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Lobel JH, Ingolia NT. Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578453. [PMID: 38370681 PMCID: PMC10871298 DOI: 10.1101/2024.02.01.578453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Disordered regions within RNA binding proteins are required to control mRNA decay and protein synthesis. To understand how these disordered regions modulate gene expression, we surveyed regulatory activity across the entire disordered proteome using a high-throughput functional assay. We identified hundreds of regulatory sequences within intrinsically disordered regions and demonstrate how these elements cooperate with core mRNA decay machinery to promote transcript turnover. Coupling high-throughput functional profiling with mutational scanning revealed diverse molecular features, ranging from defined motifs to overall sequence composition, underlying the regulatory effects of disordered peptides. Machine learning analysis implicated aromatic residues in particular contexts as critical determinants of repressor activity, consistent with their roles in forming protein-protein interactions with downstream effectors. Our results define the molecular principles and biochemical mechanisms that govern post-transcriptional gene regulation by disordered regions and exemplify the encoding of diverse yet specific functions in the absence of well-defined structure.
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Affiliation(s)
- Joseph H Lobel
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Lead contact
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2
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Torkzaban B, Sponaugle A, Coller J. Tethered mRNA Amplifier: A Novel Approach to Increase Protein Expression. Methods Mol Biol 2024; 2723:161-172. [PMID: 37824070 DOI: 10.1007/978-1-0716-3481-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Posttranscriptional RNA modification has become a revolutionary clinical tool to improve the underlying condition in genetic disorders. The cell achieves translational regulation through sequence and/or structural elements that recruit specific positive- or negative-acting factors to mRNAs. Targeting mRNA expression offers a less invasive therapeutic approach than other well-known gene therapy approaches. We have utilized our understanding of mRNA translational regulation to develop a novel disease-modifying treatment called the "Tethered mRNA Amplifier." Specifically, our approach forces a key positive-acting mRNA regulator, polyadenosine binding protein (PABPC1), to bind and remain resident on the target mRNA. This enhances the target mRNA's expression precisely and restores deficient protein levels to normal. This approach effectively increases the steady-state expression level of several transcripts associated with haploinsufficiency disorders in cell culture.
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Affiliation(s)
- Bahareh Torkzaban
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Austin Sponaugle
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jeff Coller
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA.
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA.
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3
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Liu Z, Jillette N, Robson P, Cheng AW. Simultaneous multifunctional transcriptome engineering by CRISPR RNA scaffold. Nucleic Acids Res 2023; 51:e77. [PMID: 37395412 PMCID: PMC10415119 DOI: 10.1093/nar/gkad547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023] Open
Abstract
RNA processing and metabolism are subjected to precise regulation in the cell to ensure integrity and functions of RNA. Though targeted RNA engineering has become feasible with the discovery and engineering of the CRISPR-Cas13 system, simultaneous modulation of different RNA processing steps remains unavailable. In addition, off-target events resulting from effectors fused with dCas13 limit its application. Here we developed a novel platform, Combinatorial RNA Engineering via Scaffold Tagged gRNA (CREST), which can simultaneously execute multiple RNA modulation functions on different RNA targets. In CREST, RNA scaffolds are appended to the 3' end of Cas13 gRNA and their cognate RNA binding proteins are fused with enzymatic domains for manipulation. Taking RNA alternative splicing, A-to-G and C-to-U base editing as examples, we developed bifunctional and tri-functional CREST systems for simultaneously RNA manipulation. Furthermore, by fusing two split fragments of the deaminase domain of ADAR2 to dCas13 and/or PUFc respectively, we reconstituted its enzyme activity at target sites. This split design can reduce nearly 99% of off-target events otherwise induced by a full-length effector. The flexibility of the CREST framework will enrich the transcriptome engineering toolbox for the study of RNA biology.
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Affiliation(s)
- Zukai Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | | | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME 04609, USA
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Albert Wu Cheng
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
- The Jackson Laboratory Cancer Center, Bar Harbor, ME 04609, USA
- Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT 06030, USA
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
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4
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Cao Y, Ye Q, Ma M, She QB. Enhanced bypass of PD-L1 translation reduces the therapeutic response to mTOR kinase inhibitors. Cell Rep 2023; 42:112764. [PMID: 37405918 PMCID: PMC10491412 DOI: 10.1016/j.celrep.2023.112764] [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: 12/11/2022] [Revised: 04/23/2023] [Accepted: 06/22/2023] [Indexed: 07/07/2023] Open
Abstract
Increased PD-L1 expression in cancer cells is known to enhance immunosuppression, but the mechanism underlying PD-L1 upregulation is incompletely characterized. We show that PD-L1 expression is upregulated through internal ribosomal entry site (IRES)-mediated translation upon mTORC1 inhibition. We identify an IRES element in the PD-L1 5'-UTR that permits cap-independent translation and promotes continuous production of PD-L1 protein despite effective inhibition of mTORC1. eIF4A is found to be a key PD-L1 IRES-binding protein that enhances PD-L1 IRES activity and protein production in tumor cells treated with mTOR kinase inhibitors (mTORkis). Notably, treatment with mTORkis in vivo elevates PD-L1 levels and reduces the number of tumor-infiltrating lymphocytes in immunogenic tumors, but anti-PD-L1 immunotherapy restores antitumor immunity and enhances the therapeutic efficacy of mTORkis. These findings report a molecular mechanism for regulating PD-L1 expression through bypassing mTORC1-mediated cap-dependent translation and provide a rationale for targeting PD-L1 immune checkpoint to improve mTOR-targeted therapy.
