1
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Yang H, Thompson B. Widespread changes to the translational landscape in a maize microRNA biogenesis mutant. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38963711 DOI: 10.1111/tpj.16902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 06/08/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
MicroRNAs are short, non-coding RNAs that repress gene expression in both plants and animals and have diverse functions related to growth, development, and stress responses. The ribonuclease, DICER-LIKE1 (DCL1) is required for two steps in plant miRNA biogenesis: cleavage of the primary miRNAs (pri-miRNAs) to release a hairpin structure, called the precursor miRNA (pre-miRNA) and cleavage of the pre-miRNA to generate the miRNA/miRNA* duplex. The mature miRNA guides the RNA-induced silencing complex to target RNAs with complementary sequences, resulting in translational repression and/or RNA cleavage of target mRNAs. However, the relative contribution of translational repression versus mRNA degradation by miRNAs remains unknown at the genome-level in crops, especially in maize. The maize fuzzy tassel (fzt) mutant contains a hypomorphic mutation in DCL1 resulting in broad developmental defects. While most miRNAs are reduced in fzt, the levels of miRNA-targeted mRNAs are not dramatically increased, suggesting that translational regulation by miRNAs may be common. To gain insight into the repression mechanism of plant miRNAs, we combined ribosome profiling and RNA-sequencing to globally survey miRNA activities in maize. Our data indicate that translational repression contributes significantly to regulation of most miRNA targets and that approximately one-third of miRNA targets are regulated primarily at the translational level. Surprisingly, ribosomes appear altered in fzt mutants suggesting that DCL1 may also have a role in ribosome biogenesis. Thus, DICER-LIKE1 shapes the translational landscape in plants through both miRNA-dependent and miRNA-independent mechanisms.
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Affiliation(s)
- Hailong Yang
- Biology Department, East Carolina University, Greenville, North Carolina, USA
| | - Beth Thompson
- Biology Department, East Carolina University, Greenville, North Carolina, USA
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2
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Shatskikh AS, Fefelova EA, Klenov MS. Functions of RNAi Pathways in Ribosomal RNA Regulation. Noncoding RNA 2024; 10:19. [PMID: 38668377 PMCID: PMC11054153 DOI: 10.3390/ncrna10020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.
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Affiliation(s)
- Aleksei S. Shatskikh
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia;
| | - Elena A. Fefelova
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Mikhail S. Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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3
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Fiore APZP, Maity S, Jeffery L, An D, Rendleman J, Iannitelli D, Choi H, Mazzoni E, Vogel C. Identification of molecular signatures defines the differential proteostasis response in induced spinal and cranial motor neurons. Cell Rep 2024; 43:113885. [PMID: 38457337 PMCID: PMC11018139 DOI: 10.1016/j.celrep.2024.113885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 12/12/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024] Open
Abstract
Amyotrophic lateral sclerosis damages proteostasis, affecting spinal and upper motor neurons earlier than a subset of cranial motor neurons. To aid disease understanding, we exposed induced cranial and spinal motor neurons (iCrMNs and iSpMNs) to proteotoxic stress, under which iCrMNs showed superior survival, quantifying the transcriptome and proteome for >8,200 genes at 0, 12, and 36 h. Two-thirds of the proteome showed cell-type differences. iSpMN-enriched proteins related to DNA/RNA metabolism, and iCrMN-enriched proteins acted in the endoplasmic reticulum (ER)/ER chaperone complex, tRNA aminoacylation, mitochondria, and the plasma/synaptic membrane, suggesting that iCrMNs expressed higher levels of proteins supporting proteostasis and neuronal function. When investigating the increased proteasome levels in iCrMNs, we showed that the activity of the 26S proteasome, but not of the 20S proteasome, was higher in iCrMNs than in iSpMNs, even after a stress-induced decrease. We identified Ublcp1 as an iCrMN-specific regulator of the nuclear 26S activity.
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Affiliation(s)
| | - Shuvadeep Maity
- New York University, Department of Biology, New York, NY 10003, USA; Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Lauren Jeffery
- New York University, Department of Biology, New York, NY 10003, USA
| | - Disi An
- New York University, Department of Biology, New York, NY 10003, USA
| | - Justin Rendleman
- New York University, Department of Biology, New York, NY 10003, USA
| | - Dylan Iannitelli
- New York University, Department of Biology, New York, NY 10003, USA
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Esteban Mazzoni
- New York University, Department of Biology, New York, NY 10003, USA; Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Christine Vogel
- New York University, Department of Biology, New York, NY 10003, USA.
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4
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Bryant CJ, McCool MA, Rosado González G, Abriola L, Surovtseva Y, Baserga S. Discovery of novel microRNA mimic repressors of ribosome biogenesis. Nucleic Acids Res 2024; 52:1988-2011. [PMID: 38197221 PMCID: PMC10899765 DOI: 10.1093/nar/gkad1235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 12/03/2023] [Accepted: 12/16/2023] [Indexed: 01/11/2024] Open
Abstract
While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A (p21) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We provide evidence that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.
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Affiliation(s)
- Carson J Bryant
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Mason A McCool
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
| | | | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, 06516, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, 06520, USA
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5
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Wei X, Tang J, Lin C, Jiang X. Review: Non-canonical role of Drosha ribonuclease III. Int J Biol Macromol 2023; 253:127202. [PMID: 37793530 DOI: 10.1016/j.ijbiomac.2023.127202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023]
Abstract
The typical function of Drosha is participating in cleaving pri-miRNA, the initial step of miRNA biogenesis, in the nucleus. Since Drosha has a double-stranded RNA-binding domain and two RNase III domains, when it binds and/or cleaves other RNA species other than pri-miRNA, Drosha is able to induce a variety of novel biological effects. Moreover, by interacting with other protein, Drosha is able to modify the function of other protein complexes. Recently, diverse non-classical functions of Drosha have been demonstrated, such as promoting DNA damage repair, transcriptional activation and inhibition, pre-mRNA splicing regulation, mRNA destabilization, and virus-host interaction. In this review, we describe these newly discovered functions of Drosha in order to present a panoramic picture of the novel biological processes that Drosha is involved in.
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Affiliation(s)
- Xuanshuo Wei
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Jin Tang
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Chuwen Lin
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China
| | - Xuan Jiang
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, 518107, Guangdong, China.
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6
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Kour S, Fortuna T, Anderson EN, Mawrie D, Bilstein J, Sivasubramanian R, Ward C, Roy R, Rajasundaram D, Sterneckert J, Pandey UB. Drosha-dependent microRNAs modulate FUS-mediated neurodegeneration in vivo. Nucleic Acids Res 2023; 51:11258-11276. [PMID: 37791873 PMCID: PMC10639082 DOI: 10.1093/nar/gkad774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/03/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
Mutations in the Fused in Sarcoma (FUS) gene cause the familial and progressive form of amyotrophic lateral sclerosis (ALS). FUS is a nuclear RNA-binding protein involved in RNA processing and the biogenesis of a specific set of microRNAs. Here we report that Drosha and two previously uncharacterized Drosha-dependent miRNAs are strong modulators of FUS expression and prevent the cytoplasmic segregation of insoluble mutant FUS in vivo. We demonstrate that depletion of Drosha mitigates FUS-mediated degeneration, survival and motor defects in Drosophila. Mutant FUS strongly interacts with Drosha and causes its cytoplasmic mis-localization into the insoluble FUS inclusions. Reduction in Drosha levels increases the solubility of mutant FUS. Interestingly, we found two Drosha dependent microRNAs, miR-378i and miR-6832-5p, which differentially regulate the expression, solubility and cytoplasmic aggregation of mutant FUS in iPSC neurons and mammalian cells. More importantly, we report different modes of action of these miRNAs against mutant FUS. Whereas miR-378i may regulate mutant FUS inclusions by preventing G3BP-mediated stress granule formation, miR-6832-5p may affect FUS expression via other proteins or pathways. Overall, our research reveals a possible association between ALS-linked FUS mutations and the Drosha-dependent miRNA regulatory circuit, as well as a useful perspective on potential ALS treatment via microRNAs.
