51
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Puno MR, Lima CD. Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex. Cell 2022; 185:2132-2147.e26. [PMID: 35688134 PMCID: PMC9210550 DOI: 10.1016/j.cell.2022.04.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/04/2022] [Accepted: 04/08/2022] [Indexed: 02/07/2023]
Abstract
RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined cryogenic electron microscopy structures of human nuclear exosome targeting (NEXT) complexes bound to RNA that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 surveying sequences upstream of the 3' end to facilitate RNA capture by MTR4. ZCCHC8 obscures MTR4 surfaces important for RNA binding and extrusion as well as MPP6-dependent recruitment and docking onto the RNA exosome core, interactions that contribute to RNA surveillance by coordinating RNA capture, translocation, and extrusion from the helicase to the exosome for decay.
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Affiliation(s)
- M Rhyan Puno
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA.
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52
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Chen C, Gao Y, Liu W, Gao S. Epigenetic regulation of cell fate transition: learning from early embryo development and somatic cell reprogramming. Biol Reprod 2022; 107:183-195. [PMID: 35526125 PMCID: PMC9310515 DOI: 10.1093/biolre/ioac087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/29/2022] [Accepted: 04/25/2022] [Indexed: 11/12/2022] Open
Abstract
Epigenetic regulations play a central role in governing the embryo development and somatic cell reprogramming. Taking advantage of recent advances in low-input sequencing techniques, researchers have uncovered a comprehensive view of the epigenetic landscape during rapid transcriptome transitions involved in the cell fate commitment. The well-organized epigenetic reprogramming also highlights the essential roles of specific epigenetic regulators to support efficient regulation of transcription activity and chromatin remodeling. This review briefly introduces the recent progress in the molecular dynamics and regulation mechanisms implicated in mouse early embryo development and somatic cell reprograming, as well as the multi-omics regulatory mechanisms of totipotency mediated by several key factors, which provide valuable resources for further investigations on the complicated regulatory network in essential biological events.
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Affiliation(s)
- Chuan Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yawei Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Wenqiang Liu
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China.,Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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53
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Faulkner GJ. HUSH, retrotransposon RNA, you're NEXT to decay. Mol Cell 2022; 82:1610-1612. [PMID: 35523126 DOI: 10.1016/j.molcel.2022.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Garland et al. (2022) discover a physical and functional connection between the HUSH silencing complex and the NEXT nuclear RNA decay complex in mouse embryonic stem cells and conclude HUSH recruits NEXT to degrade prematurely terminated retrotransposon RNAs.
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Affiliation(s)
- Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, Woolloongabba, QLD, 4102, Australia; Queensland Brain Institute, University of Queensland, St. Lucia, QLD, 4067, Australia.
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54
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Gerlach P, Garland W, Lingaraju M, Salerno-Kochan A, Bonneau F, Basquin J, Jensen TH, Conti E. Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome. Mol Cell 2022; 82:2505-2518.e7. [PMID: 35688157 PMCID: PMC9278407 DOI: 10.1016/j.molcel.2022.04.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/07/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting (NEXT) complex plays a central role in directing non-functional transcripts to exosome-mediated degradation, but the structural and molecular mechanisms remain enigmatic. Here, we elucidated the architecture of the human NEXT complex, showing that it exists as a dimer of MTR4-ZCCHC8-RBM7 heterotrimers. Dimerization preconfigures the major MTR4-binding region of ZCCHC8 and arranges the two MTR4 helicases opposite to each other, with each protomer able to function on many types of RNAs. In the inactive state of the complex, the 3′ end of an RNA substrate is enclosed in the MTR4 helicase channel by a ZCCHC8 C-terminal gatekeeping domain. The architecture of a NEXT-exosome assembly points to the molecular and regulatory mechanisms with which the NEXT complex guides RNA substrates to the exosome. NEXT homodimerizes through two intertwined ZCCHC8 subunits ZCCHC8 binds MTR4 with both constitutive and regulatory interactions Stable MTR4 arch interactions orient the two helicases in opposite directions Regulatory interactions at the MTR4 helicase domain guide RNA to the exosome
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Affiliation(s)
- Piotr Gerlach
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany.
| | - William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Mahesh Lingaraju
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Anna Salerno-Kochan
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Jérôme Basquin
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, Munich, Germany.
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55
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Garland W, Müller I, Wu M, Schmid M, Imamura K, Rib L, Sandelin A, Helin K, Jensen TH. Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression. Mol Cell 2022; 82:1691-1707.e8. [PMID: 35349793 PMCID: PMC9433625 DOI: 10.1016/j.molcel.2022.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) are widespread genetic parasites known to be kept under tight transcriptional control. Here, we describe a functional connection between the mouse-orthologous “nuclear exosome targeting” (NEXT) and “human silencing hub” (HUSH) complexes, involved in nuclear RNA decay and the epigenetic silencing of TEs, respectively. Knocking out the NEXT component ZCCHC8 in embryonic stem cells results in elevated TE RNA levels. We identify a physical interaction between ZCCHC8 and the MPP8 protein of HUSH and establish that HUSH recruits NEXT to chromatin at MPP8-bound TE loci. However, while NEXT and HUSH both dampen TE RNA expression, their activities predominantly affect shorter non-polyadenylated and full-length polyadenylated transcripts, respectively. Indeed, our data suggest that the repressive action of HUSH promotes a condition favoring NEXT RNA decay activity. In this way, transcriptional and post-transcriptional machineries synergize to suppress the genotoxic potential of TE RNAs. Garland et al. report a physical and functional connection between the NEXT complex, involved in RNA decay, and the HUSH complex, involved in chromatin regulation. Together, NEXT and HUSH cooperate to control transposable element (TE) RNA expression in embryonic stem cells, suppressing pA− and pA+ transcripts, respectively.
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Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iris Müller
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mengjun Wu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Leonor Rib
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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56
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Liu X, Guo Z, Han J, Peng B, Zhang B, Li H, Hu X, David CJ, Chen M. The PAF1 complex promotes 3' processing of pervasive transcripts. Cell Rep 2022; 38:110519. [PMID: 35294889 DOI: 10.1016/j.celrep.2022.110519] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/06/2022] [Accepted: 02/18/2022] [Indexed: 11/03/2022] Open
Abstract
The PAF1 complex (PAF1C) functions in multiple transcriptional processes involving RNA polymerase II (RNA Pol II). Enhancer RNAs (eRNAs) and promoter upstream transcripts (PROMPTs) are pervasive transcripts transcribed by RNA Pol II and degraded rapidly by the nuclear exosome complex after 3' endonucleolytic cleavage by the Integrator complex (Integrator). Here we show that PAF1C has a role in termination of eRNAs and PROMPTs that are cleaved 1-3 kb downstream of the transcription start site. Mechanistically, PAF1C facilitates recruitment of Integrator to sites of pervasive transcript cleavage, promoting timely cleavage and transcription termination. We also show that PAF1C recruits Integrator to coding genes, where PAF1C then dissociates from Integrator upon entry into processive elongation. Our results demonstrate a function of PAF1C in limiting the length and accumulation of pervasive transcripts that result from non-productive transcription.
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Affiliation(s)
- Xinhong Liu
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Ziwei Guo
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Jing Han
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Bo Peng
- Tsinghua University School of Medicine, Beijing 100084, China
| | - Bin Zhang
- Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China; Institute for Immunology, Tsinghua University School of Medicine, Beijing 100084, China
| | - Haitao Li
- Tsinghua University School of Medicine, Beijing 100084, China; Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China; MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Xiaoyu Hu
- Tsinghua University School of Medicine, Beijing 100084, China; Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China; Institute for Immunology, Tsinghua University School of Medicine, Beijing 100084, China
| | - Charles J David
- Tsinghua University School of Medicine, Beijing 100084, China; Peking University-Tsinghua Center for Life Sciences, Beijing 100084, China
| | - Mo Chen
- Tsinghua University School of Medicine, Beijing 100084, China.
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57
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Lange H, Gagliardi D. Catalytic activities, molecular connections, and biological functions of plant RNA exosome complexes. THE PLANT CELL 2022; 34:967-988. [PMID: 34954803 PMCID: PMC8894942 DOI: 10.1093/plcell/koab310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 05/08/2023]
Abstract
RNA exosome complexes provide the main 3'-5'-exoribonuclease activities in eukaryotic cells and contribute to the maturation and degradation of virtually all types of RNA. RNA exosomes consist of a conserved core complex that associates with exoribonucleases and with multimeric cofactors that recruit the enzyme to its RNA targets. Despite an overall high level of structural and functional conservation, the enzymatic activities and compositions of exosome complexes and their cofactor modules differ among eukaryotes. This review highlights unique features of plant exosome complexes, such as the phosphorolytic activity of the core complex, and discusses the exosome cofactors that operate in plants and are dedicated to the maturation of ribosomal RNA, the elimination of spurious, misprocessed, and superfluous transcripts, or the removal of mRNAs cleaved by the RNA-induced silencing complex and other mRNAs prone to undergo silencing.