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Affiliation(s)
- Yanan Cao
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40506, USA; Department of Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, Lexington, KY 40506, USA
| | - Qing Ye
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40506, USA; Department of Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, Lexington, KY 40506, USA
| | - Murong Ma
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40506, USA; Department of Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, Lexington, KY 40506, USA
| | - Qing-Bai She
- Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40506, USA; Department of Pharmacology and Nutritional Sciences, University of Kentucky College of Medicine, Lexington, KY 40506, USA.
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5
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Reynaud K, McGeachy AM, Noble D, Meacham ZA, Ingolia NT. Surveying the global landscape of post-transcriptional regulators. Nat Struct Mol Biol 2023; 30:740-752. [PMID: 37231154 PMCID: PMC10279529 DOI: 10.1038/s41594-023-00999-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
Numerous proteins regulate gene expression by modulating mRNA translation and decay. To uncover the full scope of these post-transcriptional regulators, we conducted an unbiased survey that quantifies regulatory activity across the budding yeast proteome and delineates the protein domains responsible for these effects. Our approach couples a tethered function assay with quantitative single-cell fluorescence measurements to analyze ~50,000 protein fragments and determine their effects on a tethered mRNA. We characterize hundreds of strong regulators, which are enriched for canonical and unconventional mRNA-binding proteins. Regulatory activity typically maps outside the RNA-binding domains themselves, highlighting a modular architecture that separates mRNA targeting from post-transcriptional regulation. Activity often aligns with intrinsically disordered regions that can interact with other proteins, even in core mRNA translation and degradation factors. Our results thus reveal networks of interacting proteins that control mRNA fate and illuminate the molecular basis for post-transcriptional gene regulation.
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Affiliation(s)
- Kendra Reynaud
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Anna M McGeachy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - David Noble
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Zuriah A Meacham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T Ingolia
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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6
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Hou S, Wang W, Hao T, Lei H. MS2-MBP-Based Affinity Purification of Nucleus- or Cytoplasm-Localized lncRNA-Protein Complexes Formed In Vivo. Methods Mol Biol 2023; 2666:231-245. [PMID: 37166669 DOI: 10.1007/978-1-0716-3191-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
With recent emergence of huge number of long noncoding RNAs (lncRNAs), purification of lncRNA-protein (lncRNP) complexes is fundamental to understand the role of lncRNA and its biological function. However, lncRNP purification is still a daunting challenge. Here we describe a protocol to purify lncRNP formed in vivo with MS2-MBP-based affinity purification. Inducible lncRNA tagged with MS2 RNA hairpins is introduced into cells of interest, and RNP on tagged lncRNA is formed in vivo. MS2-MBP fusion protein is expressed in Escherichia coli and purified with amylose resin and HiTrap heparin column. The MS2 part of MS2-MBP fusion protein binds to the hairpins, and MBP part binds to amylose resin. We also describe a protocol to separate the nucleus and the cytoplasm so that lncRNP localized in the nucleus or cytoplasm can be individually purified. The amount of lncRNP purified is well sufficient for mass spectrometry analysis.
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Affiliation(s)
- Shuai Hou
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Weijie Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
- Institute of Pediatrics, Children's Hospital of Fudan University, Shanghai, China
| | - Tian Hao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Haixin Lei
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.