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Affiliation(s)
- Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Tyler Fortuna
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Darilang Mawrie
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Jessica Bilstein
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, 01307, Germany
| | - Ramakrishnan Sivasubramanian
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, 01307, Germany
| | - Caroline Ward
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Rishit Roy
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, 01307, Germany
- Medical Faculty Carl Gustav Carus of TU Dresden, Dresden, 01307, Germany
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
- Children's Neuroscience Institute, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA 15224, USA
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7
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Bryant CJ, McCool MA, Rosado-González GT, Abriola L, Surovtseva YV, Baserga SJ. Discovery of novel microRNA mimic repressors of ribosome biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.526327. [PMID: 36824951 PMCID: PMC9949135 DOI: 10.1101/2023.02.17.526327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
While microRNAs and other non-coding RNAs are the next frontier of novel regulators of mammalian ribosome biogenesis (RB), a systematic exploration of microRNA-mediated RB regulation has not yet been undertaken. We carried out a high-content screen in MCF10A cells for changes in nucleolar number using a library of 2,603 mature human microRNA mimics. Following a secondary screen for nucleolar rRNA biogenesis inhibition, we identified 72 novel microRNA negative regulators of RB after stringent hit calling. Hits included 27 well-conserved microRNAs present in MirGeneDB, and were enriched for mRNA targets encoding proteins with nucleolar localization or functions in cell cycle regulation. Rigorous selection and validation of a subset of 15 microRNA hits unexpectedly revealed that most of them caused dysregulated pre-rRNA processing, elucidating a novel role for microRNAs in RB regulation. Almost all hits impaired global protein synthesis and upregulated CDKN1A ( p21 ) levels, while causing diverse effects on RNA Polymerase 1 (RNAP1) transcription and TP53 protein levels. We discovered that the MIR-28 siblings, hsa-miR-28-5p and hsa-miR-708-5p, directly and potently target the ribosomal protein mRNA RPS28 via tandem primate-specific 3' UTR binding sites, causing a severe pre-18S pre-rRNA processing defect. Our work illuminates novel microRNA attenuators of RB, forging a promising new path for microRNA mimic chemotherapeutics.
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8
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RNase III, Ribosome Biogenesis and Beyond. Microorganisms 2021; 9:microorganisms9122608. [PMID: 34946208 PMCID: PMC8708148 DOI: 10.3390/microorganisms9122608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022] Open
Abstract
The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved through a plethora of effectors involved in the maturation and assembly of ribosomal RNAs and proteins. Conserved from bacteria to eukaryotes, double-stranded specific RNase III enzymes play a large role in the regulation of gene expression and the processing of ribosomal RNAs. In this review, we describe the canonical role of RNase III in the biogenesis of the ribosome comparing conserved and unique features from bacteria to eukaryotes. Furthermore, we report additional roles in ribosome biogenesis re-enforcing the importance of RNase III.
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9
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Guan L, Grigoriev A. Computational meta-analysis of ribosomal RNA fragments: potential targets and interaction mechanisms. Nucleic Acids Res 2021; 49:4085-4103. [PMID: 33772581 PMCID: PMC8053083 DOI: 10.1093/nar/gkab190] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
The most abundant cellular RNA species, ribosomal RNA (rRNA), appears to be a source of massive amounts of non-randomly generated fragments. We found rRNA fragments (rRFs) in immunoprecipitated Argonaute (Ago-IP) complexes in human and mouse cells and in small RNA sequencing datasets. In human Ago1-IP, guanine-rich rRFs were preferentially cut in single-stranded regions of mature rRNAs between pyrimidines and adenosine, and non-randomly paired with cellular transcripts in crosslinked chimeras. Numerous identical rRFs were found in the cytoplasm and nucleus in mouse Ago2-IP. We report specific interaction motifs enriched in rRF-target pairs. Locations of such motifs on rRFs were compatible with the Ago structural features and patterns of the Ago-RNA crosslinking in both species. Strikingly, many of these motifs may bind to double-stranded regions on target RNAs, suggesting a potential pathway for regulating translation by unwinding mRNAs. Occurring on either end of rRFs and matching intronic, untranslated or coding regions in targets, such interaction sites extend the concept of microRNA seed regions. Targeting both borders of certain short introns, rRFs may be involved in their biogenesis or function, facilitated by Ago. Frequently dismissed as noise, rRFs are poised to greatly enrich the known functional spectrum of small RNA regulation.
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Affiliation(s)
- Lingyu Guan
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA
| | - Andrey Grigoriev
- Department of Biology, Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA
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10
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Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases. Int J Mol Sci 2021; 22:ijms22020616. [PMID: 33435485 PMCID: PMC7827160 DOI: 10.3390/ijms22020616] [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: 11/30/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/12/2022] Open
Abstract
Ribonuclease Dicer belongs to the family of RNase III endoribonucleases, the enzymes that specifically hydrolyze phosphodiester bonds found in double-stranded regions of RNAs. Dicer enzymes are mostly known for their essential role in the biogenesis of small regulatory RNAs. A typical Dicer-type RNase consists of a helicase domain, a domain of unknown function (DUF283), a PAZ (Piwi-Argonaute-Zwille) domain, two RNase III domains, and a double-stranded RNA binding domain; however, the domain composition of Dicers varies among species. Dicer and its homologues developed only in eukaryotes; nevertheless, the two enzymatic domains of Dicer, helicase and RNase III, display high sequence similarity to their prokaryotic orthologs. Evolutionary studies indicate that a combination of the helicase and RNase III domains in a single protein is a eukaryotic signature and is supposed to be one of the critical events that triggered the consolidation of the eukaryotic RNA interference. In this review, we provide the genetic insight into the domain organization and structure of Dicer proteins found in vertebrate and invertebrate animals, plants and fungi. We also discuss, in the context of the individual domains, domain deletion variants and partner proteins, a variety of Dicers’ functions not only related to small RNA biogenesis pathways.
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11
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Stolyarenko AD. Nuclear Argonaute Piwi Gene Mutation Affects rRNA by Inducing rRNA Fragment Accumulation, Antisense Expression, and Defective Processing in Drosophila Ovaries. Int J Mol Sci 2020; 21:ijms21031119. [PMID: 32046213 PMCID: PMC7037970 DOI: 10.3390/ijms21031119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/27/2020] [Accepted: 02/04/2020] [Indexed: 12/26/2022] Open
Abstract
Drosophila key nuclear piRNA silencing pathway protein Piwi of the Argonaute family has been classically studied as a factor controlling transposable elements and fertility. Piwi has been shown to concentrate in the nucleolus for reasons largely unknown. Ribosomal RNA is the main component of the nucleolus. In this work the effect of a piwi mutation on rRNA is described. This work led to three important conclusions: A mutation in piwi induces antisense 5S rRNA expression, a processing defect of 2S rRNA orthologous to the 3′-end of eukaryotic 5.8S rRNA, and accumulation of fragments of all five rRNAs in Drosophilamelanogaster ovaries. Hypotheses to explain these phenomena are proposed, possibly involving the interaction of the components of the piRNA pathway with the RNA surveillance machinery.
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Affiliation(s)
- Anastasia D Stolyarenko
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., Moscow 123182, Russia
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12
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Weiner AMJ, Scampoli NL, Steeman TJ, Dooley CM, Busch-Nentwich EM, Kelsh RN, Calcaterra NB. Dicer1 is required for pigment cell and craniofacial development in zebrafish. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:472-485. [PMID: 30840854 DOI: 10.1016/j.bbagrm.2019.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 02/22/2019] [Accepted: 02/23/2019] [Indexed: 12/22/2022]
Abstract
The multidomain RNase III endoribonuclease DICER is required for the generation of most functional microRNAs (miRNAs). Loss of Dicer affects developmental processes at different levels. Here, we characterized the zebrafish Dicer1 mutant, dicer1sa9205, which has a single point mutation induced by N-ethyl-N-nitrosourea mutagenesis. Heterozygous dicer1sa9205 developed normally, being phenotypically indistinguishable from wild-type siblings. Homozygous dicer1sa9205 mutants display smaller eyes, abnormal craniofacial development and aberrant pigmentation. Reduced numbers of both iridophores and melanocytes were observed in the head and ventral trunk of dicer1sa9205 homozygotes; the effect on melanocytes was stronger and detectable earlier in development. The expression of microphthalmia-associated transcription factor a (mitfa), the master gene for melanocytes differentiation, was enhanced in dicer1-depleted fish. Similarly, the expression of SRY-box containing gene 10 (sox10), required for mitfa activation, was higher in mutants than in wild types. In silico and in vivo analyses of either sox10 or mitfa 3'UTRs revealed conserved potential miRNA binding sites likely involved in the post-transcriptional regulation of both genes. Based on these findings, we propose that dicer1 participates in the gene regulatory network governing zebrafish melanocyte differentiation by controlling the expression of mitfa and sox10.
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Affiliation(s)
- Andrea M J Weiner
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina.
| | - Nadia L Scampoli
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina
| | - Tomás J Steeman
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina
| | - Christopher M Dooley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Robert N Kelsh
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, S2000EZP Rosario, Argentina.