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Affiliation(s)
- Heike Lange
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
- Author for correspondence:
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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58
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Control of non-productive RNA polymerase II transcription via its early termination in metazoans. Biochem Soc Trans 2022; 50:283-295. [PMID: 35166324 DOI: 10.1042/bst20201140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
Transcription establishes the universal first step of gene expression where RNA is produced by a DNA-dependent RNA polymerase. The most versatile of eukaryotic RNA polymerases, RNA polymerase II (Pol II), transcribes a broad range of DNA including protein-coding and a variety of non-coding transcription units. Although Pol II can be configured as a durable enzyme capable of transcribing hundreds of kilobases, there is reliable evidence of widespread abortive Pol II transcription termination shortly after initiation, which is often followed by rapid degradation of the associated RNA. The molecular details underlying this phenomenon are still vague but likely reflect the action of quality control mechanisms on the early Pol II complex. Here, we summarize current knowledge of how and when such promoter-proximal quality control is asserted on metazoan Pol II.
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59
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Gockert M, Schmid M, Jakobsen L, Jens M, Andersen JS, Jensen TH. Rapid factor depletion highlights intricacies of nucleoplasmic RNA degradation. Nucleic Acids Res 2022; 50:1583-1600. [PMID: 35048984 PMCID: PMC8860595 DOI: 10.1093/nar/gkac001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/13/2021] [Accepted: 01/05/2022] [Indexed: 12/15/2022] Open
Abstract
Turnover of nucleoplasmic transcripts by the mammalian multi-subunit RNA exosome is mediated by two adaptors: the Nuclear EXosome Targeting (NEXT) complex and the Poly(A) tail eXosome Targeting (PAXT) connection. Functional analyses of NEXT and PAXT have largely utilized long-term factor depletion strategies, facilitating the appearance of indirect phenotypes. Here, we rapidly deplete NEXT, PAXT and core exosome components, uncovering the direct consequences of their acute losses. Generally, proteome changes are sparse and largely dominated by co-depletion of other exosome and adaptor subunits, reflecting possible subcomplex compositions. While parallel high-resolution 3′ end sequencing of newly synthesized RNA confirms previously established factor specificities, it concomitantly demonstrates an inflation of long-term depletion datasets by secondary effects. Most strikingly, a general intron degradation phenotype, observed in long-term NEXT depletion samples, is undetectable upon short-term depletion, which instead emphasizes NEXT targeting of snoRNA-hosting introns. Further analysis of these introns uncovers an unusual mode of core exosome-independent RNA decay. Our study highlights the accumulation of RNAs as an indirect result of long-term decay factor depletion, which we speculate is, at least partly, due to the exhaustion of alternative RNA decay pathways.
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Affiliation(s)
- Maria Gockert
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Marvin Jens
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, 68-271A, Cambridge, MA 02139-4307, USA
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
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60
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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: 2] [Impact Index Per Article: 1.0] [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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61
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Puno MR, Lima CD. Methods to assess helicase and translocation activities of human nuclear RNA exosome and RNA adaptor complexes. Methods Enzymol 2022; 673:453-473. [PMID: 35965016 PMCID: PMC9382703 DOI: 10.1016/bs.mie.2022.03.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The nuclear RNA exosome collaborates with the MTR4 helicase and RNA adaptor complexes to process, surveil, and degrade RNA. Here we outline methods to characterize RNA translocation and strand displacement by exosome-associated helicases and adaptor complexes using fluorescence-based strand displacement assays. The design and preparation of substrates suitable for analysis of helicase and decay activities of reconstituted MTR4–exosome complexes are described. To aid structural and biophysical studies, we present strategies for engineering substrates that can stall helicases during translocation, providing a means to capture snapshots of interactions and molecular steps involved in substrate translocation and delivery to the exosome.
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62
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Ogami K, Suzuki HI. Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function. Int J Mol Sci 2021; 22:13401. [PMID: 34948199 PMCID: PMC8707817 DOI: 10.3390/ijms222413401] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023] Open
Abstract
The genome is pervasively transcribed across various species, yielding numerous non-coding RNAs. As a counterbalance for pervasive transcription, various organisms have a nuclear RNA exosome complex, whose structure is well conserved between yeast and mammalian cells. The RNA exosome not only regulates the processing of stable RNA species, such as rRNAs, tRNAs, small nucleolar RNAs, and small nuclear RNAs, but also plays a central role in RNA surveillance by degrading many unstable RNAs and misprocessed pre-mRNAs. In addition, associated cofactors of RNA exosome direct the exosome to distinct classes of RNA substrates, suggesting divergent and/or multi-layer control of RNA quality in the cell. While the RNA exosome is essential for cell viability and influences various cellular processes, mutations and alterations in the RNA exosome components are linked to the collection of rare diseases and various diseases including cancer, respectively. The present review summarizes the relationships between pervasive transcription and RNA exosome, including evolutionary crosstalk, mechanisms of RNA exosome-mediated RNA surveillance, and physiopathological effects of perturbation of RNA exosome.
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Affiliation(s)
- Koichi Ogami
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8550, Japan;
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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63
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Papadopoulos D, Solvie D, Baluapuri A, Endres T, Ha SA, Herold S, Kalb J, Giansanti C, Schülein-Völk C, Ade CP, Schneider C, Gaballa A, Vos S, Fischer U, Dobbelstein M, Wolf E, Eilers M. MYCN recruits the nuclear exosome complex to RNA polymerase II to prevent transcription-replication conflicts. Mol Cell 2021; 82:159-176.e12. [PMID: 34847357 DOI: 10.1016/j.molcel.2021.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 01/05/2023]
Abstract
The MYCN oncoprotein drives the development of numerous neuroendocrine and pediatric tumors. Here we show that MYCN interacts with the nuclear RNA exosome, a 3'-5' exoribonuclease complex, and recruits the exosome to its target genes. In the absence of the exosome, MYCN-directed elongation by RNA polymerase II (RNAPII) is slow and non-productive on a large group of cell-cycle-regulated genes. During the S phase of MYCN-driven tumor cells, the exosome is required to prevent the accumulation of stalled replication forks and of double-strand breaks close to the transcription start sites. Upon depletion of the exosome, activation of ATM causes recruitment of BRCA1, which stabilizes nuclear mRNA decapping complexes, leading to MYCN-dependent transcription termination. Disruption of mRNA decapping in turn activates ATR, indicating transcription-replication conflicts. We propose that exosome recruitment by MYCN maintains productive transcription elongation during S phase and prevents transcription-replication conflicts to maintain the rapid proliferation of neuroendocrine tumor cells.
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Affiliation(s)
- Dimitrios Papadopoulos
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Daniel Solvie
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Theresa Endres
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Stefanie Anh Ha
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Steffi Herold
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jacqueline Kalb
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Celeste Giansanti
- Institute of Molecular Oncology, Center of Molecular Biosciences, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Christina Schülein-Völk
- Core Unit High-Content Microscopy, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Carsten Patrick Ade
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Cornelius Schneider
- Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Abdallah Gaballa
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Seychelle Vos
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02142, USA
| | - Utz Fischer
- Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Matthias Dobbelstein
- Institute of Molecular Oncology, Center of Molecular Biosciences, University of Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Martin Eilers
- Theodor Boveri Institute, Department of Biochemistry and Molecular Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
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Wang Y, Fan J, Wang J, Zhu Y, Xu L, Tong D, Cheng H. ZFC3H1 prevents RNA trafficking into nuclear speckles through condensation. Nucleic Acids Res 2021; 49:10630-10643. [PMID: 34530450 PMCID: PMC8501945 DOI: 10.1093/nar/gkab774] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 01/23/2023] Open
Abstract
Controlling proper RNA pool for nuclear export is important for accurate gene expression. ZFC3H1 is a key controller that not only facilitates nuclear exosomal degradation, but also retains its bound polyadenylated RNAs in the nucleus upon exosome inactivation. However, how ZFC3H1 retains RNAs and how its roles in RNA retention and degradation are related remain largely unclear. Here, we found that upon degradation inhibition, ZFC3H1 forms nuclear condensates to prevent RNA trafficking to nuclear speckles (NSs) where many RNAs gain export competence. Systematic mapping of ZFC3H1 revealed that it utilizes distinct domains for condensation and RNA degradation. Interestingly, ZFC3H1 condensation activity is required for preventing RNA trafficking to NSs, but not for RNA degradation. Considering that no apparent ZFC3H1 condensates are formed in normal cells, our study suggests that nuclear RNA degradation and retention are two independent mechanisms with different preference for controlling proper export RNA pool—degradation is preferred in normal cells, and condensation retention is activated upon degradation inhibition.
