of several putative components of the human nuclear RNA decay machinery, including the TRAMP complex protein Mtr4 and the nuclear exosome constituents PM/Scl-100 and PM/Scl-75, with components of the U4/U6.U5 tri-snRNP complex required for pre-mRNA splicing. The tri-snRNP component Prp31 interacts indirectly with Mtr4 and PM/Scl-100 in a manner that is dependent on the phosphorylation sites in the middle of the protein, while Prp3 and Prp4 interact with the nuclear decay complex independent of Prp31. Together our results suggest recruitment of the nuclear decay machinery to the spliceosome to ensure production of properly spliced mRNA.
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Affiliation(s)
- Anita Nag
- Department of Molecular Biophysics and Biochemistry-MB&B, Howard Hughes Medical Institute-HHMI, Yale University School of Medicine, Boyer Center for Molecular Medicine, New Haven, CT, USA
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Stepanov G, Semenov D, Kuligina E, Koval O, Rabinov I, Kit Y, Richter V. Analogues of Artificial Human Box C/D Small Nucleolar RNA As Regulators of Alternative Splicing
of a pre-mRNA Target. Acta Naturae 2012; 4:32-41. [PMID: 22708061 PMCID: PMC3372990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Small nucleolar RNAs (snoRNAs) play a key role in ribosomal RNA (rRNA) biogenesis. Box C/D snoRNAs guide the site-specific 2'-O-ribose methylation of nucleotides in rRNAs and small nuclear RNAs (snRNAs). A number of box C/D snoRNAs and their fragments have recently been reported to regulate post-transcriptional modifications and the alternative splicing of pre-mRNA. Artificial analogues of U24 snoRNAs directed to nucleotides in 28S and 18S rRNAs, as well as pre-mRNAs and mature mRNAs of human heat shock cognate protein (hsc70), were designed and synthesized in this study. It was found that after the transfection of MCF-7 human cells with artificial box C/D RNAs in complex with lipofectamine, snoRNA analogues penetrated into cells and accumulated in the cytoplasm and nucleus. It was demonstrated that the transfection of cultured human cells with artificial box C/D snoRNA targeted to pre-mRNAs induce partial splicing impairments. It was found that transfection with artificial snoRNAs directed to 18S and 28S rRNA nucleotides, significant for ribosome functioning, induce a decrease in MCF-7 cell viability.
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Affiliation(s)
- G.A. Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch,
Russian Academy of Sciences
| | - D.V. Semenov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch,
Russian Academy of Sciences
| | - E.V. Kuligina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch,
Russian Academy of Sciences
| | - O.A. Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch,
Russian Academy of Sciences
| | - I.V. Rabinov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch,
Russian Academy of Sciences
| | - Y.Y. Kit
- Institute of Cell Biology, National Academy of Sciences of Ukraine
| | - V.A. Richter
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch,
Russian Academy of Sciences
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48
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Collart MA, Panasenko OO. The Ccr4--not complex. Gene 2011; 492:42-53. [PMID: 22027279 DOI: 10.1016/j.gene.2011.09.033] [Citation(s) in RCA: 226] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 09/06/2011] [Accepted: 09/29/2011] [Indexed: 12/11/2022]
Abstract
The Ccr4-Not complex is a unique, essential and conserved multi-subunit complex that acts at the level of many different cellular functions to regulate gene expression. Two enzymatic activities, namely ubiquitination and deadenylation, are provided by different subunits of the complex. However, studies over the last decade have demonstrated a tantalizing multi-functionality of this complex that extends well beyond its identified enzymatic activities. Most of our initial knowledge about the Ccr4-Not complex stemmed from studies in yeast, but an increasing number of reports on this complex in other species are emerging. In this review we will discuss the structure and composition of the complex, and describe the different cellular functions with which the Ccr4-Not complex has been connected in different organisms. Finally, based upon our current state of knowledge, we will propose a model to explain how one complex can provide such multi-functionality. This model suggests that the Ccr4-Not complex might function as a "chaperone platform".
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Affiliation(s)
- Martine A Collart
- Dpt Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1 rue Michel Servet, 1211 Geneva 4, Switzerland.
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Fiesel FC, Kahle PJ. TDP-43 and FUS/TLS: cellular functions and implications for neurodegeneration. FEBS J 2011; 278:3550-68. [PMID: 21777389 DOI: 10.1111/j.1742-4658.2011.08258.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
TDP-43 (transactive response binding protein of 43 kDa) and FUS (fused in sarcoma) comprise the neuropathological protein aggregates of distinct subtypes of the neurodegenerative diseases frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Moreover, the genes encoding TDP-43 and FUS are linked to these diseases. Both TDP-43 and FUS contain RNA binding motifs, and specific targets are being identified. Potential actions of TDP-43 and FUS include transcriptional regulation, mRNA processing and micro RNA biogenesis. These activities are probably modulated by interacting proteins in cell type specific manners as well as distinctly within the nucleus and cytosol, as both proteins shuttle between these compartments. In this minireview the specific functions of TDP-43 and FUS are described and discussed in the context of how TDP-43 and FUS may contribute to the pathogenesis of frontotemporal lobar degeneration and amyotrophic lateral sclerosis.
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Affiliation(s)
- Fabienne C Fiesel
- Department of Neurodegeneration, Faculty of Medicine, University of Tuebingen, Tuebingen, Germany.
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50
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Perna D, Fagà G, Verrecchia A, Gorski MM, Barozzi I, Narang V, Khng J, Lim KC, Sung WK, Sanges R, Stupka E, Oskarsson T, Trumpp A, Wei CL, Müller H, Amati B. Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts. Oncogene 2011; 31:1695-709. [PMID: 21860422 PMCID: PMC3324106 DOI: 10.1038/onc.2011.359] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The transition from quiescence to proliferation is a key regulatory step that can be induced by serum stimulation in cultured fibroblasts. The transcription factor Myc is directly induced by serum mitogens and drives a secondary gene expression program that remains largely unknown. Using mRNA profiling, we identify close to 300 Myc-dependent serum response (MDSR) genes, which are induced by serum in a Myc-dependent manner in mouse fibroblasts. Mapping of genomic Myc-binding sites by ChIP-seq technology revealed that most MDSR genes were directly targeted by Myc, but represented a minor fraction (5.5%) of all Myc-bound promoters (which were 22.4% of all promoters). Other target loci were either induced by serum in a Myc-independent manner, were not significantly regulated or were negatively regulated. MDSR gene products were involved in a variety of processes, including nucleotide biosynthesis, ribosome biogenesis, DNA replication and RNA control. Of the 29 MDSR genes targeted by RNA interference, three showed a requirement for cell-cycle entry upon serum stimulation and 11 for long-term proliferation and/or survival. Hence, proper coordination of key regulatory and biosynthetic pathways following mitogenic stimulation relies upon the concerted regulation of multiple Myc-dependent genes.
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Affiliation(s)
- D Perna
- Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, Milan, Italy
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