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7
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Li M, Yan C, Jiao Y, Xu Y, Bai C, Miao R, Jiang J, Liu J. Site-directed RNA editing by harnessing ADARs: advances and challenges. Funct Integr Genomics 2022; 22:1089-1103. [DOI: 10.1007/s10142-022-00910-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/04/2022]
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8
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Khong A, Matheny T, Huynh TN, Babl V, Parker R. Limited effects of m 6A modification on mRNA partitioning into stress granules. Nat Commun 2022; 13:3735. [PMID: 35768440 PMCID: PMC9243116 DOI: 10.1038/s41467-022-31358-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/13/2022] [Indexed: 11/16/2022] Open
Abstract
The presence of the m6A modification in mammalian mRNAs is proposed to promote mRNA recruitment to stress granules through the interaction with YTHDF proteins. We test this possibility by examining the accumulation of mRNAs in stress granules in both WT and ∆METTL3 mES cells, which are deficient in m6A modification. A critical observation is that all m6A modified mRNAs partition similarly into stress granules in both wild-type and m6A-deficient cells by single-molecule FISH. Moreover, multiple linear regression analysis indicates m6A modification explains only 6% of the variance in stress granule localization when controlled for length. Finally, the artificial tethering of 25 YTHDF proteins on reporter mRNAs leads to only a modest increase in mRNA partitioning to stress granules. Since most mammalian mRNAs have 4 or fewer m6A sites, and those sites are not fully modified, this argues m6A modifications are unlikely to play a significant role in recruiting mRNAs to stress granules. Taken together, these observations argue that m6A modifications play a minimal, if any, role in mRNA partitioning into stress granules. Recent studies proposed that m6A modification in mammalian mRNAs increases their recruitment to stress granule. However, here the authors observed that m6A modification has a limited effect on mRNA entry into stress granules.
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Affiliation(s)
- Anthony Khong
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Tyler Matheny
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Thao Ngoc Huynh
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Vincent Babl
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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9
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Hallacli E, Kayatekin C, Nazeen S, Wang XH, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, Di Maio R, Wang W, Keeney MT, Felsky D, Sandoe J, Vahdatshoar A, Udeshi ND, Mani DR, Carr SA, Lindquist S, De Jager PL, Bartel DP, Myers CL, Greenamyre JT, Feany MB, Sunyaev SR, Chung CY, Khurana V. The Parkinson's disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability. Cell 2022; 185:2035-2056.e33. [PMID: 35688132 DOI: 10.1016/j.cell.2022.05.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/05/2022] [Accepted: 05/06/2022] [Indexed: 12/13/2022]
Abstract
Alpha-synuclein (αS) is a conformationally plastic protein that reversibly binds to cellular membranes. It aggregates and is genetically linked to Parkinson's disease (PD). Here, we show that αS directly modulates processing bodies (P-bodies), membraneless organelles that function in mRNA turnover and storage. The N terminus of αS, but not other synucleins, dictates mutually exclusive binding either to cellular membranes or to P-bodies in the cytosol. αS associates with multiple decapping proteins in close proximity on the Edc4 scaffold. As αS pathologically accumulates, aberrant interaction with Edc4 occurs at the expense of physiologic decapping-module interactions. mRNA decay kinetics within PD-relevant pathways are correspondingly disrupted in PD patient neurons and brain. Genetic modulation of P-body components alters αS toxicity, and human genetic analysis lends support to the disease-relevance of these interactions. Beyond revealing an unexpected aspect of αS function and pathology, our data highlight the versatility of conformationally plastic proteins with high intrinsic disorder.
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Affiliation(s)
- Erinc Hallacli
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Can Kayatekin
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sumaiya Nazeen
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Xiou H Wang
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zoe Sheinkopf
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shubhangi Sathyakumar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Souvarish Sarkar
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xin Jiang
- Yumanity Therapeutics, Boston, MA 02135, USA
| | - Xianjun Dong
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Genomics and Bioinformatics Hub, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Roberto Di Maio
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew T Keeney
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics and Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Department of Psychiatry, Temerty Faculty of Medicine, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, 155 College Street, Toronto, ON M5T 3M7, Canada
| | - Jackson Sandoe
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Aazam Vahdatshoar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | | | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Philip L De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David P Bartel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - J Timothy Greenamyre
- Pittsburgh Institute for Neurodegenerative Diseases and Department of Neurology, Pittsburgh, PA 15213, USA
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | | | - Vikram Khurana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Movement Disorders, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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10
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Baron Y, Sens J, Lange L, Nassauer L, Klatt D, Hoffmann D, Kleppa MJ, Barbosa PV, Keisker M, Steinberg V, Suerth JD, Vondran FW, Meyer J, Morgan M, Schambach A, Galla M. Improved alpharetrovirus-based Gag.MS2 particles for efficient and transient delivery of CRISPR-Cas9 into target cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:810-823. [PMID: 35141043 PMCID: PMC8801357 DOI: 10.1016/j.omtn.2021.12.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/29/2021] [Indexed: 12/12/2022]
Abstract
DNA-modifying technologies, such as the CRISPR-Cas9 system, are promising tools in the field of gene and cell therapies. However, high and prolonged expression of DNA-modifying enzymes may cause cytotoxic and genotoxic side effects and is therefore unwanted in therapeutic approaches. Consequently, development of new and potent short-term delivery methods is of utmost importance. Recently, we developed non-integrating gammaretrovirus- and MS2 bacteriophage-based Gag.MS2 (g.Gag.MS2) particles for transient transfer of non-retroviral CRISPR-Cas9 RNA into target cells. In the present study, we further improved the technique by transferring the system to the alpharetroviral vector platform (a.Gag.MS2), which significantly increased CRISPR-Cas9 delivery into target cells and allowed efficient targeted knockout of endogenous TP53/Trp53 genes in primary murine fibroblasts as well as primary human fibroblasts, hepatocytes, and cord-blood-derived CD34+ stem and progenitor cells. Strikingly, co-packaging of Cas9 mRNA and multiple single guide RNAs (sgRNAs) into a.Gag.MS2 chimera displayed efficient targeted knockout of up to three genes. Co-transfection of single-stranded DNA donor oligonucleotides during CRISPR-Cas9 particle production generated all-in-one particles, which mediated up to 12.5% of homology-directed repair in primary cell cultures. In summary, optimized a.Gag.MS2 particles represent a versatile tool for short-term delivery of DNA-modifying enzymes into a variety of target cells, including primary murine and human cells.