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Affiliation(s)
- Yimin Wang
- State Key Laboratory of Molecular Biology, 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 200031, China
| | - Jing Fan
- State Key Laboratory of Molecular Biology, 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 200031, China
| | - Jianshu Wang
- State Key Laboratory of Molecular Biology, 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 200031, China
| | - Yi Zhu
- State Key Laboratory of Molecular Biology, 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 200031, China
| | - Lin Xu
- State Key Laboratory of Molecular Biology, 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 200031, China
| | - Deng Tong
- State Key Laboratory of Molecular Biology, 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 200031, China
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, 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 200031, China.,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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65
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Nair L, Zhang W, Laffleur B, Jha MK, Lim J, Lee H, Wu L, Alvarez NS, Liu ZP, Munteanu EL, Swayne T, Hanna JH, Ding L, Rothschild G, Basu U. Mechanism of noncoding RNA-associated N 6-methyladenosine recognition by an RNA processing complex during IgH DNA recombination. Mol Cell 2021; 81:3949-3964.e7. [PMID: 34450044 PMCID: PMC8571800 DOI: 10.1016/j.molcel.2021.07.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/04/2021] [Accepted: 07/28/2021] [Indexed: 01/13/2023]
Abstract
Immunoglobulin heavy chain (IgH) locus-associated G-rich long noncoding RNA (SμGLT) is important for physiological and pathological B cell DNA recombination. We demonstrate that the METTL3 enzyme-catalyzed N6-methyladenosine (m6A) RNA modification drives recognition and 3' end processing of SμGLT by the RNA exosome, promoting class switch recombination (CSR) and suppressing chromosomal translocations. The recognition is driven by interaction of the MPP6 adaptor protein with nuclear m6A reader YTHDC1. MPP6 and YTHDC1 promote CSR by recruiting AID and the RNA exosome to actively transcribe SμGLT. Direct suppression of m6A modification of SμGLT or of m6A reader YTHDC1 reduces CSR. Moreover, METTL3, an essential gene for B cell development in the bone marrow and germinal center, suppresses IgH-associated aberrant DNA breaks and prevents genomic instability. Taken together, we propose coordinated and central roles for MPP6, m6A modification, and m6A reader proteins in controlling long noncoding RNA processing, DNA recombination, and development in B cells.
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Affiliation(s)
- Lekha Nair
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Mukesh K Jha
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Heather Lee
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lijing Wu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Nehemiah S Alvarez
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan 250061, Shandong, China
| | - Emilia L Munteanu
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Theresa Swayne
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Lei Ding
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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66
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Hojka-Osinska A, Chlebowski A, Grochowska J, Owczarek EP, Affek K, Kłosowska-Kosicka K, Szczesny RJ, Dziembowski A. Landscape of functional interactions of human processive ribonucleases revealed by high-throughput siRNA screenings. iScience 2021; 24:103036. [PMID: 34541468 PMCID: PMC8437785 DOI: 10.1016/j.isci.2021.103036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/09/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Processive exoribonucleases are executors of RNA decay. In humans, their physical but not functional interactions were thoughtfully investigated. Here we have screened cells deficient in DIS3, XRN2, EXOSC10, DIS3L, and DIS3L2 with a custom siRNA library and determined their genetic interactions (GIs) with diverse pathways of RNA metabolism. We uncovered a complex network of positive interactions that buffer alterations in RNA degradation and reveal reciprocal cooperation with genes involved in transcription, RNA export, and splicing. Further, we evaluated the functional distinctness of nuclear DIS3 and cytoplasmic DIS3L using a library of all known genes associated with RNA metabolism. Our analysis revealed that DIS3 mutation suppresses RNA splicing deficiency, while DIS3L GIs disclose the interplay of cytoplasmic RNA degradation with nuclear RNA processing. Finally, genome-wide DIS3 GI map uncovered relations with genes not directly involved in RNA metabolism, like microtubule organization or regulation of telomerase activity.
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Affiliation(s)
- Anna Hojka-Osinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Joanna Grochowska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Ewelina P. Owczarek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Kamila Affek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Roman J. Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
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67
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Sterrett MC, Enyenihi L, Leung SW, Hess L, Strassler SE, Farchi D, Lee RS, Withers ES, Kremsky I, Baker RE, Basrai MA, van Hoof A, Fasken MB, Corbett AH. A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex. RNA (NEW YORK, N.Y.) 2021; 27:1046-1067. [PMID: 34162742 PMCID: PMC8370739 DOI: 10.1261/rna.078618.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
RNA exosomopathies, a growing family of diseases, are linked to missense mutations in genes encoding structural subunits of the evolutionarily conserved, 10-subunit exoribonuclease complex, the RNA exosome. This complex consists of a three-subunit cap, a six-subunit, barrel-shaped core, and a catalytic base subunit. While a number of mutations in RNA exosome genes cause pontocerebellar hypoplasia, mutations in the cap subunit gene EXOSC2 cause an apparently distinct clinical presentation that has been defined as a novel syndrome SHRF (short stature, hearing loss, retinitis pigmentosa, and distinctive facies). We generated the first in vivo model of the SHRF pathogenic amino acid substitutions using budding yeast by modeling pathogenic EXOSC2 missense mutations (p.Gly30Val and p.Gly198Asp) in the orthologous S. cerevisiae gene RRP4 The resulting rrp4 mutant cells show defects in cell growth and RNA exosome function. Consistent with altered RNA exosome function, we detect significant transcriptomic changes in both coding and noncoding RNAs in rrp4-G226D cells that model EXOSC2 p.Gly198Asp, suggesting defects in nuclear surveillance. Biochemical and genetic analyses suggest that the Rrp4 G226D variant subunit shows impaired interactions with key RNA exosome cofactors that modulate the function of the complex. These results provide the first in vivo evidence that pathogenic missense mutations present in EXOSC2 impair the function of the RNA exosome. This study also sets the stage to compare exosomopathy models to understand how defects in RNA exosome function underlie distinct pathologies.
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Affiliation(s)
- Maria C Sterrett
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia 30322, USA
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Liz Enyenihi
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Sara W Leung
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Laurie Hess
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Sarah E Strassler
- Biochemistry, Cell and Developmental Biology Graduate Program, Emory University, Atlanta, Georgia 30322, USA
- Department of Biochemistry, Emory University, Atlanta, Georgia 30322, USA
| | - Daniela Farchi
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Richard S Lee
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Elise S Withers
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Isaac Kremsky
- Loma Linda University School of Medicine, Loma Linda, California 92350, USA
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Milo B Fasken
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, Georgia 30322, USA
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68
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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: 6] [Impact Index Per Article: 2.0] [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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69
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Abstract
Biological mass spectrometry (MS) encompasses a range of methods for characterizing proteins and other biomolecules. MS is uniquely powerful for the structural analysis of endogenous protein complexes, which are often heterogeneous, poorly abundant, and refractive to characterization by other methods. Here, we focus on how biological MS can contribute to the study of endogenous protein complexes, which we define as complexes expressed in the physiological host and purified intact, as opposed to reconstituted complexes assembled from heterologously expressed components. Biological MS can yield information on complex stoichiometry, heterogeneity, topology, stability, activity, modes of regulation, and even structural dynamics. We begin with a review of methods for isolating endogenous complexes. We then describe the various biological MS approaches, focusing on the type of information that each method yields. We end with future directions and challenges for these MS-based methods.
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Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
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70
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Machado de Amorim A, Chakrabarti S. Assembly of multicomponent machines in RNA metabolism: A common theme in mRNA decay pathways. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1684. [PMID: 34351053 DOI: 10.1002/wrna.1684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/05/2022]
Abstract
Multicomponent protein-RNA complexes comprising a ribonuclease and partner RNA helicase facilitate the turnover of mRNA in all domains of life. While these higher-order complexes provide an effective means of physically and functionally coupling the processes of RNA remodeling and decay, most ribonucleases and RNA helicases do not exhibit sequence specificity in RNA binding. This raises the question as to how these assemblies select substrates for processing and how the activities are orchestrated at the precise moment to ensure efficient decay. The answers to these apparent puzzles lie in the auxiliary components of the assemblies that might relay decay-triggering signals. Given their function within the assemblies, these components may be viewed as "sensors." The functions and mechanisms of action of the sensor components in various degradation complexes in bacteria and eukaryotes are highlighted here to discuss their roles in RNA decay processes. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
| | - Sutapa Chakrabarti
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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71
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Kan RL, Chen J, Sallam T. Crosstalk between epitranscriptomic and epigenetic mechanisms in gene regulation. Trends Genet 2021; 38:182-193. [PMID: 34294427 PMCID: PMC9093201 DOI: 10.1016/j.tig.2021.06.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/26/2022]
Abstract
Epigenetic modifications occur on genomic DNA and histones to influence gene expression. More recently, the discovery that mRNA undergoes similar chemical modifications that powerfully impact transcript turnover and translation adds another layer of dynamic gene regulation. Central to precise and synchronized regulation of gene expression is intricate crosstalk between multiple checkpoints involved in transcript biosynthesis and processing. There are more than 100 internal modifications of RNA in mammalian cells. The most common is N6-methyladenosine (m6A) methylation. Although m6A is established to influence RNA stability dynamics and translation efficiency, rapidly accumulating evidence shows significant crosstalk between RNA methylation and histone/DNA epigenetic mechanisms. These interactions specify transcriptional outputs, translation, recruitment of chromatin modifiers, as well as the deployment of the m6A methyltransferase complex (MTC) at target sites. In this review, we dissect m6A-orchestrated feedback circuits that regulate histone modifications and the activity of regulatory RNAs, such as long noncoding (lnc)RNA and chromosome-associated regulatory RNA. Collectively, this body of evidence suggests that m6A acts as a versatile checkpoint that can couple different layers of gene regulation with one another.