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13
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Neuronal activity regulates DROSHA via autophagy in spinal muscular atrophy. Sci Rep 2018; 8:7907. [PMID: 29784949 PMCID: PMC5962575 DOI: 10.1038/s41598-018-26347-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 05/10/2018] [Indexed: 02/06/2023] Open
Abstract
Dysregulated miRNA expression and mutation of genes involved in miRNA biogenesis have been reported in motor neuron diseases including spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Therefore, identifying molecular mechanisms governing miRNA expression is important to understand these diseases. Here, we report that expression of DROSHA, which is a critical enzyme in the microprocessor complex and essential for miRNA biogenesis, is reduced in motor neurons from an SMA mouse model. We show that DROSHA is degraded by neuronal activity induced autophagy machinery, which is also dysregulated in SMA. Blocking neuronal activity or the autophagy-lysosome pathway restores DROSHA levels in SMA motor neurons. Moreover, reducing DROSHA levels enhances axonal growth. As impaired axonal growth is a well described phenotype of SMA motor neurons, these data suggest that DROSHA reduction by autophagy may mitigate the phenotype of SMA. In summary, these findings suggest that autophagy regulates RNA metabolism and neuronal growth via the DROSHA/miRNA pathway and this pathway is dysregulated in SMA.
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14
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Abstract
MicroRNA (miRNA) is the noncoding gene: therefore, the miRNA gene inheritably controls protein gene expression through transcriptional and post-transcriptional levels. Aberrant expression of miRNA genes causes various human diseases, especially cancers. Although cancer is a complex disease, cancer/miRNA implication has yet been grasped from the perspective of miRNA profile in bed side. Since miRNA is the mobile genetic element, the clinical verification of miRNA in microvesicle of blood is too much straggle to predict potential cancer/miRNA associations without bioinformatical computing. Further, experimental investigation of miRNA/cancer pathways is expensive and time-consuming. While the accumulated data (big data) of miRNA profiles has been on line as the databases in cancers, using the database algorithms for miRNA target prediction have reduced required time for conventional experiments and have cut the cost. Computational prediction of miRNA/target mRNA has shown numerous significant outcomes that are unobtainable only by experimental approaches. However, ID of miRNA in the annotation is an arbitrary number and the ID is not related with miRNA its functions. Therefore, it has not been physicochemically shown why multiple miRNAs in blood or tissues are useful for diagnosis and porgnosis of human diseases or why function of single miRNA in cancer is rendered to oncomir or tumopr suppressor. In addition, it is less cleared why environmental factors, such as temperature, radiation, therapeutic anti-cancer immune or chemical agents can alter the expression of miRNAs in the cell. The ceRNA theory would not be enough for the investigation of such subjects. Given miRNA/target prediction tools, to elucidate such issues with computer simulation we have previously introduced the quantum miRNA/miRNA interaction as a new scoring using big database. The quantum score was implicated in miRNA synergisms in cancer and participated in the miRNA/target interaction on human diseases. On the other hand, ribosomal RNA (rRNA) is the dominant RNA species of the cells. It is well known that ribosomopathies, such as Diamond-Blackfan anemia, dyskeratiosis congenital, Shwachman-Diamond syndrome, 5q-myelodysplastic syndrome, Treacher Collins syndrome, cartilage-hair hypoplasia, North American Indian childhood cirrhosis, isolated congenital asplenia, Bowen-Conradi syndrome and cancer are caused by altered expression of ribosomal proteins or rRNA genes. We have proposed the hypothesis that the interaction among miRNAs from rRNA and/or other cellular miRNAs would be involved into cancer as the ribosomopathy. Subsequently, we found rRNA-derived miRNAs (rmiRNAs) by using the sequence homology search (miPS) with miRNA database (miRBase). Further, the pathway related with cancer between rmiRNA/target protein gene was predicted by miRNA entangling target sorting (METS) algorithm. In this chapter, we describe about the usage of in silico miRNA identification program, miRNA/target prediction search through the database and quantum language of miRNA by the METS, and the ontology analysis. In particular, the METS algorithm according to the quantum value would be useful simulator to discover a new therapeutic target aganist cancer. It may also partly contribute to the elucidation of complex mechanisms and development of agents of anti-cancer.
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Affiliation(s)
- Yoichi Robertus Fujii
- Retroviral Genetics Group, Pharmaco-MicroRNA Genomics, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan.
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15
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Abstract
DROSHA is the catalytic subunit of the Microprocessor complex, which initiates microRNA (miRNA) maturation in the nucleus by recognizing and cleaving hairpin precursors embedded in primary transcripts. However, accumulating evidence suggests that not all hairpin substrates of DROSHA are associated with the generation of functional small RNAs. By targeting those hairpins, DROSHA regulates diverse aspects of RNA metabolism across the transcriptome, serves as a line of defense against the expression of potentially deleterious elements, and permits cell fate determination and differentiation. DROSHA is also versatile in the way that it executes these noncanonical functions, occasionally depending on its RNA-binding activity rather than its catalytic activity. Herein, we discuss the functional and mechanistic diversity of DROSHA beyond the miRNA biogenesis pathway in light of recent findings.
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Affiliation(s)
- Dooyoung Lee
- a Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea
| | - Chanseok Shin
- a Department of Agricultural Biotechnology , Seoul National University , Seoul , Republic of Korea.,b Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute , Seoul National University , Seoul , Republic of Korea
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16
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Liang XH, Sun H, Shen W, Wang S, Yao J, Migawa MT, Bui HH, Damle SS, Riney S, Graham MJ, Crooke RM, Crooke ST. Antisense oligonucleotides targeting translation inhibitory elements in 5' UTRs can selectively increase protein levels. Nucleic Acids Res 2017; 45:9528-9546. [PMID: 28934489 PMCID: PMC5766168 DOI: 10.1093/nar/gkx632] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 07/05/2017] [Accepted: 07/10/2017] [Indexed: 12/31/2022] Open
Abstract
A variety of diseases are caused by deficiencies in amounts or activity of key proteins. An approach that increases the amount of a specific protein might be of therapeutic benefit. We reasoned that translation could be specifically enhanced using trans-acting agents that counter the function of negative regulatory elements present in the 5' UTRs of some mRNAs. We recently showed that translation can be enhanced by antisense oligonucleotides (ASOs) that target upstream open reading frames. Here we report the amount of a protein can also be selectively increased using ASOs designed to hybridize to other translation inhibitory elements in 5' UTRs. Levels of human RNASEH1, LDLR, and ACP1 and of mouse ACP1 and ARF1 were increased up to 2.7-fold in different cell types and species upon treatment with chemically modified ASOs targeting 5' UTR inhibitory regions in the mRNAs encoding these proteins. The activities of ASOs in enhancing translation were sequence and position dependent and required helicase activity. The ASOs appear to improve the recruitment of translation initiation factors to the target mRNA. Importantly, ASOs targeting ACP1 mRNA significantly increased the level of ACP1 protein in mice, suggesting that this approach has therapeutic and research potentials.
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Affiliation(s)
- Xue-hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Hong Sun
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Shiyu Wang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Joyee Yao
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Michael T. Migawa
- Department of Medicinal Chemistry, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Huynh-Hoa Bui
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Sagar S. Damle
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Stan Riney
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Mark J. Graham
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Rosanne M. Crooke
- Department of Antisense Drug Discovery, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
| | - Stanley T. Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., Carlsbad, CA, USA
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17
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Abstract
The nucleolus is a distinct compartment of the nucleus responsible for ribosome biogenesis. Mis-regulation of nucleolar functions and of the cellular translation machinery has been associated with disease, in particular with many types of cancer. Indeed, many tumor suppressors (p53, Rb, PTEN, PICT1, BRCA1) and proto-oncogenes (MYC, NPM) play a direct role in the nucleolus, and interact with the RNA polymerase I transcription machinery and the nucleolar stress response. We have identified Dicer and the RNA interference pathway as having an essential role in the nucleolus of quiescent Schizosaccharomyces pombe cells, distinct from pericentromeric silencing, by controlling RNA polymerase I release. We propose that this novel function is evolutionarily conserved and may contribute to the tumorigenic pre-disposition of DICER1 mutations in mammals.