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Affiliation(s)
- Yvonne Baron
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Johanna Sens
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Lucas Lange
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Larissa Nassauer
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Denise Klatt
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Dirk Hoffmann
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Marc-Jens Kleppa
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Philippe Vollmer Barbosa
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover 30625, Germany
| | - Maximilian Keisker
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Viviane Steinberg
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Julia D. Suerth
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Florian W.R. Vondran
- ReMediES, Department of General, Visceral and Transplant Surgery, Hannover Medical School, Hannover 30625, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover Medical School, Hannover 30625, Germany
| | - Johann Meyer
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
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11
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Tagging and Capturing of Lentiviral Vectors Using Short RNAs. Int J Mol Sci 2021; 22:ijms221910263. [PMID: 34638603 PMCID: PMC8508951 DOI: 10.3390/ijms221910263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 09/19/2021] [Indexed: 11/22/2022] Open
Abstract
Lentiviral (LV) vectors have emerged as powerful tools for transgene delivery ex vivo but in vivo gene therapy applications involving LV vectors have faced a number of challenges, including the low efficiency of transgene delivery, a lack of tissue specificity, immunogenicity to both the product encoded by the transgene and the vector, and the inactivation of the vector by the human complement cascade. To mitigate these issues, several engineering approaches, involving the covalent modification of vector particles or the incorporation of specific protein domains into the vector’s envelope, have been tested. Short synthetic oligonucleotides, including aptamers bound to the surface of LV vectors, may provide a novel means with which to retarget LV vectors to specific cells and to shield these vectors from neutralization by sera. The purpose of this study was to develop strategies to tether nucleic acid sequences, including short RNA sequences, to LV vector particles in a specific and tight fashion. To bind short RNA sequences to LV vector particles, a bacteriophage lambda N protein-derived RNA binding domain (λN), fused to the measles virus hemagglutinin protein, was used. The λN protein bound RNA sequences bearing a boxB RNA hairpin. To test this approach, we used an RNA aptamer specific to the human epidermal growth factor receptor (EGFR), which was bound to LV vector particles via an RNA scaffold containing a boxB RNA motif. The results obtained confirmed that the EGFR-specific RNA aptamer bound to cells expressing EGFR and that the boxB containing the RNA scaffold was bound specifically to the λN RNA binding domain attached to the vector. These results show that LV vectors can be equipped with nucleic acid sequences to develop improved LV vectors for in vivo applications.
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12
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Lalwani Prakash D, Gosavi S. Understanding the Folding Mediated Assembly of the Bacteriophage MS2 Coat Protein Dimers. J Phys Chem B 2021; 125:8722-8732. [PMID: 34339197 DOI: 10.1021/acs.jpcb.1c03928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The capsids of RNA viruses such as MS2 are great models for studying protein self-assembly because they are made almost entirely of multiple copies of a single coat protein (CP). Although CP is the minimal repeating unit of the capsid, previous studies have shown that CP exists as a homodimer (CP2) even in an acid-disassembled system, indicating that CP2 is an obligate dimer. Here, we investigate the molecular basis of this obligate dimerization using coarse-grained structure-based models and molecular dynamics simulations. We find that, unlike monomeric proteins of similar size, CP populates a single partially folded ensemble whose "foldedness" is sensitive to denaturing conditions. In contrast, CP2 folds similarly to single-domain proteins populating only the folded and the unfolded ensembles, separated by a prominent folding free energy barrier. Several intramonomer contacts form early, but the CP2 folding barrier is crossed only when the intermonomer contacts are made. A dissection of the structure of CP2 through mutant folding simulations shows that the folding barrier arises both from the topology of CP and the interface contacts of CP2. Together, our results show that CP2 is an obligate dimer because of kinetic stability, that is, dimerization induces a folding barrier and that makes it difficult for proteins in the dimer minimum to partially unfold and access the monomeric state without completely unfolding. We discuss the advantages of this obligate dimerization in the context of dimer design and virus stability.