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Affiliation(s)
- Ryan L Kan
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA; Molecular Biology Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA; City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
| | - Tamer Sallam
- Division of Cardiology, Department of Medicine, University of California, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, CA, USA; Molecular Biology Interdepartmental Program, University of California, Los Angeles, CA, USA.
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72
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Fukushima K, Akira S. Novel insights into the pathogenesis of lung fibrosis: the RBM7-NEAT1-CXCL12-SatM axis at fibrosis onset. Int Immunol 2021; 33:659-663. [PMID: 34165514 DOI: 10.1093/intimm/dxab034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022] Open
Abstract
Fibrosis is a life-threatening disorder with significant morbidity and mortality and is caused by excessive formation of connective tissue that can affect several important organs. Fibrosis in organ tissues is caused by an abnormal wound-healing process from repeated injuries. In our recent study using a mouse model of bleomycin-induced lung fibrosis, we examined the role of RNA-binding protein 7 (RBM7) on the development of lung fibrosis. RBM7 is upregulated in the injured lung epithelium and disturbs normal epithelial cell repair and regeneration by promoting apoptosis of damaged epithelial cells. RBM7 causes the decay of nuclear-enriched abundant transcript 1 (NEAT1), which results in apoptosis of lung epithelial cells. These apoptotic cells then produce C-X-C motif chemokine ligand 12 (CXCL12), which leads to the recruitment of a fibrosis-promoting monocyte population called segregated-nucleus-containing atypical monocytes (SatM) to the damaged area, followed by the initiation and promotion of lung fibrosis. Here, we review recent insights into the crosstalk between lung parenchymal cells and hematopoietic cells during the development of pulmonary fibrosis.
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Affiliation(s)
- Kiyoharu Fukushima
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan.,Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan.,Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan.,Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
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73
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The zinc-finger protein Red1 orchestrates MTREC submodules and binds the Mtl1 helicase arch domain. Nat Commun 2021; 12:3456. [PMID: 34103492 PMCID: PMC8187409 DOI: 10.1038/s41467-021-23565-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/05/2021] [Indexed: 12/02/2022] Open
Abstract
Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome in a process requiring the RNA helicase Mtr4 and specific adaptor complexes for RNA substrate recognition. The PAXT and MTREC complexes have recently been identified as homologous exosome adaptors in human and fission yeast, respectively. The eleven-subunit MTREC comprises the zinc-finger protein Red1 and the Mtr4 homologue Mtl1. Here, we use yeast two-hybrid and pull-down assays to derive a detailed interaction map. We show that Red1 bridges MTREC submodules and serves as the central scaffold. In the crystal structure of a minimal Mtl1/Red1 complex an unstructured region adjacent to the Red1 zinc-finger domain binds to both the Mtl1 KOW domain and stalk helices. This interaction extends the canonical interface seen in Mtr4-adaptor complexes. In vivo mutational analysis shows that this interface is essential for cell survival. Our results add to Mtr4 versatility and provide mechanistic insights into the MTREC complex. The human PAXT complex and the MTREC complex in fission yeast are important exosome cofactors, serving in the degradation of specific noncoding RNAs. Here, the authors combine structural, biochemical and in vivo methods to show how Red1 recruits the Mtl1 helicase by an interface not seen before in helicase-adaptor complexes.
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74
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Yuan J, Botchway BOA, Zhang Y, Wang X, Liu X. Combined bioscaffold with stem cells and exosomes can improve traumatic brain injury. Stem Cell Rev Rep 2021; 16:323-334. [PMID: 31808037 DOI: 10.1007/s12015-019-09927-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The intricacy of the brain, along with the existence of blood brain barrier (BBB) does complicate the delivery of effective therapeutics through simple intravascular injection. Hence, an effective delivery mechanism of therapeutics in the event of either traumatic brain injury (TBI) or other brain injuries is needed. Stem cells can promote regeneration and repair injury. The usage of biomaterials and exosomes in transporting stem cells to target lesion sites has been suggested as a potential option. The combination of biomaterials with modified exosomes can help in transporting stem cells to injury sites, whiles also increasing their survival and promoting effective treatment. Herein, we review the current researches pertinent to biological scaffolds and exosomes in repairing TBI and present the current progress and new direction in the clinical setting. We begin with the role of bioscaffold in treating neuronal conditions, the effect of exosomes in injury, and conclude with the improvement of TBI via the employment of combined exosomes, bioscaffold and stem cells.
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Affiliation(s)
- Jiaying Yuan
- Department of Histology and Embryology, Medical College, Shaoxing University, 312000, Shaoxing, Zhejiang, China
| | - Benson O A Botchway
- Institute of Neuroscience, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Zhang
- Department of Histology and Embryology, Medical College, Shaoxing University, 312000, Shaoxing, Zhejiang, China
| | - Xizhi Wang
- Department of Histology and Embryology, Medical College, Shaoxing University, 312000, Shaoxing, Zhejiang, China
| | - Xuehong Liu
- Department of Histology and Embryology, Medical College, Shaoxing University, 312000, Shaoxing, Zhejiang, China.
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75
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ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control. Biochem Soc Trans 2021; 49:1325-1336. [PMID: 34060620 DOI: 10.1042/bst20201008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/26/2023]
Abstract
ARS2/SRRT is an essential eukaryotic protein that has emerged as a critical factor in the sorting of functional from non-functional RNA polymerase II (Pol II) transcripts. Through its interaction with the Cap Binding Complex (CBC), it associates with the cap of newly made RNAs and acts as a hub for competitive exchanges of protein factors that ultimately determine the fate of the associated RNA. The central position of the protein within the nuclear gene expression machinery likely explains why its depletion causes a broad range of phenotypes, yet an exact function of the protein remains elusive. Here, we consider the literature on ARS2/SRRT with the attempt to garner the threads into a unifying working model for ARS2/SRRT function at the nexus of Pol II transcription, transcript maturation and quality control.
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76
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Abstract
Telomere biology disorders (TBD) are a heterogeneous group of diseases arising from germline mutations affecting genes involved in telomere maintenance. Telomeres are DNA-protein structures at chromosome ends that maintain chromosome stability; their length affects cell replicative potential and senescence. A constellation of bone marrow failure, pulmonary fibrosis, liver cirrhosis and premature greying is suggestive, however incomplete penetrance results in highly variable manifestations, with idiopathic pulmonary fibrosis as the most common presentation. Currently, the true extent of TBD burden is unknown as there is no established diagnostic criteria and the disorder often is unrecognised and underdiagnosed. There is no gold standard for measuring telomere length and not all TBD-related mutations have been identified. There is no specific cure and the only treatment is organ transplantation, which has poor outcomes. This review summarises the current literature and discusses gaps in understanding and areas of need in managing TBD.
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77
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Wang G, Zheng C. Zinc finger proteins in the host-virus interplay: multifaceted functions based on their nucleic acid-binding property. FEMS Microbiol Rev 2021; 45:fuaa059. [PMID: 33175962 DOI: 10.1093/femsre/fuaa059] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/07/2020] [Indexed: 12/14/2022] Open
Abstract
Zinc finger proteins (ZFPs) are a huge family comprised of massive, structurally diverse proteins characterized by zinc ion coordinating. They engage in the host-virus interplay in-depth and occupy a significant portion of the host antiviral arsenal. Nucleic acid-binding is the basic property of certain ZFPs, which draws increasing attention due to their immense influence on viral infections. ZFPs exert multiple roles on the viral replications and host cell transcription profiles by recognizing viral genomes and host mRNAs. Their roles could be either antiviral or proviral and were separately discussed. Our review covers the recent research progress and provides a comprehensive understanding of ZFPs in antiviral immunity based on their DNA/RNA binding property.
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Affiliation(s)
- Guanming Wang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Dr NW, Calgary, Alberta, Canada, AB T2N 4N1
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78
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Wang Y, Yu Y, Pang Y, Yu H, Zhang W, Zhao X, Yu J. The distinct roles of zinc finger CCHC-type (ZCCHC) superfamily proteins in the regulation of RNA metabolism. RNA Biol 2021; 18:2107-2126. [PMID: 33787465 DOI: 10.1080/15476286.2021.1909320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The zinc finger CCHC-type (ZCCHC) superfamily proteins, characterized with the consensus sequence C-X2-C-X4-H-X4-C, are accepted to have high-affinity binding to single-stranded nucleic acids, especially single-stranded RNAs. In human beings 25 ZCCHC proteins have been annotated in the HGNC database. Of interest is that among the family, most members are involved in the multiple steps of RNA metabolism. In this review, we focus on the diverged roles of human ZCCHC proteins on RNA transcription, biogenesis, splicing, as well as translation and degradation.