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Affiliation(s)
- Benjamin Roche
- a Martienssen Lab, Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA
| | - Benoît Arcangioli
- b Genome Dynamics Unit, UMR 3525 CNRS, Institut Pasteur , Paris , France
| | - Rob Martienssen
- a Martienssen Lab, Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA.,c Howard Hughes Medical Institute, Cold Spring Harbor Laboratory , Cold Spring Harbor , NY , USA
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18
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Tomecki R, Sikorski PJ, Zakrzewska-Placzek M. Comparison of preribosomal RNA processing pathways in yeast, plant and human cells - focus on coordinated action of endo- and exoribonucleases. FEBS Lett 2017; 591:1801-1850. [PMID: 28524231 DOI: 10.1002/1873-3468.12682] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/14/2017] [Accepted: 05/15/2017] [Indexed: 12/17/2022]
Abstract
Proper regulation of ribosome biosynthesis is mandatory for cellular adaptation, growth and proliferation. Ribosome biogenesis is the most energetically demanding cellular process, which requires tight control. Abnormalities in ribosome production have severe consequences, including developmental defects in plants and genetic diseases (ribosomopathies) in humans. One of the processes occurring during eukaryotic ribosome biogenesis is processing of the ribosomal RNA precursor molecule (pre-rRNA), synthesized by RNA polymerase I, into mature rRNAs. It must not only be accurate but must also be precisely coordinated with other phenomena leading to the synthesis of functional ribosomes: RNA modification, RNA folding, assembly with ribosomal proteins and nucleocytoplasmic RNP export. A multitude of ribosome biogenesis factors ensure that these events take place in a correct temporal order. Among them are endo- and exoribonucleases involved in pre-rRNA processing. Here, we thoroughly present a wide spectrum of ribonucleases participating in rRNA maturation, focusing on their biochemical properties, regulatory mechanisms and substrate specificity. We also discuss cooperation between various ribonucleolytic activities in particular stages of pre-rRNA processing, delineating major similarities and differences between three representative groups of eukaryotes: yeast, plants and humans.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Poland
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19
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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20
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Molecular mechanisms of Dicer: endonuclease and enzymatic activity. Biochem J 2017; 474:1603-1618. [PMID: 28473628 PMCID: PMC5415849 DOI: 10.1042/bcj20160759] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 12/12/2022]
Abstract
The enzyme Dicer is best known for its role as a riboendonuclease in the small RNA pathway. In this canonical role, Dicer is a critical regulator of the biogenesis of microRNA and small interfering RNA, as well as a growing number of additional small RNAs derived from various sources. Emerging evidence demonstrates that Dicer's endonuclease role extends beyond the generation of small RNAs; it is also involved in processing additional endogenous and exogenous substrates, and is becoming increasingly implicated in regulating a variety of other cellular processes, outside of its endonuclease function. This review will describe the canonical and newly identified functions of Dicer.
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21
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Human Ribosomal RNA-Derived Resident MicroRNAs as the Transmitter of Information upon the Cytoplasmic Cancer Stress. BIOMED RESEARCH INTERNATIONAL 2016; 2016:7562085. [PMID: 27517048 PMCID: PMC4969525 DOI: 10.1155/2016/7562085] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/19/2016] [Indexed: 12/13/2022]
Abstract
Dysfunction of ribosome biogenesis induces divergent ribosome-related diseases including ribosomopathy and occasionally results in carcinogenesis. Although many defects in ribosome-related genes have been investigated, little is known about contribution of ribosomal RNA (rRNA) in ribosome-related disorders. Meanwhile, microRNA (miRNA), an important regulator of gene expression, is derived from both coding and noncoding region of the genome and is implicated in various diseases. Therefore, we performed in silico analyses using M-fold, TargetScan, GeneCoDia3, and so forth to investigate RNA relationships between rRNA and miRNA against cellular stresses. We have previously shown that miRNA synergism is significantly correlated with disease and the miRNA package is implicated in memory for diseases; therefore, quantum Dynamic Nexus Score (DNS) was also calculated using MESer program. As a result, seventeen RNA sequences identical with known miRNAs were detected in the human rRNA and termed as rRNA-hosted miRNA analogs (rmiRNAs). Eleven of them were predicted to form stem-loop structures as pre-miRNAs, and especially one stem-loop was completely identical with hsa-pre-miR-3678 located in the non-rDNA region. Thus, these rmiRNAs showed significantly high DNS values, participation in regulation of cancer-related pathways, and interaction with nucleolar RNAs, suggesting that rmiRNAs may be stress-responsible resident miRNAs which transmit stress-tuning information in multiple levels.
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22
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Atwood BL, Woolnough JL, Lefevre GM, Saint Just Ribeiro M, Felsenfeld G, Giles KE. Human Argonaute 2 Is Tethered to Ribosomal RNA through MicroRNA Interactions. J Biol Chem 2016; 291:17919-28. [PMID: 27288410 DOI: 10.1074/jbc.m116.725051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Indexed: 11/06/2022] Open
Abstract
The primary role of the RNAi machinery is to promote mRNA degradation within the cytoplasm in a microRNA-dependent manner. However, both Dicer and the Argonaute protein family have expanded roles in gene regulation within the nucleus. To further our understanding of this role, we have identified chromatin binding sites for AGO2 throughout the 45S region of the human rRNA gene. The location of these sites was mirrored by the positions of AGO2 cross-linking sites identified via PAR-CLIP-seq. AGO2 binding to the rRNA within the nucleus was confirmed by RNA immunoprecipitation and quantitative-PCR. To explore a possible mechanism by which AGO2 could be recruited to the rRNA, we identified 1174 regions within the 45S rRNA transcript that have the ability to form a perfect duplex with position 2-6 (seed sequence) of each microRNA expressed in HEK293T cells. Of these potential AGO2 binding sites, 479 occurred within experimentally verified AGO2-rRNA cross-linking sites. The ability of AGO2 to cross-link to rRNA was almost completely lost in a DICER knock-out cell line. The transfection of miR-92a-2-3p into the noDICE cell line facilitated AGO2 cross-linking at a region of the rRNA that has a perfect seed match at positions 3-8, including a single G-U base pair. Knockdown of AGO2 within HEK293T cells causes a slight, but statistically significant increase in the overall rRNA synthesis rate but did not impact the ratio of processing intermediates or the recruitment of the Pol I transcription factor UBTF.
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Affiliation(s)
- Blake L Atwood
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| | - Jessica L Woolnough
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| | - Gaelle M Lefevre
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Mariana Saint Just Ribeiro
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland
| | - Keith E Giles
- From the UAB Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35209 and
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23
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Link S, Grund SE, Diederichs S. Alternative splicing affects the subcellular localization of Drosha. Nucleic Acids Res 2016; 44:5330-43. [PMID: 27185895 PMCID: PMC4914122 DOI: 10.1093/nar/gkw400] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/29/2016] [Indexed: 12/21/2022] Open
Abstract
The RNase III enzyme Drosha is a key factor in microRNA (miRNA) biogenesis and as such indispensable for cellular homeostasis and developmental processes. Together with its co-factor DGCR8, it converts the primary transcript (pri-miRNA) into the precursor hairpin (pre-miRNA) in the nucleus. While the middle and the C-terminal domain are crucial for pri-miRNA processing and DGCR8 binding, the function of the N-terminus remains cryptic. Different studies have linked this region to the subcellular localization of Drosha, stabilization and response to stress. In this study, we identify alternatively spliced Drosha transcripts that are devoid of a part of the arginine/serine-rich (RS-rich) domain and expressed in a large set of human cells. In contrast to their expected habitation, we find two isoforms also present in the cytoplasm, while the other two isoforms reside exclusively in the nucleus. Their processing activity for pri-miRNAs and the binding to co-factors remains unaltered. In multiple cell lines, the endogenous mRNA expression of the Drosha isoforms correlates with the localization of endogenous Drosha proteins. The pri-miRNA processing efficiency is not significantly different between groups of cells with or without cytoplasmic Drosha expression. In summary, we discovered novel isoforms of Drosha with differential subcellular localization pointing toward additional layers of complexity in the regulation of its activity.