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Affiliation(s)
- Digvijay Lalwani Prakash
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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13
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Bhakta S, Tsukahara T. Artificial RNA Editing with ADAR for Gene Therapy. Curr Gene Ther 2021; 20:44-54. [PMID: 32416688 DOI: 10.2174/1566523220666200516170137] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/14/2022]
Abstract
Editing mutated genes is a potential way for the treatment of genetic diseases. G-to-A mutations are common in mammals and can be treated by adenosine-to-inosine (A-to-I) editing, a type of substitutional RNA editing. The molecular mechanism of A-to-I editing involves the hydrolytic deamination of adenosine to an inosine base; this reaction is mediated by RNA-specific deaminases, adenosine deaminases acting on RNA (ADARs), family protein. Here, we review recent findings regarding the application of ADARs to restoring the genetic code along with different approaches involved in the process of artificial RNA editing by ADAR. We have also addressed comparative studies of various isoforms of ADARs. Therefore, we will try to provide a detailed overview of the artificial RNA editing and the role of ADAR with a focus on the enzymatic site directed A-to-I editing.
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Affiliation(s)
- Sonali Bhakta
- Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomicity, Ishikawa, 923-1292, Japan
| | - Toshifumi Tsukahara
- Area of Bioscience and Biotechnology, School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomicity, Ishikawa, 923-1292, Japan
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14
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Weissinger R, Heinold L, Akram S, Jansen RP, Hermesh O. RNA Proximity Labeling: A New Detection Tool for RNA-Protein Interactions. Molecules 2021; 26:2270. [PMID: 33919831 PMCID: PMC8070807 DOI: 10.3390/molecules26082270] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/26/2022] Open
Abstract
Multiple cellular functions are controlled by the interaction of RNAs and proteins. Together with the RNAs they control, RNA interacting proteins form RNA protein complexes, which are considered to serve as the true regulatory units for post-transcriptional gene expression. To understand how RNAs are modified, transported, and regulated therefore requires specific knowledge of their interaction partners. To this end, multiple techniques have been developed to characterize the interaction between RNAs and proteins. In this review, we briefly summarize the common methods to study RNA-protein interaction including crosslinking and immunoprecipitation (CLIP), and aptamer- or antisense oligonucleotide-based RNA affinity purification. Following this, we focus on in vivo proximity labeling to study RNA-protein interactions. In proximity labeling, a labeling enzyme like ascorbate peroxidase or biotin ligase is targeted to specific RNAs, RNA-binding proteins, or even cellular compartments and uses biotin to label the proteins and RNAs in its vicinity. The tagged molecules are then enriched and analyzed by mass spectrometry or RNA-Seq. We highlight the latest studies that exemplify the strength of this approach for the characterization of RNA protein complexes and distribution of RNAs in vivo.
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Affiliation(s)
| | | | | | | | - Orit Hermesh
- Interfaculty Institute for Biochemistry (IFIB), Tübingen University, 72076 Tübingen, Germany; (R.W.); (L.H.); (S.A.); (R.-P.J.)