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Affiliation(s)
- Yishu Wang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Yu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yidan Pang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haojun Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenqi Zhang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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79
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Sapio RT, Burns CJ, Pestov DG. Effects of Hydrogen Peroxide Stress on the Nucleolar Redox Environment and Pre-rRNA Maturation. Front Mol Biosci 2021; 8:678488. [PMID: 33981726 PMCID: PMC8107432 DOI: 10.3389/fmolb.2021.678488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/06/2021] [Indexed: 12/16/2022] Open
Abstract
Identifying biologically relevant molecular targets of oxidative stress may provide new insights into disease mechanisms and accelerate development of novel biomarkers. Ribosome biogenesis is a fundamental prerequisite for cellular protein synthesis, but how oxidative stress affects ribosome biogenesis has not been clearly established. To monitor and control the redox environment of ribosome biogenesis, we targeted a redox-sensitive roGFP reporter and catalase, a highly efficient H2O2 scavenger, to the nucleolus, the primary site for transcription and processing of rRNA in eukaryotic cells. Imaging of mouse 3T3 cells exposed to non-cytotoxic H2O2 concentrations revealed increased oxidation of the nucleolar environment accompanied by a detectable increase in the oxidative damage marker 8-oxo-G in nucleolar RNA. Analysis of pre-rRNA processing showed a complex pattern of alterations in pre-rRNA maturation in the presence of H2O2, including inhibition of the transcription and processing of the primary 47S transcript, accumulation of 18S precursors, and inefficient 3'-end processing of 5.8S rRNA. This work introduces new tools for studies of the redox biology of the mammalian nucleolus and identifies pre-rRNA maturation steps sensitive to H2O2 stress.
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Affiliation(s)
- Russell T Sapio
- Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States.,Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
| | - Chelsea J Burns
- Graduate School of Biomedical Sciences, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
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80
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Rambout X, Maquat LE. The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing. Genes Dev 2021; 34:1113-1127. [PMID: 32873578 PMCID: PMC7462061 DOI: 10.1101/gad.339986.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Rambout and Maquat discuss known roles of the nuclear cap-binding complex (CBC) during the transcription of genes that encode proteins, stitching together past studies from diverse groups to describe the continuum of CBC-mediated checks and balances in eukaryotic cells. The largely nuclear cap-binding complex (CBC) binds to the 5′ caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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81
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Dai XY, Shi L, Li Z, Yang HY, Wei JF, Ding Q. Main N6-Methyladenosine Readers: YTH Family Proteins in Cancers. Front Oncol 2021; 11:635329. [PMID: 33928028 PMCID: PMC8076607 DOI: 10.3389/fonc.2021.635329] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
Among the over 150 RNA modifications, N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic RNAs, not only in messenger RNAs, but also in microRNAs and long non-coding RNAs. It is a dynamic and reversible process in mammalian cells, which is installed by “writers,” consisting of METTL3, METTL14, WTAP, RBM15/15B, and KIAA1429 and removed by “erasers,” including FTO and ALKBH5. Moreover, m6A modification is recognized by “readers,” which play the key role in executing m6A functions. IYT521-B homology (YTH) family proteins are the first identified m6A reader proteins. They were reported to participate in cancer tumorigenesis and development through regulating the metabolism of targeted RNAs, including RNA splicing, RNA export, translation, and degradation. There are many reviews about function of m6A and its role in various diseases. However, reviews only focusing on m6A readers, especially YTH family proteins are few. In this review, we systematically summarize the recent advances in structure and biological function of YTH family proteins, and their roles in human cancer and potential application in cancer therapy.
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Affiliation(s)
- Xin-Yuan Dai
- Jiangsu Breast Disease Center, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Liang Shi
- Jiangsu Breast Disease Center, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Zhi Li
- Jiangsu Breast Disease Center, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Hai-Yan Yang
- Jiangsu Breast Disease Center, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Qiang Ding
- Jiangsu Breast Disease Center, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
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82
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Das M, Zattas D, Zinder JC, Wasmuth EV, Henri J, Lima CD. Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome. Proc Natl Acad Sci U S A 2021; 118:e2024846118. [PMID: 33782132 PMCID: PMC8040639 DOI: 10.1073/pnas.2024846118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Quality control requires discrimination between functional and aberrant species to selectively target aberrant substrates for destruction. Nuclear RNA quality control in Saccharomyces cerevisiae includes the TRAMP complex that marks RNA for decay via polyadenylation followed by helicase-dependent 3' to 5' degradation by the RNA exosome. Using reconstitution biochemistry, we show that polyadenylation and helicase activities of TRAMP cooperate with processive and distributive exoribonuclease activities of the nuclear RNA exosome to protect stable RNA from degradation while selectively targeting and degrading less stable RNA. Substrate discrimination is lost when the distributive exoribonuclease activity of Rrp6 is inactivated, leading to degradation of stable and unstable RNA species. These data support a proofreading mechanism in which deadenylation by Rrp6 competes with Mtr4-dependent degradation to protect stable RNA while selectively targeting and degrading unstable RNA.
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Affiliation(s)
- Mom Das
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Dimitrios Zattas
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - John C Zinder
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Elizabeth V Wasmuth
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Julien Henri
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065;
- HHMI, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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83
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Wang L, Hu B, Pan K, Chang J, Zhao X, Chen L, Lin H, Wang J, Zhou G, Xu W, Yuan J. SYVN1-MTR4-MAT2A Signaling Axis Regulates Methionine Metabolism in Glioma Cells. Front Cell Dev Biol 2021; 9:633259. [PMID: 33859984 PMCID: PMC8042234 DOI: 10.3389/fcell.2021.633259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/08/2021] [Indexed: 12/14/2022] Open
Abstract
Methionine is one of the essential amino acids. How tumor cells adapt and adjust their signal transduction networks to avoid apoptosis in a methionine-restricted environment is worthy of further exploration. In this study, we investigated the molecular mechanism of glioma response to methionine restriction, providing a theoretical basis for new treatment strategies for glioma.
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Affiliation(s)
- Lude Wang
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Bin Hu
- Department of Pathology, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Kailing Pan
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jie Chang
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaoya Zhao
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Lin Chen
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Haiping Lin
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jing Wang
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Gezhi Zhou
- Department of Neurosurgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Wenxia Xu
- Central Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jianlie Yuan
- Department of Neurosurgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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84
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Norppa AJ, Frilander MJ. The integrity of the U12 snRNA 3' stem-loop is necessary for its overall stability. Nucleic Acids Res 2021; 49:2835-2847. [PMID: 33577674 PMCID: PMC7968993 DOI: 10.1093/nar/gkab048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 01/14/2021] [Accepted: 02/07/2021] [Indexed: 12/20/2022] Open
Abstract
Disruption of minor spliceosome functions underlies several genetic diseases with mutations in the minor spliceosome-specific small nuclear RNAs (snRNAs) and proteins. Here, we define the molecular outcome of the U12 snRNA mutation (84C>U) resulting in an early-onset form of cerebellar ataxia. To understand the molecular consequences of the U12 snRNA mutation, we created cell lines harboring the 84C>T mutation in the U12 snRNA gene (RNU12). We show that the 84C>U mutation leads to accelerated decay of the snRNA, resulting in significantly reduced steady-state U12 snRNA levels. Additionally, the mutation leads to accumulation of 3′-truncated forms of U12 snRNA, which have undergone the cytoplasmic steps of snRNP biogenesis. Our data suggests that the 84C>U-mutant snRNA is targeted for decay following reimport into the nucleus, and that the U12 snRNA fragments are decay intermediates that result from the stalling of a 3′-to-5′ exonuclease. Finally, we show that several other single-nucleotide variants in the 3′ stem-loop of U12 snRNA that are segregating in the human population are also highly destabilizing. This suggests that the 3′ stem-loop is important for the overall stability of the U12 snRNA and that additional disease-causing mutations are likely to exist in this region.