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Affiliation(s)
- Steffen Link
- Division of RNA Biology and Cancer (B150), German Cancer Research Center (DKFZ), Heidelberg, Germany Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Stefanie E Grund
- Division of RNA Biology and Cancer (B150), German Cancer Research Center (DKFZ), Heidelberg, Germany Institute of Pathology, University of Heidelberg, Heidelberg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center-University of Freiburg, Freiburg, Germany Faculty of Medicine, University of Freiburg, Freiburg, Germany Division of RNA Biology and Cancer (B150), German Cancer Research Center (DKFZ), Heidelberg, Germany German Cancer Consortium (DKTK), Freiburg, Germany Institute of Pathology, University of Heidelberg, Heidelberg, Germany Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
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24
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Liang XH, Shen W, Sun H, Kinberger GA, Prakash TP, Nichols JG, Crooke ST. Hsp90 protein interacts with phosphorothioate oligonucleotides containing hydrophobic 2'-modifications and enhances antisense activity. Nucleic Acids Res 2016; 44:3892-907. [PMID: 26945041 PMCID: PMC4856991 DOI: 10.1093/nar/gkw144] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/25/2016] [Indexed: 02/05/2023] Open
Abstract
RNase H1-dependent antisense oligonucleotides (ASOs) are chemically modified to enhance pharmacological properties. Major modifications include phosphorothioate (PS) backbone and different 2′-modifications in 2–5 nucleotides at each end (wing) of an ASO. Chemical modifications can affect protein binding and understanding ASO-protein interactions is important for better drug design. Recently we identified many intracellular ASO-binding proteins and found that protein binding could affect ASO potency. Here, we analyzed the structure-activity-relationships of ASO-protein interactions and found 2′-modifications significantly affected protein binding, including La, P54nrb and NPM. PS-ASOs containing more hydrophobic 2′-modifications exhibit higher affinity for proteins in general, although certain proteins, e.g. Ku70/Ku80 and TCP1, are less affected by 2′-modifications. We found that Hsp90 protein binds PS-ASOs containing locked-nucleic-acid (LNA) or constrained-ethyl-bicyclic-nucleic-acid ((S)-cEt) modifications much more avidly than 2′-O-methoxyethyl (MOE). ASOs bind the mid-domain of Hsp90 protein. Hsp90 interacts with more hydrophobic 2′ modifications, e.g. (S)-cEt or LNA, in the 5′-wing of the ASO. Reduction of Hsp90 protein decreased activity of PS-ASOs with 5′-LNA or 5′-cEt wings, but not with 5′-MOE wing. Together, our results indicate Hsp90 protein enhances the activity of PS/LNA or PS/(S)-cEt ASOs, and imply that altering protein binding of ASOs using different chemical modifications can improve therapeutic performance of PS-ASOs.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Wen Shen
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Garth A Kinberger
- Department of Medicinal Chemistry, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Department of Medicinal Chemistry, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, IONIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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25
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Caudron-Herger M, Pankert T, Seiler J, Németh A, Voit R, Grummt I, Rippe K. Alu element-containing RNAs maintain nucleolar structure and function. EMBO J 2015; 34:2758-74. [PMID: 26464461 DOI: 10.15252/embj.201591458] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023] Open
Abstract
Non-coding RNAs play a key role in organizing the nucleus into functional subcompartments. By combining fluorescence microscopy and RNA deep-sequencing-based analysis, we found that RNA polymerase II transcripts originating from intronic Alu elements (aluRNAs) were enriched in the nucleolus. Antisense-oligo-mediated depletion of aluRNAs or drug-induced inhibition of RNA polymerase II activity disrupted nucleolar structure and impaired RNA polymerase I-dependent transcription of rRNA genes. In contrast, overexpression of a prototypic aluRNA sequence increased both nucleolus size and levels of pre-rRNA, suggesting a functional link between aluRNA, nucleolus integrity and pre-rRNA synthesis. Furthermore, we show that aluRNAs interact with nucleolin and target ectopic genomic loci to the nucleolus. Our study suggests an aluRNA-based mechanism that links RNA polymerase I and II activities and modulates nucleolar structure and rRNA production.
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Affiliation(s)
- Maïwen Caudron-Herger
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Teresa Pankert
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
| | - Jeanette Seiler
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Attila Németh
- Department of Biochemistry III, Biochemistry Center Regensburg University of Regensburg, Regensburg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center, Heidelberg, Germany
| | - Karsten Rippe
- Genome Organization & Function, German Cancer Research Center (DKFZ) Bioquant Center, Heidelberg, Germany
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26
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Bisset DR, Stepniak-Konieczna EA, Zavaljevski M, Wei J, Carter GT, Weiss MD, Chamberlain JR. Therapeutic impact of systemic AAV-mediated RNA interference in a mouse model of myotonic dystrophy. Hum Mol Genet 2015; 24:4971-83. [PMID: 26082468 DOI: 10.1093/hmg/ddv219] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/08/2015] [Indexed: 01/22/2023] Open
Abstract
RNA interference (RNAi) offers a promising therapeutic approach for dominant genetic disorders that involve gain-of-function mechanisms. One candidate disease for RNAi therapy application is myotonic dystrophy type 1 (DM1), which results from toxicity of a mutant mRNA. DM1 is caused by expansion of a CTG repeat in the 3' UTR of the DMPK gene. The expression of DMPK mRNA containing an expanded CUG repeat (CUG(exp)) leads to defects in RNA biogenesis and turnover. We designed miRNA-based RNAi hairpins to target the CUG(exp) mRNA in the human α-skeletal muscle actin long-repeat (HSA(LR)) mouse model of DM1. RNAi expression cassettes were delivered to HSA(LR) mice using recombinant adeno-associated viral (rAAV) vectors injected intravenously as a route to systemic gene therapy. Vector delivery significantly reduced disease pathology in muscles of the HSA(LR) mice, including a reduction in the CUG(exp) mRNA, a reduction in myotonic discharges, a shift toward adult pre-mRNA splicing patterns, reduced myofiber hypertrophy and a decrease in myonuclear foci containing the CUG(exp) mRNA. Significant reversal of hallmarks of DM1 in the rAAV RNAi-treated HSA(LR) mice indicate that defects characteristic of DM1 can be mitigated with a systemic RNAi approach targeting the nuclei of terminally differentiated myofibers. Efficient rAAV-mediated delivery of RNAi has the potential to provide a long-term therapy for DM1 and other dominant muscular dystrophies.
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Affiliation(s)
| | | | | | - Jessica Wei
- Division of Medical Genetics, Department of Medicine
| | | | - Michael D Weiss
- Department of Neurology, University of Washington, Seattle, WA 98195, USA
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27
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Burger K, Gullerova M. Swiss army knives: non-canonical functions of nuclear Drosha and Dicer. Nat Rev Mol Cell Biol 2015; 16:417-30. [DOI: 10.1038/nrm3994] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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28
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Liang XH, Sun H, Shen W, Crooke ST. Identification and characterization of intracellular proteins that bind oligonucleotides with phosphorothioate linkages. Nucleic Acids Res 2015; 43:2927-45. [PMID: 25712094 PMCID: PMC4357732 DOI: 10.1093/nar/gkv143] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Although the RNase H-dependent mechanism of inhibition of gene expression by chemically modified antisense oligonucleotides (ASOs) has been well characterized, little is known about the interactions between ASOs and intracellular proteins that may alter cellular localization and/or potency of ASOs. Here, we report the identification of 56 intracellular ASO-binding proteins using multi-step affinity selection approaches. Many of the tested proteins had no significant effect on ASO activity; however, some proteins, including La/SSB, NPM1, ANXA2, VARS and PC4, appeared to enhance ASO activities, likely through mechanisms related to subcellular distribution. VARS and ANXA2 co-localized with ASOs in endocytic organelles, and reduction in the level of VARS altered lysosome/ASO localization patterns, implying that these proteins may facilitate ASO release from the endocytic pathway. Depletion of La and NPM1 reduced nuclear ASO levels, suggesting potential roles in ASO nuclear accumulation. On the other hand, Ku70 and Ku80 proteins inhibited ASO activity, most likely by competition with RNase H1 for ASO/RNA duplex binding. Our results demonstrate that phosphorothioate-modified ASOs bind a set of cellular proteins that affect ASO activity via different mechanisms.
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Affiliation(s)
- Xue-hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Wen Shen
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Carlsbad, CA 92010, USA
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29
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Shen W, Liang XH, Crooke ST. Phosphorothioate oligonucleotides can displace NEAT1 RNA and form nuclear paraspeckle-like structures. Nucleic Acids Res 2014; 42:8648-62. [PMID: 25013176 PMCID: PMC4117792 DOI: 10.1093/nar/gku579] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nuclear paraspeckles are built co-transcriptionally around a long non-coding RNA, NEAT1. Here we report that transfected 20-mer phosphorothioate-modified (PS) antisense oligonucleotides (ASOs) can recruit paraspeckle proteins to form morphologically normal and apparently functional paraspeckle-like structures containing no NEAT1 RNA. PS-ASOs can associate with paraspeckle proteins, including P54nrb, PSF, PSPC1 and hnRNPK. NEAT1 RNA can be displaced by transfected PS-ASO from paraspeckles and rapidly degraded. Co-localization of PS-ASOs with P54nrb was observed in canonical NEAT1-containing paraspeckles, in perinucleolar caps upon transcriptional inhibition, and importantly, in paraspeckle-like or filament structures lacking NEAT1 RNA. The induced formation of paraspeckle-like and filament structures occurred in mouse embryonic stem cells expressing little or no NEAT1 RNA, suggesting that PS-ASOs can serve as seeding molecules to assemble paraspeckle-like foci in the absence of NEAT1 RNA. Moreover, CTN, an RNA reported to be functionally retained in paraspeckles, was also observed to localize to paraspeckle-like structures, implying that paraspeckle-like structures assembled on PS-ASOs are functional. Together, our results indicate that functional paraspeckles can form with short nucleic acids other than NEAT1 RNA.