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15
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Kenny A, Morgan MB, Macdonald PM. Different roles for the adjoining and structurally similar A-rich and poly(A) domains of oskar mRNA: Only the A-rich domain is required for oskar noncoding RNA function, which includes MTOC positioning. Dev Biol 2021; 476:117-127. [PMID: 33798537 DOI: 10.1016/j.ydbio.2021.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 11/17/2022]
Abstract
Drosophila oskar (osk) mRNA has both coding and noncoding functions, with the latter required for progression through oogenesis. Noncoding activity is mediated by the osk 3' UTR. Three types of cis elements act most directly and are clustered within the final ~120 nucleotides of the 3' UTR: multiple binding sites for the Bru1 protein, a short highly conserved region, and A-rich sequences abutting the poly(A) tail. Here we extend the characterization of these elements and their functions, providing new insights into osk noncoding RNA function and the makeup of the cis elements. We show that all three elements are required for correct positioning of the microtubule organizing center (MTOC), a defect not previously reported for any osk mutant. Normally, the MTOC is located at the posterior of the oocyte during previtellogenic stages of oogenesis, and this distribution underlies the strong posterior enrichment of many mRNAs transported into the oocyte from the nurse cells. When osk noncoding function was disrupted the MTOC was dispersed in the oocyte and osk mRNA failed to be enriched at the posterior, although transport to the oocyte was not affected. A previous study did not detect loss of posterior enrichment for certain osk mutants lacking noncoding activity (Kanke et al., 2015). This discrepancy may be due to use of imaging aimed at monitoring transport to the oocyte rather than posterior enrichment. Involvement in MTOC positioning suggests that the osk noncoding function may act in conjunction with genes whose loss has similar effects, and that osk function may extend to other processes requiring those genes. Further characterization of the cis elements required for osk noncoding function included completion of saturation mutagenesis of the most highly conserved region, providing critical information for evaluating the possible contribution of candidate binding factors. The 3'-most cis element is a cluster of A-rich sequences, the ARS. The close juxtaposition and structural similarity of the ARS and poly(A) tail raised the possibility that they comprise an extended A-rich element required for osk noncoding function. We found that absence of the poly(A) tail did not mimic the effects of mutation of the ARS, causing neither arrest of oogenesis nor mispositioning of osk mRNA in previtellogenic stage oocytes. Thus, the ARS and the poly(A) tail are not interchangeable for osk noncoding RNA function, suggesting that the role of the ARS is not in recruitment of Poly(A) binding protein (PABP), the protein that binds the poly(A) tail. Furthermore, although PABP has been implicated in transport of osk mRNA from the nurse cells to the oocyte, mutation of the ARS in combination with loss of the poly(A) tail did not disrupt transport of osk mRNA into the oocyte. We conclude that PABP acts indirectly in osk mRNA transport, or is associated with osk mRNA independent of an A-rich binding site. Although the poly(A) tail was not required for osk mRNA transport into the oocyte, its absence was associated with a novel osk mRNA localization defect later in oogenesis, potentially revealing a previously unrecognized step in the localization process.
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Affiliation(s)
- Andrew Kenny
- Department of Molecular Biosciences, The University of Texas at Austin, United States
| | - Miles B Morgan
- Department of Molecular Biosciences, The University of Texas at Austin, United States
| | - Paul M Macdonald
- Department of Molecular Biosciences, The University of Texas at Austin, United States.
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16
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Macias VM, Palatini U, Bonizzoni M, Rasgon JL. Leaning Into the Bite: The piRNA Pathway as an Exemplar for the Genetic Engineering Need in Mosquitoes. Front Cell Infect Microbiol 2021; 10:614342. [PMID: 33520739 PMCID: PMC7840538 DOI: 10.3389/fcimb.2020.614342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022] Open
Abstract
The piRNA pathway is a specialized small RNA interference that in mosquitoes is mechanistically distant from analogous biology in the Drosophila model. Current genetic engineering methods, such as targeted genome manipulation, have a high potential to tease out the functional complexity of this intricate molecular pathway. However, progress in utilizing these methods in arthropod vectors has been geared mostly toward the development of new vector control strategies rather than to study cellular functions. Herein we propose that genetic engineering methods will be essential to uncover the full functionality of PIWI/piRNA biology in mosquitoes and that extending the applications of genetic engineering on other aspects of mosquito biology will grant access to a much larger pool of knowledge in disease vectors that is just out of reach. We discuss motivations for and impediments to expanding the utility of genetic engineering to study the underlying biology and disease transmission and describe specific areas where efforts can be placed to achieve the full potential for genetic engineering in basic biology in mosquito vectors. Such efforts will generate a refreshed intellectual source of novel approaches to disease control and strong support for the effective use of approaches currently in development.
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Affiliation(s)
- Vanessa M. Macias
- Department of Entomology, The Pennsylvania State University, University Park, PA, United States
| | - Umberto Palatini
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | | | - Jason L. Rasgon
- Department of Entomology, The Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA, United States
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17
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Marina RJ, Brannan KW, Dong KD, Yee BA, Yeo GW. Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing. Cell Rep 2020; 33:108350. [PMID: 33147453 PMCID: PMC8985550 DOI: 10.1016/j.celrep.2020.108350] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/30/2020] [Accepted: 10/13/2020] [Indexed: 12/17/2022] Open
Abstract
Site-directed RNA editing approaches offer great potential to correct genetic mutations in somatic cells while avoiding permanent off-target genomic edits. Nuclease-dead RNA-targeting CRISPR-Cas systems recruit functional effectors to RNA molecules in a programmable fashion. Here, we demonstrate a Streptococcus pyogenes Cas9-ADAR2 fusion system that uses a 3' modified guide RNA (gRNA) to enable adenosine-to-inosine (A-to-I) editing of specific bases on reporter and endogenously expressed mRNAs. Due to the sufficient nature of the 3' gRNA extension sequence, we observe that Cas9 gRNA spacer sequences are dispensable for directed RNA editing, revealing that Cas9 can act as an RNA-aptamer-binding protein. We demonstrate that Cas9-based A-to-I editing is comparable in on-target efficiency and off-target specificity with Cas13 RNA editing versions. This study provides a systematic benchmarking of RNA-targeting CRISPR-Cas designs for reversible nucleotide-level conversion at the transcriptome level.