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Affiliation(s)
- Antto J Norppa
- Institute of Biotechnology, P.O. Box 56, Viikinkaari 5, University of Helsinki, FI-00014 Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, P.O. Box 56, Viikinkaari 5, University of Helsinki, FI-00014 Helsinki, Finland
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85
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Wu G, Schmid M, Rib L, Polak P, Meola N, Sandelin A, Jensen TH. A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome. Cell Rep 2021; 30:2387-2401.e5. [PMID: 32075771 DOI: 10.1016/j.celrep.2020.01.068] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/09/2019] [Accepted: 01/22/2020] [Indexed: 12/14/2022] Open
Abstract
Degradation of transcripts in human nuclei is primarily facilitated by the RNA exosome. To obtain substrate specificity, the exosome is aided by adaptors; in the nucleoplasm, those adaptors are the nuclear exosome-targeting (NEXT) complex and the poly(A) (pA) exosome-targeting (PAXT) connection. How these adaptors guide exosome targeting remains enigmatic. Employing high-resolution 3' end sequencing, we demonstrate that NEXT substrates arise from heterogenous and predominantly pA- 3' ends often covering kilobase-wide genomic regions. In contrast, PAXT targets harbor well-defined pA+ 3' ends defined by canonical pA site use. Irrespective of this clear division, NEXT and PAXT act redundantly in two ways: (1) regional redundancy, where the majority of exosome-targeted transcription units produce NEXT- and PAXT-sensitive RNA isoforms, and (2) isoform redundancy, where the PAXT connection ensures fail-safe decay of post-transcriptionally polyadenylated NEXT targets. In conjunction, this provides a two-layered targeting mechanism for efficient nuclear sorting of the human transcriptome.
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Affiliation(s)
- Guifen Wu
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Leonor Rib
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Patrik Polak
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Nicola Meola
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology and Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Building 1130, 8000 Aarhus C, Denmark.
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86
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Qin J, Autexier C. Regulation of human telomerase RNA biogenesis and localization. RNA Biol 2021; 18:305-315. [PMID: 32813614 PMCID: PMC7954027 DOI: 10.1080/15476286.2020.1809196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/03/2020] [Accepted: 08/08/2020] [Indexed: 12/16/2022] Open
Abstract
Maintenance of telomeres is essential for genome integrity and replicative capacity in eukaryotic cells. Telomerase, the ribonucleoprotein complex that catalyses telomere synthesis is minimally composed of a reverse transcriptase and an RNA component. The sequence and structural domains of human telomerase RNA (hTR) have been extensively characterized, while the regulation of hTR transcription, maturation, and localization, is not fully understood. Here, we provide an up-to-date review of hTR, with an emphasis on current breakthroughs uncovering the mechanisms of hTR maturation and localization.
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Affiliation(s)
- Jian Qin
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, Canada
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87
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Ishida YI, Miyao S, Saito M, Hiraishi N, Nagahama M. Interactome analysis of the Tudor domain-containing protein SPF30 which associates with the MTR4-exosome RNA-decay machinery under the regulation of AAA-ATPase NVL2. Int J Biochem Cell Biol 2021; 132:105919. [PMID: 33422691 DOI: 10.1016/j.biocel.2021.105919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022]
Abstract
The AAA-ATPase NVL2 associates with an RNA helicase MTR4 and the nuclear RNA exosome in the course of ribosome biogenesis. In our proteomic screen, we had identified a ribosome biogenesis factor WDR74 as a MTR4-interacting partner, whose dissociation is stimulated by the ATP hydrolysis of NVL2. In this study, we report the identification of splicing factor 30 (SPF30), another MTR4-interacting protein with a similar regulatory mechanism. SPF30 is a pre-mRNA splicing factor harboring a Tudor domain in its central region, which regulates various cellular events by binding to dimethylarginine-modified proteins. The interaction between SPF30 and the exosome core is mediated by MTR4 and RRP6, a catalytic component of the nuclear exosome. The N- and C-terminal regions, but not the Tudor domain, of SPF30 are involved in the association with MTR4 and the exosome. The knockdown of SPF30 caused subtle delay in the 12S pre-rRNA processing to mature 5.8S rRNA, even though no obvious effect was observed on the ribosome subunit profile in the cells. Shotgun proteomic analysis to search for SPF30-interacting proteins indicated its role in ribosome biogenesis, pre-mRNA splicing, and box C/D snoRNA biogenesis. These results suggest that SPF30 collaborates with the MTR4-exosome machinery to play a functional role in multiple RNA metabolic pathways, some of which may be regulated by the ATP hydrolysis of NVL2.
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Affiliation(s)
- Yo-Ichi Ishida
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Sotaro Miyao
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Mitsuaki Saito
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Nobuhiro Hiraishi
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan
| | - Masami Nagahama
- Laboratory of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan.
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88
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Kulsuptrakul J, Wang R, Meyers NL, Ott M, Puschnik AS. A genome-wide CRISPR screen identifies UFMylation and TRAMP-like complexes as host factors required for hepatitis A virus infection. Cell Rep 2021; 34:108859. [PMID: 33730579 PMCID: PMC8893346 DOI: 10.1016/j.celrep.2021.108859] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/21/2020] [Accepted: 02/19/2021] [Indexed: 12/17/2022] Open
Abstract
Hepatitis A virus (HAV) is a positive-sense RNA virus causing acute inflammation of the liver. Here, using a genome-scale CRISPR screen, we provide a comprehensive picture of the cellular factors that are exploited by HAV. We identify genes involved in sialic acid/ganglioside biosynthesis and members of the eukaryotic translation initiation factor complex, corroborating their putative roles for HAV. Additionally, we uncover all components of the cellular machinery for UFMylation, a ubiquitin-like protein modification. We show that HAV translation specifically depends on UFM1 conjugation of the ribosomal protein RPL26. Furthermore, we find that components related to the yeast Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex are required for viral translation independent of controlling viral poly(A) tails or RNA stability. Finally, we demonstrate that pharmacological inhibition of the TRAMP-like complex decreases HAV replication in hepatocyte cells and human liver organoids, thus providing a strategy for host-directed therapy of HAV infection. To identify host factors required for the infection with hepatitis A virus, Kulsuptrakul et al. conducted a genome-wide CRISPR knockout screen in human hepatocytes. They reveal that UFMylation of the ribosomal protein RPL26 as well as the polyadenylation activity of a TRAMP-like complex enhance viral translation.
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Affiliation(s)
| | - Ruofan Wang
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | | | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
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89
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Wu P, Zhang M, Webster NJG. Alternative RNA Splicing in Fatty Liver Disease. Front Endocrinol (Lausanne) 2021; 12:613213. [PMID: 33716968 PMCID: PMC7953061 DOI: 10.3389/fendo.2021.613213] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Alternative RNA splicing is a process by which introns are removed and exons are assembled to construct different RNA transcript isoforms from a single pre-mRNA. Previous studies have demonstrated an association between dysregulation of RNA splicing and a number of clinical syndromes, but the generality to common disease has not been established. Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease affecting one-third of adults worldwide, increasing the risk of cirrhosis and hepatocellular carcinoma (HCC). In this review we focus on the change in alternative RNA splicing in fatty liver disease and the role for splicing regulation in disease progression.
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Affiliation(s)
- Panyisha Wu
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA, United States
| | - Moya Zhang
- University of California Los Angeles, Los Angeles, CA, United States
| | - Nicholas J. G. Webster
- VA San Diego Healthcare System, San Diego, CA, United States
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
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90
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Ulmke PA, Xie Y, Sokpor G, Pham L, Shomroni O, Berulava T, Rosenbusch J, Basu U, Fischer A, Nguyen HP, Staiger JF, Tuoc T. Post-transcriptional regulation by the exosome complex is required for cell survival and forebrain development via repression of P53 signaling. Development 2021; 148:dev.188276. [PMID: 33462115 DOI: 10.1242/dev.188276] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
Fine-tuned gene expression is crucial for neurodevelopment. The gene expression program is tightly controlled at different levels, including RNA decay. N6-methyladenosine (m6A) methylation-mediated degradation of RNA is essential for brain development. However, m6A methylation impacts not only RNA stability, but also other RNA metabolism processes. How RNA decay contributes to brain development is largely unknown. Here, we show that Exosc10, a RNA exonuclease subunit of the RNA exosome complex, is indispensable for forebrain development. We report that cortical cells undergo overt apoptosis, culminating in cortical agenesis upon conditional deletion of Exosc10 in mouse cortex. Mechanistically, Exosc10 directly binds and degrades transcripts of the P53 signaling-related genes, such as Aen and Bbc3. Overall, our findings suggest a crucial role for Exosc10 in suppressing the P53 pathway, in which the rapid turnover of the apoptosis effectors Aen and Bbc3 mRNAs is essential for cell survival and normal cortical histogenesis.