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Affiliation(s)
- Wen Shen
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Xue-hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc. 2855 Gazelle Court, Carlsbad, CA 92010, USA
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Thomas MF, L'Etoile ND, Ansel KM. Eri1: a conserved enzyme at the crossroads of multiple RNA-processing pathways. Trends Genet 2014; 30:298-307. [PMID: 24929628 DOI: 10.1016/j.tig.2014.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
Abstract
Eri1 is an evolutionarily conserved 3'-5' exoribonuclease that participates in 5.8S rRNA 3' end processing and turnover of replication-dependent histone mRNAs. Over the course of evolution, Eri1 has also been recruited into a variety of conserved and species-specific regulatory small RNA pathways that include endogenous small interfering (si)RNAs and miRNAs. Recent advances in Eri1 biology illustrate the importance of RNA metabolism in epigenetic gene regulation and illuminate common principles and players in RNA biogenesis and turnover. In this review, we highlight Eri1 as a member of a growing class of ribosome- and histone mRNA-associated proteins that have been recruited into divergent RNA metabolic pathways. We summarize recent advances in the understanding of Eri1 function in these pathways and discuss how Eri1 impacts gene expression and physiology in a variety of eukaryotic species. This emerging view highlights the possibility for crosstalk and coregulation of diverse cellular processes regulated by RNA.
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Affiliation(s)
- Molly F Thomas
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Noelle D L'Etoile
- Department of Cell & Tissue Biology, University of California San Francisco, San Francisco, CA 94143, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA.
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31
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Liang XH, Shen W, Sun H, Prakash TP, Crooke ST. TCP1 complex proteins interact with phosphorothioate oligonucleotides and can co-localize in oligonucleotide-induced nuclear bodies in mammalian cells. Nucleic Acids Res 2014; 42:7819-32. [PMID: 24861627 PMCID: PMC4081088 DOI: 10.1093/nar/gku484] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Phosphorothioate (PS) antisense oligonucleotides (ASOs) have been successfully developed as drugs to reduce the expression of disease-causing genes. PS-ASOs can be designed to induce degradation of complementary RNAs via the RNase H pathway and much is understood about that process. However, interactions of PS-ASOs with other cellular proteins are not well characterized. Here we report that in cells transfected with PS-ASOs, the chaperonin T-complex 1 (TCP1) proteins interact with PS-ASOs and enhance antisense activity. The TCP1-β subunit co-localizes with PS-ASOs in distinct nuclear structures, termed phosphorothioate bodies or PS-bodies. Upon Ras-related nuclear protein (RAN) depletion, cytoplasmic PS-body-like structures were observed and nuclear concentrations of PS-ASOs were reduced, suggesting that TCP1-β can interact with PS-ASOs in the cytoplasm and that the nuclear import of PS-ASOs is at least partially through the RAN-mediated pathway. Upon free uptake, PS-ASOs co-localize with TCP1 proteins in cytoplasmic foci related to endosomes/lysosomes. Together, our results indicate that the TCP1 complex binds oligonucleotides with TCP1-β subunit being a nuclear PS-body component and suggest that the TCP1 complex may facilitate PS-ASO uptake and/or release from the endocytosis pathway.
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Affiliation(s)
- Xue-hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Wen Shen
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Hong Sun
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Thazha P Prakash
- Department of Medicinal Chemistry, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., Carlsbad, CA 92010, USA
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32
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García-López J, Hourcade JDD, Alonso L, Cárdenas DB, del Mazo J. Global characterization and target identification of piRNAs and endo-siRNAs in mouse gametes and zygotes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:463-75. [PMID: 24769224 DOI: 10.1016/j.bbagrm.2014.04.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 03/24/2014] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
Abstract
A set of small RNAs known as rasRNAs (repeat-associated small RNAs) have been related to the down-regulation of Transposable Elements (TEs) to safeguard genome integrity. Two key members of the rasRNAs group are piRNAs and endo-siRNAs. We have performed a comparative analysis of piRNAs and endo-siRNAs present in mouse oocytes, spermatozoa and zygotes, identified by deep sequencing and bioinformatic analysis. The detection of piRNAs and endo-siRNAs in the spermatozoa and revealed also in zygotes, hints to their potential delivery to oocytes during fertilization. However, a comparative assessment of the three cell types indicates that both piRNAs and endo-siRNAs are mainly maternally inherited. Finally, we have assessed the role of the different rasRNA molecules in connection with amplification processes by way of the "ping-pong cycle". Our results suggest that the ping-pong cycle can act on other rasRNAs, such as tRNA- and rRNA-derived fragments, thus not only being restricted to TEs during gametogenesis.
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Affiliation(s)
- Jesús García-López
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Juan de Dios Hourcade
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Lola Alonso
- Bioinformatics Service, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - David B Cárdenas
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jesús del Mazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
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Liang XH, Crooke ST. RNA helicase A is not required for RISC activity. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:1092-101. [PMID: 23895878 DOI: 10.1016/j.bbagrm.2013.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/29/2013] [Accepted: 07/22/2013] [Indexed: 01/13/2023]
Abstract
It has been shown that siRNAs can compete with each other or with endogenous miRNAs for RISC components. This competition may complicate the interpretations of phenotypes observed through siRNA-mediated knockdown of genes, especially those genes implicated in the RISC pathway. In this study, we re-examined the function of RNA helicase A (RHA), which has been previously proposed to function in RISC loading based on siRNA-mediated knockdown studies. Here we show that reduced RISC activity or loading of siRNAs was observed only in cells depleted of RHA using siRNA, but not using RNaseH-dependent antisense oligonucleotides (ASOs), suggesting that the impaired RISC function stems from the competition between pre-existing and newly transfected siRNAs, but not from reduction of the RHA protein. This view is further supported by the findings that cells depleted of a control protein, NCL1, using siRNA, but not ASO, exhibited similar defects on the loading and activity of a subsequently transfected siRNA. Transfection of RHA or NCL1 siRNAs, but not ASOs, reduced the levels of endogenous miRNAs, suggesting a competition mechanism. As a positive control, we showed that reduction of MOV10 by either siRNA or ASO decreased siRNA activity, confirming its role in RISC function. Together, our results indicate that RHA is not required for RISC activity or loading, and suggest that proper controls are required when using siRNAs to functionalize genes to avoid competition effects.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA.
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34
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Gómez-Cabello D, Adrados I, Gamarra D, Kobayashi H, Takatsu Y, Takatsu K, Gil J, Palmero I. DGCR8-mediated disruption of miRNA biogenesis induces cellular senescence in primary fibroblasts. Aging Cell 2013; 12:923-31. [PMID: 23773483 DOI: 10.1111/acel.12117] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2013] [Indexed: 12/21/2022] Open
Abstract
The regulation of gene expression by microRNAs (miRNAs) is critical for normal development and physiology. Conversely, miRNA function is frequently impaired in cancer, and other pathologies, either by aberrant expression of individual miRNAs or dysregulation of miRNA synthesis. Here, we have investigated the impact of global disruption of miRNA biogenesis in primary fibroblasts of human or murine origin, through the knockdown of DGCR8, an essential mediator of the synthesis of canonical miRNAs. We find that the inactivation of DGCR8 in these cells results in a dramatic antiproliferative response, with the acquisition of a senescent phenotype. Senescence triggered by DGCR8 loss is accompanied by the upregulation of the cell-cycle inhibitor p21CIP1. We further show that a subset of senescence-associated miRNAs with the potential to target p21CIP1 is downregulated during DGCR8-mediated senescence. Interestingly, the antiproliferative response to miRNA biogenesis disruption is retained in human tumor cells, irrespective of p53 status. In summary, our results show that defective synthesis of canonical microRNAs results in cell-cycle arrest and cellular senescence in primary fibroblasts mediated by specific miRNAs, and thus identify global miRNA disruption as a novel senescence trigger.