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Affiliation(s)
- Ryan J Marina
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Kristopher W Brannan
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Kevin D Dong
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA; Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA 92093, USA.
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18
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Zhang W, Wu Q. Applications of phage-derived RNA-based technologies in synthetic biology. Synth Syst Biotechnol 2020; 5:343-360. [PMID: 33083579 PMCID: PMC7564126 DOI: 10.1016/j.synbio.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.
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Affiliation(s)
- Wenhui Zhang
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- Corresponding author. MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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19
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McDonel P, Guttman M. Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene Expression. Cold Spring Harb Perspect Biol 2019; 11:11/12/a032151. [PMID: 31791999 DOI: 10.1101/cshperspect.a032151] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mammalian genomes encode tens of thousands of long noncoding RNAs (lncRNAs) that have been implicated in a diverse array of biological processes and human diseases. In recent years, the development of new tools for studying lncRNAs has enabled important progress in defining the mechanisms by which Xist and other lncRNAs function. This collective work provides a framework for how to define the mechanisms by which lncRNAs act. This includes defining lncRNA function, identifying and characterizing lncRNA-protein interactions, and lncRNA localization in the cell. In this review, we discuss various experimental approaches for deciphering lncRNA mechanisms and discuss issues and limitations in interpreting these results. We explore what these data can reveal about lncRNA function and mechanism as well as emerging insights into lncRNA biology that have been derived from these studies.
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Affiliation(s)
- Patrick McDonel
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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20
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Azad MTA, Qulsum U, Tsukahara T. Comparative Activity of Adenosine Deaminase Acting on RNA (ADARs) Isoforms for Correction of Genetic Code in Gene Therapy. Curr Gene Ther 2019; 19:31-39. [DOI: 10.2174/1566523218666181114122116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/26/2022]
Abstract
Introduction:
Members of the adenosine deaminase acting on RNA (ADAR) family of enzymes
consist of double-stranded RNA-binding domains (dsRBDs) and a deaminase domain (DD)
that converts adenosine (A) into inosine (I), which acts as guanosine (G) during translation. Using the
MS2 system, we engineered the DD of ADAR1 to direct it to a specific target. The aim of this work
was to compare the deaminase activities of ADAR1-DD and various isoforms of ADAR2-DD.
Materials and Methods:
We measured the binding affinity of the artificial enzyme system on a Biacore
™ X100. ADARs usually target dsRNA, so we designed a guide RNA complementary to the target
RNA, and then fused the guide sequence to the MS2 stem-loop. A mutated amber (TAG) stop
codon at 58 amino acid (TGG) of EGFP was targeted. After transfection of these three factors into
HEK 293 cells, we observed fluorescence signals of various intensities.
Results:
ADAR2-long without the Alu-cassette yielded a much higher fluorescence signal than
ADAR2-long with the Alu-cassette. With another isoform, ADAR2-short, which is 81 bp shorter at
the C-terminus, the fluorescence signal was undetectable. A single amino acid substitution of
ADAR2-long-DD (E488Q) rendered the enzyme more active than the wild type. The results of fluorescence
microscopy suggested that ADAR1-DD is more active than ADAR2-long-DD. Western blots
and sequencing confirmed that ADAR1-DD was more active than any other DD.
Conclusion:
This study provides information that should facilitate the rational use of ADAR variants
for genetic restoration and treatment of genetic diseases.