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Affiliation(s)
- Pauline Antonie Ulmke
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Yuanbin Xie
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany.,Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Gannan Medical University, 341000 Ganzhou, The People's Republic of China
| | - Godwin Sokpor
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany.,Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
| | - Linh Pham
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany.,Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
| | - Orr Shomroni
- Microarray and Deep-Sequencing Core Facility, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Tea Berulava
- German Center for Neurodegenerative Diseases, Goettingen 37075, Germany
| | - Joachim Rosenbusch
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Andre Fischer
- German Center for Neurodegenerative Diseases, Goettingen 37075, Germany.,Department for Psychiatry and Psychotherapy, University Medical Center, Georg-August-University Goettingen, Goettingen 37075, Germany.,Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Goettingen, Goettingen 37075, Germany
| | - Huu Phuc Nguyen
- Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
| | - Jochen F Staiger
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany
| | - Tran Tuoc
- University Medical Center, Georg-August- University Goettingen, Goettingen 37075, Germany .,Department of Human Genetics, Ruhr University of Bochum, Bochum 44801, Germany
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91
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Yang Q, Lyu X, Zhao F, Liu Y. Effects of codon usage on gene expression are promoter context dependent. Nucleic Acids Res 2021; 49:818-831. [PMID: 33410890 PMCID: PMC7826287 DOI: 10.1093/nar/gkaa1253] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 12/16/2020] [Indexed: 12/21/2022] Open
Abstract
Codon usage bias is a universal feature of all genomes. Although codon usage has been shown to regulate mRNA and protein levels by influencing mRNA decay and transcription in eukaryotes, little or no genome-wide correlations between codon usage and mRNA levels are detected in mammalian cells, raising doubt on the significance of codon usage effect on gene expression. Here we show that gene-specific regulation reduces the genome-wide codon usage and mRNA correlations: Constitutively expressed genes exhibit much higher genome-wide correlations than differentially expressed genes from fungi to human cells. Using Drosophila S2 cells as a model system, we showed that the effect of codon usage on mRNA expression level is promoter-dependent. Regions downstream of the core promoters of differentially expressed genes can repress the codon usage effects on mRNA expression. An element in the Hsp70 promoter was identified to be necessary and sufficient for this inhibitory effect. The promoter-dependent codon usage effects on mRNA levels are regulated at the transcriptional level through modulation of histone modifications, nucleosome densities and premature termination. Together, our results demonstrate that promoters play a major role in determining whether codon usage influences gene expression and further establish the transcription-dependent codon usage effects on gene expression.
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Affiliation(s)
- Qian Yang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Xueliang Lyu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.,State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Fangzhou Zhao
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
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92
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Olsen KJ, Johnson SJ. Mtr4 RNA helicase structures and interactions. Biol Chem 2021; 402:605-616. [PMID: 33857361 DOI: 10.1515/hsz-2020-0329] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/10/2020] [Indexed: 01/19/2023]
Abstract
Mtr4 is a Ski2-like RNA helicase that plays a central role in RNA surveillance and degradation pathways as an activator of the RNA exosome. Multiple crystallographic and cryo-EM studies over the past 10 years have revealed important insight into the Mtr4 structure and interactions with protein and nucleic acid binding partners. These structures place Mtr4 at the center of a dynamic process that recruits RNA substrates and presents them to the exosome. In this review, we summarize the available Mtr4 structures and highlight gaps in our current understanding.
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Affiliation(s)
- Keith J Olsen
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT84322-0300, USA
| | - Sean J Johnson
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT84322-0300, USA
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93
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Tazi J, Begon-Pescia C, Campos N, Apolit C, Garcel A, Scherrer D. Specific and selective induction of miR-124 in immune cells by the quinoline ABX464: a transformative therapy for inflammatory diseases. Drug Discov Today 2020; 26:1030-1039. [PMID: 33387693 DOI: 10.1016/j.drudis.2020.12.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/02/2020] [Accepted: 12/24/2020] [Indexed: 12/17/2022]
Abstract
Inflammatory diseases are believed to develop as a result of dysregulated inflammatory responses to environmental factors on susceptible genetic backgrounds. Operating at the level of post-transcriptional gene regulation, miRNAs are a class of endogenous, small noncoding RNAs that can promote downregulation of protein expression by translational repression and/or mRNA degradation of target mRNAs involved in inflammation. MiR-124 is a crucial modulator of inflammation and innate immunity that could provide therapeutic restitution of physiological pathways lost in inflammatory diseases. A recently discovered small quinoline, ABX464, was shown to upregulate miR-124 in human immune cells. In vivo, in a proof-of-concept clinical study, ABX464 showed robust and consistent efficacy in ulcerative colitis (UC). In this review, we examine the current therapeutic options proposed for UC and discuss the drug candidate ABX464 in this context.
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Affiliation(s)
- Jamal Tazi
- Cooperative Laboratory CNRS-Montpellier University, Montpellier, France; ABIVAX, 1919 Route de Mende, 34293 Montpellier, France.
| | | | - Noëlie Campos
- Cooperative Laboratory CNRS-Montpellier University, Montpellier, France; ABIVAX, 1919 Route de Mende, 34293 Montpellier, France
| | - Cécile Apolit
- Cooperative Laboratory CNRS-Montpellier University, Montpellier, France
| | - Aude Garcel
- Cooperative Laboratory CNRS-Montpellier University, Montpellier, France; ABIVAX, 1919 Route de Mende, 34293 Montpellier, France
| | - Didier Scherrer
- Cooperative Laboratory CNRS-Montpellier University, Montpellier, France; ABIVAX, 1919 Route de Mende, 34293 Montpellier, France
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94
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Fraga de Andrade I, Mehta C, Bresnick EH. Post-transcriptional control of cellular differentiation by the RNA exosome complex. Nucleic Acids Res 2020; 48:11913-11928. [PMID: 33119769 PMCID: PMC7708067 DOI: 10.1093/nar/gkaa883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/21/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Given the complexity of intracellular RNA ensembles and vast phenotypic remodeling intrinsic to cellular differentiation, it is instructive to consider the role of RNA regulatory machinery in controlling differentiation. Dynamic post-transcriptional regulation of protein-coding and non-coding transcripts is vital for establishing and maintaining proteomes that enable or oppose differentiation. By contrast to extensively studied transcriptional mechanisms governing differentiation, many questions remain unanswered regarding the involvement of post-transcriptional mechanisms. Through its catalytic activity to selectively process or degrade RNAs, the RNA exosome complex dictates the levels of RNAs comprising multiple RNA classes, thereby regulating chromatin structure, gene expression and differentiation. Although the RNA exosome would be expected to control diverse biological processes, studies to elucidate its biological functions and how it integrates into, or functions in parallel with, cell type-specific transcriptional mechanisms are in their infancy. Mechanistic analyses have demonstrated that the RNA exosome confers expression of a differentiation regulatory receptor tyrosine kinase, downregulates the telomerase RNA component TERC, confers genomic stability and promotes DNA repair, which have considerable physiological and pathological implications. In this review, we address how a broadly operational RNA regulatory complex interfaces with cell type-specific machinery to control cellular differentiation.
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Affiliation(s)
- Isabela Fraga de Andrade
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Charu Mehta
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
| | - Emery H Bresnick
- Wisconsin Blood Cancer Research Institute, Department of Cell and Regenerative Biology, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, 1111 Highland Avenue, 4009 WIMR, Madison, WI 53705, USA
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95
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The Dihydroquinolizinone Compound RG7834 Inhibits the Polyadenylase Function of PAPD5 and PAPD7 and Accelerates the Degradation of Matured Hepatitis B Virus Surface Protein mRNA. Antimicrob Agents Chemother 2020; 65:AAC.00640-20. [PMID: 33046485 DOI: 10.1128/aac.00640-20] [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] [Received: 04/02/2020] [Accepted: 09/30/2020] [Indexed: 12/13/2022] Open
Abstract
Hepatitis B virus (HBV) mRNA metabolism is dependent upon host proteins PAPD5 and PAPD7 (PAPD5/7). PAPD5/7 are cellular, noncanonical, poly(A) polymerases (PAPs) whose main function is to oligoadenylate the 3' end of noncoding RNA (ncRNA) for exosome degradation. HBV seems to exploit these two ncRNA quality-control factors for viral mRNA stabilization, rather than degradation. RG7834 is a small-molecule compound that binds PAPD5/7 and inhibits HBV gene production in both tissue culture and animal study. We reported that RG7834 was able to destabilize multiple HBV mRNA species, ranging from the 3.5-kb pregenomic/precore mRNAs to the 2.4/2.1-kb hepatitis B virus surface protein (HBs) mRNAs, except for the smallest 0.7-kb X protein (HBx) mRNA. Compound-induced HBV mRNA destabilization was initiated by a shortening of the poly(A) tail, followed by an accelerated degradation process in both the nucleus and cytoplasm. In cells expressing HBV mRNA, both PAPD5/7 were found to be physically associated with the viral RNA, and the polyadenylating activities of PAPD5/7 were susceptible to RG7834 repression in a biochemical assay. Moreover, in PAPD5/7 double-knockout cells, viral transcripts with a regular length of the poly(A) sequence could be initially synthesized but became shortened in hours, suggesting that participation of PAPD5/7 in RNA 3' end processing, either during adenosine oligomerization or afterward, is crucial for RNA stabilization.
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96
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Out or decay: fate determination of nuclear RNAs. Essays Biochem 2020; 64:895-905. [DOI: 10.1042/ebc20200005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/12/2020] [Accepted: 08/24/2020] [Indexed: 02/08/2023]
Abstract
Abstract
In eukaryotes, RNAs newly synthesized by RNA polymerase II (RNAPII) undergo several processing steps prior to transport to the cytoplasm. It has long been known that RNAs with defects in processing or export are removed in the nucleus. Recent studies revealed that RNAs without apparent defects are also subjected to nuclear degradation, indicating that nuclear RNA fate is determined in a more complex and dynamic way than previously thought. Nuclear RNA sorting directly determines the quality and quantity of RNA pools for future translation and thus is of significant importance. In this essay, we will summarize recent studies on this topic, mainly focusing on findings in mammalian system, and discuss about important remaining questions and possible biological relevance for nuclear RNA fate determination.