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Affiliation(s)
| | - Isabel Adrados
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’ CSIC-UAM; Madrid; Spain
| | - David Gamarra
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’ CSIC-UAM; Madrid; Spain
| | - Hikaru Kobayashi
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’ CSIC-UAM; Madrid; Spain
| | - Yoshihiro Takatsu
- Cell Proliferation Group; MRC Clinical Sciences Centre; Imperial College London; London; UK
| | - Kyoko Takatsu
- Cell Proliferation Group; MRC Clinical Sciences Centre; Imperial College London; London; UK
| | - Jesús Gil
- Cell Proliferation Group; MRC Clinical Sciences Centre; Imperial College London; London; UK
| | - Ignacio Palmero
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’ CSIC-UAM; Madrid; Spain
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35
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Maute RL, Dalla-Favera R, Basso K. RNAs with multiple personalities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:1-13. [DOI: 10.1002/wrna.1193] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/19/2013] [Accepted: 07/25/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Roy L. Maute
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center; Columbia University; New York NY USA
- Department of Genetics and Development; Columbia University; New York NY USA
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center; Columbia University; New York NY USA
- Department of Genetics and Development; Columbia University; New York NY USA
- Department of Pathology and Cell Biology; Columbia University; New York NY USA
- Department of Microbiology and Immunology; Columbia University; New York NY USA
| | - Katia Basso
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center; Columbia University; New York NY USA
- Department of Pathology and Cell Biology; Columbia University; New York NY USA
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36
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Helwak A, Kudla G, Dudnakova T, Tollervey D. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 2013; 153:654-65. [PMID: 23622248 PMCID: PMC3650559 DOI: 10.1016/j.cell.2013.03.043] [Citation(s) in RCA: 942] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 12/21/2012] [Accepted: 03/20/2013] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.
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Affiliation(s)
- Aleksandra Helwak
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh, UK
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37
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Makarova JA, Ivanova SM, Tonevitsky AG, Grigoriev AI. New functions of small nucleolar RNAs. BIOCHEMISTRY (MOSCOW) 2013; 78:638-50. [DOI: 10.1134/s0006297913060096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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38
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Sloan KE, Mattijssen S, Lebaron S, Tollervey D, Pruijn GJM, Watkins NJ. Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human ribosomal RNA processing. ACTA ACUST UNITED AC 2013; 200:577-88. [PMID: 23439679 PMCID: PMC3587827 DOI: 10.1083/jcb.201207131] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Human ribosome production is up-regulated during tumorogenesis and is defective in many genetic diseases (ribosomopathies). We have undertaken a detailed analysis of human precursor ribosomal RNA (pre-rRNA) processing because surprisingly little is known about this important pathway. Processing in internal transcribed spacer 1 (ITS1) is a key step that separates the rRNA components of the large and small ribosomal subunits. We report that this was initiated by endonuclease cleavage, which required large subunit biogenesis factors. This was followed by 3' to 5' exonucleolytic processing by RRP6 and the exosome, an enzyme complex not previously linked to ITS1 removal. In contrast, RNA interference-mediated knockdown of the endoribonuclease MRP did not result in a clear defect in ITS1 processing. Despite the apparently high evolutionary conservation of the pre-rRNA processing pathway and ribosome synthesis factors, each of these features of human ITS1 processing is distinct from those in budding yeast. These results also provide significant insight into the links between ribosomopathies and ribosome production in human cells.
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Affiliation(s)
- Katherine E Sloan
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, England, UK
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39
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Kirby BS, Bruhl A, Sullivan MN, Francis M, Dinenno FA, Earley S. Robust internal elastic lamina fenestration in skeletal muscle arteries. PLoS One 2013; 8:e54849. [PMID: 23359815 PMCID: PMC3554626 DOI: 10.1371/journal.pone.0054849] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/17/2012] [Indexed: 11/18/2022] Open
Abstract
Holes within the internal elastic lamina (IEL) of blood vessels are sites of fenestration allowing for passage of diffusible vasoactive substances and interface of endothelial cell membrane projections with underlying vascular smooth muscle. Endothelial projections are sites of dynamic Ca2+ events leading to endothelium dependent hyperpolarization (EDH)-mediated relaxations and the activity of these events increase as vessel diameter decreases. We tested the hypothesis that IEL fenestration is greater in distal vs. proximal arteries in skeletal muscle, and is unlike other vascular beds (mesentery). We also determined ion channel protein composition within the endothelium of intramuscular and non-intramuscular skeletal muscle arteries. Popliteal arteries, subsequent gastrocnemius feed arteries, and first and second order intramuscular arterioles from rat hindlimb were isolated, cut longitudinally, fixed, and imaged using confocal microscopy. Quantitative analysis revealed a significantly larger total fenestration area in second and first order arterioles vs. feed and popliteal arteries (58% and 16% vs. 5% and 3%; N = 10 images/artery), due to a noticeably greater average size of holes (9.5 and 3.9 µm2 vs 1.5 and 1.9 µm2). Next, we investigated via immunolabeling procedures whether proteins involved in EDH often embedded in endothelial cell projections were disparate between arterial segments. Specific proteins involved in EDH, such as inositol trisphosphate receptors, small and intermediate conductance Ca2+-activated K+ channels, and the canonical (C) transient receptor potential (TRP) channel TRPC3 were present in both popliteal and first order intramuscular arterioles. However due to larger IEL fenestration in first order arterioles, a larger spanning area of EDH proteins is observed proximal to the smooth muscle cell plasma membrane. These observations highlight the robust area of fenestration within intramuscular arterioles and indicate that the anatomical architecture and endothelial cell hyperpolarizing apparatus for distinct vasodilatory signaling is potentially present.
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Affiliation(s)
- Brett S. Kirby
- Department of Biomedical Sciences, Vascular Physiology Research Group, Colorado State University, Fort Collins, Colorado, United States of America
| | - Allison Bruhl
- Department of Biomedical Sciences, Vascular Physiology Research Group, Colorado State University, Fort Collins, Colorado, United States of America
| | - Michelle N. Sullivan
- Department of Biomedical Sciences, Vascular Physiology Research Group, Colorado State University, Fort Collins, Colorado, United States of America
| | - Michael Francis
- Department of Physiology, University of South Alabama College of Medicine, Mobile, Alabama, United States of America
| | - Frank A. Dinenno
- Department of Biomedical Sciences, Vascular Physiology Research Group, Colorado State University, Fort Collins, Colorado, United States of America
- Department of Health and Exercise Science, Human Cardiovascular Physiology Laboratory, Colorado State University, Fort Collins, Colorado, United States of America
| | - Scott Earley
- Department of Biomedical Sciences, Vascular Physiology Research Group, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus. Mol Cell 2012; 48:509-20. [PMID: 23084833 DOI: 10.1016/j.molcel.2012.09.010] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 07/26/2012] [Accepted: 09/07/2012] [Indexed: 11/21/2022]
Abstract
Emerging evidence suggests that Argonaute (Ago)/Piwi proteins have diverse functions in the nucleus and cytoplasm, but the molecular mechanisms employed in the nucleus remain poorly defined. The Tetrahymena thermophila Ago/Piwi protein Twi12 is essential for growth and functions in the nucleus. Twi12-bound small RNAs (sRNAs) are 3' tRNA fragments that contain modified bases and thus are attenuated for base pairing to targets. We show that Twi12 assembles an unexpected complex with the nuclear exonuclease Xrn2. Twi12 functions to stabilize and localize Xrn2, as well as to stimulate its exonuclease activity. Twi12 function depends on sRNA binding, which is required for its nuclear import. Depletion of Twi12 or Xrn2 induces a cellular ribosomal RNA processing defect known to result from limiting Xrn2 activity in other organisms. Our findings suggest a role for an Ago/Piwi protein and 3' tRNA fragments in nuclear RNA metabolism.