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97
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Wan G, Yan J, Fei Y, Pagano DJ, Kennedy S. A Conserved NRDE-2/MTR-4 Complex Mediates Nuclear RNAi in Caenorhabditis elegans. Genetics 2020; 216:1071-1085. [PMID: 33055090 PMCID: PMC7768265 DOI: 10.1534/genetics.120.303631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/05/2020] [Indexed: 12/21/2022] Open
Abstract
Small regulatory RNAs, such as small interfering RNAs (siRNAs) and PIWI-interacting RNAs, regulate splicing, transcription, and genome integrity in many eukaryotes. In Caenorhabditis elegans, siRNAs bind nuclear Argonautes (AGOs), which interact with homologous premessenger RNAs to recruit downstream silencing effectors, such as NRDE-2, to direct cotranscriptional gene silencing [or nuclear RNA interference (RNAi)]. To further our understanding of the mechanism of nuclear RNAi, we conducted immunoprecipitation-mass spectrometry on C. elegans NRDE-2 The major NRDE-2 interacting protein identified was the RNA helicase MTR-4 Co-immunoprecipitation analyses confirmed a physical association between NRDE-2 and MTR-4 MTR-4 colocalizes with NRDE-2 within the nuclei of most/all C. elegans somatic and germline cells. MTR-4 is required for nuclear RNAi, and interestingly, MTR-4 is recruited to premessenger RNAs undergoing nuclear RNAi via a process requiring nuclear siRNAs, the nuclear AGO HRDE-1, and NRDE-2, indicating that MTR-4 is a component of the C. elegans nuclear RNAi machinery. Finally, we confirm previous reports showing that human (Hs)NRDE2 and HsMTR4 also physically interact. Our data show that the NRDE-2/MTR-4 interactions are evolutionarily conserved, and that, in C. elegans, the NRDE-2/MTR-4 complex contributes to siRNA-directed cotranscriptional gene silencing.
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Affiliation(s)
- Gang Wan
- Ministry Of Education Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China 510275
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
| | - Jenny Yan
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
| | - Yuhan Fei
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China 210095
| | - Daniel J Pagano
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
| | - Scott Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, Massachusetts 02115
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98
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Block TM, Young JAT, Javanbakht H, Sofia MJ, Zhou T. Host RNA quality control as a hepatitis B antiviral target. Antiviral Res 2020; 186:104972. [PMID: 33242518 DOI: 10.1016/j.antiviral.2020.104972] [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] [Received: 07/23/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022]
Abstract
Inhibition of the host RNA polyadenylating polymerases, PAPD5 and PAPD7 (PAPD5/7), with dihydroquinolizinone, a small orally available, molecule, results in a rapid and selective degradation of hepatitis B virus (HBV) RNA, and hence reduction in the amounts of viral gene products. DHQ, is a first in class investigational agent and could represent an entirely new category of HBV antivirals. PAPD5 and PAPD7 are non-canonical, cell specified, polyadenylating polymerases, also called terminal nucleotidyl transferases 4B and 4A (TENT4B/A), respectively. They are involved in the degradation of poor-quality cell transcripts, mostly non-coding RNAs and in the maturation of a sub-set of transcripts. They also appear to play a role in shielding some mRNA from degradation. The results of studies with DHQ, along with other recent findings, provide evidence that repression of the PAPD5/7 arm of the cell "RNA quality control" pathway, causes a profound (multi-fold) reduction rather than increase, in the amount of HBV pre-genomic, pre-core and HBsAg mRNA levels in tissue culture and animal models, as well. In this review we will briefly discuss the need for new HBV therapeutics and provide background about HBV transcription. We also discuss cellular degradation of host transcripts, as it relates to a new family of anti-HBV drugs that interfere with these processes. Finally, since HBV mRNA maturation appears to be selectively sensitive to PAPD5/7 inhibition in hepatocytes, we discuss the possibility of targeting host RNA "quality control" as an antiviral strategy.
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Affiliation(s)
| | - John A T Young
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, F.Hoffmann-La Roche Ltd, Basel, Switzerland.
| | - Hassan Javanbakht
- SQZ Biotechnologies, 200 Arsenal Yards Blvd, Suite 210, Watertown, MA, 02472, USA.
| | - Michael J Sofia
- Arbutus Biopharma, Inc, 701 Veterans Circle, Warminster, PA, 18974, USA.
| | - Tianlun Zhou
- Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA.
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99
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Dou Y, Barbosa I, Jiang H, Iasillo C, Molloy KR, Schulze WM, Cusack S, Schmid M, Le Hir H, LaCava J, Jensen TH. NCBP3 positively impacts mRNA biogenesis. Nucleic Acids Res 2020; 48:10413-10427. [PMID: 32960271 PMCID: PMC7544205 DOI: 10.1093/nar/gkaa744] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/26/2022] Open
Abstract
The nuclear Cap-Binding Complex (CBC), consisting of Nuclear Cap-Binding Protein 1 (NCBP1) and 2 (NCBP2), associates with the nascent 5′cap of RNA polymerase II transcripts and impacts RNA fate decisions. Recently, the C17orf85 protein, also called NCBP3, was suggested to form an alternative CBC by replacing NCBP2. However, applying protein–protein interaction screening of NCBP1, 2 and 3, we find that the interaction profile of NCBP3 is distinct. Whereas NCBP1 and 2 identify known CBC interactors, NCBP3 primarily interacts with components of the Exon Junction Complex (EJC) and the TRanscription and EXport (TREX) complex. NCBP3-EJC association in vitro and in vivo requires EJC core integrity and the in vivo RNA binding profiles of EJC and NCBP3 overlap. We further show that NCBP3 competes with the RNA degradation factor ZC3H18 for binding CBC-bound transcripts, and that NCBP3 positively impacts the nuclear export of polyadenylated RNAs and the expression of large multi-exonic transcripts. Collectively, our results place NCBP3 with the EJC and TREX complexes in supporting mRNA expression.
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Affiliation(s)
- Yuhui Dou
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Isabelle Barbosa
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Claudia Iasillo
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Wiebke Manuela Schulze
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Hervé Le Hir
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
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100
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Xi PW, Zhang X, Zhu L, Dai XY, Cheng L, Hu Y, Shi L, Wei JF, Ding Q. Oncogenic action of the exosome cofactor RBM7 by stabilization of CDK1 mRNA in breast cancer. NPJ Breast Cancer 2020; 6:58. [PMID: 33145401 PMCID: PMC7603334 DOI: 10.1038/s41523-020-00200-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 10/01/2020] [Indexed: 12/22/2022] Open
Abstract
RNA exosome can target the specific RNAs for their processing/degradation by distinct exosome cofactors. As a key component in exosome cofactors, RNA binding motif protein 7 (RBM7) shows the binding specificity for uridine-rich sequences in mRNAs via its RNA recognition motifs. However, the specific function of RBM7 in human breast cancer remains unclear. In vitro, experiments revealed that knockdown of RBM7 dramatically inhibited breast cancer cell proliferation, while inducing G1 cell cycle arrest; the opposite was true when RBM7 was overexpressed. Meanwhile, experiments in vivo confirmed the oncogenic function of RBM7 in breast cancer. RNA sequencing and the following pathway analysis found that cyclin-dependent kinase1 (CDK1) was one of the main gene regulated by RBM7. Overexpression of RBM7 increased CDK1 expression, while RBM7 knockdown decreased it. RIP assays additionally found that RBM7 bound directly to CDK1 mRNA. It was also showed that RBM7 could directly bind to the AU-rich elements (AREs) in 3'-UTR of CDK1 mRNA, which contributed to the stability of CDK1 mRNA by lengthening its half-life. More importantly, the oncogenic activity reduced by knockdown of RBM7 could be rescued by overexpression of CDK1 both in vitro and in vivo, but mutant CDK1 failed. All the evidences implied RBM7 promoted breast cancer cell proliferation by stabilizing CDK1 mRNA via binding to AREs in its 3'-UTR. As we knew, it was the first attempt to connect the RNA exosome to the tumor development, providing new insights into the mechanisms of RNA exosome-linked diseases.
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Affiliation(s)
- Pei-Wen Xi
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Xu Zhang
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Lei Zhu
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Xin-Yuan Dai
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Lin Cheng
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Yue Hu
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Liang Shi
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Ji-Fu Wei
- Research Division of Clinical Pharmacology, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
| | - Qiang Ding
- Jiangsu Breast Disease Center, The First Affiliated Hospital with Nanjing Medical University (Jiangsu Province Hospital), 300 Guangzhou Road, 210029 Nanjing, China
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