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41
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Sohn EJ, Park J, Kang SI, Wu YP. Accumulation of pre-let-7g and downregulation of mature let-7g with the depletion of EWS. Biochem Biophys Res Commun 2012; 426:89-93. [PMID: 22910415 DOI: 10.1016/j.bbrc.2012.08.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 08/08/2012] [Indexed: 11/19/2022]
Abstract
EWS functions in RNA splicing and transcription by encoding an RNA binding protein, which results in the chromosomal translocation t(11;22)(q24;q12) found in Ewing sarcoma. EWS interacts with the microprocessor complex involving Drosha and DGCR8, which play roles as the cofactors of primary microRNA processing. However, the role of EWS in microRNA biogenesis has not been investigated. Here, we show that endogenous EWS interacts with endogenous Drosha by IP-western blotting. In addition, EWS knockout mouse decreased the expression of Drosha. The depletion of EWS results in the accumulation of precursor let-7g but down-regulates mature let-7g in U2OS cells. Consistently, mature let 7g was suppressed in both Ewing sarcoma cell and primary Ewing sarcoma. Also, expression levels of Dicer and CCND1 (Cyclin D1), which are known target genes of the let-7 family were upregulated. Our findings suggest that EWS mediates generation of mature let-7g from pre-let-7g.
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Affiliation(s)
- Eun Jung Sohn
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20871, USA.
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42
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Dundr M. Nuclear bodies: multifunctional companions of the genome. Curr Opin Cell Biol 2012; 24:415-22. [PMID: 22541757 DOI: 10.1016/j.ceb.2012.03.010] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 03/16/2012] [Accepted: 03/29/2012] [Indexed: 01/22/2023]
Abstract
It has become increasingly apparent that gene expression is regulated by the functional interplay between spatial genome organization and nuclear architecture. Within the nuclear environment a variety of distinct nuclear bodies exist. They are dynamic, self-organizing structures that do not assemble as pre-formed entities but rather emerge as a direct reflection of specific activities associated with gene expression and genome maintenance. Here I summarize recent findings on functions of some of the most prominent nuclear bodies, including the nucleolus, Cajal body, PML nuclear body, Polycomb group body and the 53BP1 nuclear body. The emerging view is that their organization is orchestrated by similar principles, and they function in fundamental cellular processes involved in homeostasis, differentiation, development and disease.
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Affiliation(s)
- Miroslav Dundr
- Department of Cell Biology, Rosalind Franklin University of Medicine & Science, North Chicago, IL 60064, United States.
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43
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Gagnon KT, Corey DR. Argonaute and the nuclear RNAs: new pathways for RNA-mediated control of gene expression. Nucleic Acid Ther 2012; 22:3-16. [PMID: 22283730 DOI: 10.1089/nat.2011.0330] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Small RNAs are a commonly used tool for gene silencing and a promising platform for nucleic acid drug development. They are almost exclusively used to silence gene expression post-transcriptionally through degradation of mRNA. Small RNAs, however, can have a broader range of function by binding to Argonaute proteins and associating with complementary RNA targets in the nucleus, including long noncoding RNAs (lncRNAs) and pre-mRNA. Argonaute-RNA complexes can regulate nuclear events like transcription, genome maintenance, and splicing. Thousands of lncRNAs and alternatively spliced pre-mRNA isoforms exist in humans, and these RNAs may serve as natural targets for regulation and therapeutic intervention. This review describes nuclear mechanisms for Argonaute proteins and small RNAs, new pathways for sequence-specific targeting, and the potential for therapeutic development of small RNAs with nuclear targets.
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Affiliation(s)
- Keith T Gagnon
- Departments of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
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44
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45
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Dicer Proteins and Their Role in Gene Silencing Pathways. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/b978-0-12-404741-9.00001-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
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46
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Pickering BF, Yu D, Van Dyke MW. Nucleolin protein interacts with microprocessor complex to affect biogenesis of microRNAs 15a and 16. J Biol Chem 2011; 286:44095-44103. [PMID: 22049078 PMCID: PMC3243533 DOI: 10.1074/jbc.m111.265439] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 10/22/2011] [Indexed: 01/09/2023] Open
Abstract
MicroRNAs (miRNA) are endogenous, short, non-coding RNA that undergo a multistep biogenesis before generating the functional, mature sequence. The core components of the microprocessor complex, consisting of Drosha and DGCR8, are both necessary and sufficient for this process, although accessory proteins have been found that modulate the biogenesis of a subset of miRNA. Curiously, many of the proteins involved in miRNA biogenesis are also needed for ribosomal RNA processing. Here we show that nucleolin, another protein critical for rRNA processing, is involved in the biogenesis of microRNA 15a/16 (miR-15a/16), specifically at the primary to precursor stage of processing. Through overexpression and knockdown studies, we show that miR-15a/16 levels are directly correlated to nucleolin expression. Furthermore, we found that cellular localization is critical for the proper functioning of nucleolin in this pathway and that nucleolin directly interacts with DGCR8 and Drosha in the nucleus. Nucleolin can bind to the primary miRNA both directly and specifically. Finally, we show that in the absence of nucleolin, cell extracts are unable to process miR-15a/16 in vitro and that this can be rescued by the addition of nucleolin. Our findings offer a new protein component in the microRNA biogenesis pathway and lend insight into miRNA dysregulation in certain cancers.
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Affiliation(s)
- Brian F Pickering
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030; Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030.
| | - Dihua Yu
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030; Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030.
| | - Michael W Van Dyke
- Department of Chemistry and Physics, Western Carolina University, Cullowhee, North Carolina 28723
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Smalheiser NR. The search for endogenous siRNAs in the mammalian brain. Exp Neurol 2011; 235:455-63. [PMID: 22062046 DOI: 10.1016/j.expneurol.2011.10.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 09/28/2011] [Accepted: 10/17/2011] [Indexed: 02/08/2023]
Abstract
A decade ago, RNA interference was proposed to serve as a physiologic means of regulating long-term gene expression in the mammalian brain. However, during the intervening years, this hypothesis appeared to be contradicted by both experimental data and theoretical considerations. More recently, the advent of deep sequencing technology has permitted a re-assessment of this issue. As reviewed here, a large population of small RNAs having features characteristic of endogenous siRNAs are detected within adult mouse hippocampus, which derive from genes involved in synaptic structure and signaling, and which show a significant, though modest (16-22%) up-regulation during olfactory discrimination training. Small RNAs derived from abundant cellular noncoding RNAs are also detected; in particular, a subpopulation of RNAs 25-30 nt. in length shows very large (>100 fold) up-regulation during olfactory discrimination training. Preliminary data suggest that the 25-30 nt. RNAs may associate with MIWI rather than Argonaute 1-4 homologues. I conclude that, despite their apparent low abundance, endogenous siRNAs and noncoding RNA-derived small RNAs are likely to play an important role in regulating synaptic plasticity.
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Affiliation(s)
- Neil R Smalheiser
- University of Illinois at Chicago, Psychiatric Institute MC912, Chicago, IL 60612, USA.
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Zalachoras I, Evers MM, van Roon-Mom WMC, Aartsma-Rus AM, Meijer OC. Antisense-mediated RNA targeting: versatile and expedient genetic manipulation in the brain. Front Mol Neurosci 2011; 4:10. [PMID: 21811437 PMCID: PMC3142880 DOI: 10.3389/fnmol.2011.00010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 07/08/2011] [Indexed: 12/28/2022] Open
Abstract
A limiting factor in brain research still is the difficulty to evaluate in vivo the role of the increasing number of proteins implicated in neuronal processes. We discuss here the potential of antisense-mediated RNA targeting approaches. We mainly focus on those that manipulate splicing (exon skipping and exon inclusion), but will also briefly discuss mRNA targeting. Classic knockdown of expression by mRNA targeting is only one possible application of antisense oligonucleotides (AON) in the control of gene function. Exon skipping and inclusion are based on the interference of AONs with splicing of pre-mRNAs. These are powerful, specific and particularly versatile techniques, which can be used to circumvent pathogenic mutations, shift splice variant expression, knock down proteins, or to create molecular models using in-frame deletions. Pre-mRNA targeting is currently used both as a research tool, e.g., in models for motor neuron disease, and in clinical trials for Duchenne muscular dystrophy and amyotrophic lateral sclerosis. AONs are particularly promising in relation to brain research, as the modified AONs are taken up extremely fast in neurons and glial cells with a long residence, and without the need for viral vectors or other delivery tools, once inside the blood brain barrier. In this review we cover (1). The principles of antisense-mediated techniques, chemistry, and efficacy. (2) The pros and cons of AON approaches in the brain compared to other techniques of interfering with gene function, such as transgenesis and short hairpin RNAs, in terms of specificity of the manipulation, spatial, and temporal control over gene expression, toxicity, and delivery issues. (3) The potential applications for Neuroscience. We conclude that there is good evidence from animal studies that the central nervous system can be successfully targeted, but the potential of the diverse AON-based approaches appears to be under-recognized.
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Affiliation(s)
- Ioannis Zalachoras
- Division of Medical Pharmacology, Leiden/Amsterdam Center for Drug Research Leiden, Netherlands
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