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Affiliation(s)
- Md. Thoufic A. Azad
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923- 1292, Japan
| | - Umme Qulsum
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923- 1292, Japan
| | - Toshifumi Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923- 1292, Japan
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21
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Montiel-Gonzalez MF, Diaz Quiroz JF, Rosenthal JJC. Current strategies for Site-Directed RNA Editing using ADARs. Methods 2019; 156:16-24. [PMID: 30502398 PMCID: PMC6814296 DOI: 10.1016/j.ymeth.2018.11.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/22/2018] [Accepted: 11/27/2018] [Indexed: 12/26/2022] Open
Abstract
Adenosine Deaminases that Act on RNA (ADARs) are a group of enzymes that catalyze the conversion of adenosines (A's) to inosines (I's) in a process known as RNA editing. Though ADARs can act on different types of RNA, editing events in coding regions of mRNA are of particular interest as I's base pair like guanosines (G's). Thus, every A-to-I change catalyzed by ADAR is read as an A-to-G change during translation, potentially altering protein sequence and function. This ability to re-code makes ADAR an attractive therapeutic tool to correct genetic mutations within mRNA. The main challenge in doing so is to re-direct ADAR's catalytic activity towards A's that are not naturally edited, a process termed Site-Directed RNA Editing (SDRE). Recently, a handful of labs have taken up this challenge and two basic strategies have emerged. The first involves redirecting endogenous ADAR to new sites by making editable structures using antisense RNA oligonucleotides. The second also utilizes antisense RNA oligonucleotides, but it uses them as guides to deliver the catalytic domain of engineered ADARs to new sites, much as CRISPR guides deliver Cas nucleases. In fact, despite the intense current focus on CRISPR-Cas9 genome editing, SDRE offers a number of distinct advantages. In the present review we will discuss these strategies in greater detail, focusing on the concepts on which they are based, how they were developed and tested, and their respective advantages and disadvantages. Though the precise and efficient re-direction of ADAR activity still remains a challenge, the systems that are being developed lay the foundation for SDRE as a powerful tool for transient genome editing.
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MESH Headings
- Adenosine/metabolism
- Adenosine Deaminase/genetics
- Adenosine Deaminase/metabolism
- Animals
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Genome, Human
- Humans
- Inosine/metabolism
- Mutagenesis, Site-Directed/methods
- Oligoribonucleotides, Antisense/genetics
- Oligoribonucleotides, Antisense/metabolism
- Protein Domains
- RNA Editing
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
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22
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Knopp Y, Geis FK, Heckl D, Horn S, Neumann T, Kuehle J, Meyer J, Fehse B, Baum C, Morgan M, Meyer J, Schambach A, Galla M. Transient Retrovirus-Based CRISPR/Cas9 All-in-One Particles for Efficient, Targeted Gene Knockout. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:256-274. [PMID: 30317165 PMCID: PMC6187057 DOI: 10.1016/j.omtn.2018.09.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 12/11/2022]
Abstract
The recently discovered CRISPR/Cas9 system is widely used in basic research and is a useful tool for disease modeling and gene editing therapies. However, long-term expression of DNA-modifying enzymes can be associated with cytotoxicity and is particularly unwanted in clinical gene editing strategies. Because current transient expression methods may still suffer from cytotoxicity and/or low efficiency, we developed non-integrating retrovirus-based CRISPR/Cas9 all-in-one particles for targeted gene knockout. By redirecting the gammaretroviral packaging machinery, we transiently delivered Streptococcus pyogenes Cas9 (SpCas9) mRNA and single-guide RNA transcripts into various (including primary) cell types. Spatiotemporal co-delivery of CRISPR/Cas9 components resulted in efficient disruption of a surrogate reporter gene, as well as functional knockout of endogenous human genes CXCR4 and TP53. Although acting in a hit-and-run fashion, knockout efficiencies of our transient particles corresponded to 52%-80% of those obtained from constitutively active integrating vectors. Stable SpCas9 overexpression at high doses in murine NIH3T3 cells caused a substantial G0/G1 arrest accompanied by reduced cell growth and metabolic activity, which was prevented by transient SpCas9 transfer. In summary, the non-integrating retrovirus-based vector particles introduced here allow efficient and dose-controlled delivery of CRISPR/Cas9 components into target cells.
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Affiliation(s)
- Yvonne Knopp
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Franziska K Geis
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Dirk Heckl
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover 30625, Germany
| | - Stefan Horn
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Thomas Neumann
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Johannes Kuehle
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Janine Meyer
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Christopher Baum
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany; Presidential Office, Hannover Medical School, Hannover 30625, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Johann Meyer
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, Hannover 30625, Germany.
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23
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Harada LK, Silva EC, Campos WF, Del Fiol FS, Vila M, Dąbrowska K, Krylov VN, Balcão VM. Biotechnological applications of bacteriophages: State of the art. Microbiol Res 2018; 212-213:38-58. [DOI: 10.1016/j.micres.2018.04.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/16/2018] [Accepted: 04/25/2018] [Indexed: 02/06/2023]
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24
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Barajas BC, Tanaka M, Robinson BA, Phuong DJ, Chutiraka K, Reed JC, Lingappa JR. Identifying the assembly intermediate in which Gag first associates with unspliced HIV-1 RNA suggests a novel model for HIV-1 RNA packaging. PLoS Pathog 2018; 14:e1006977. [PMID: 29664940 PMCID: PMC5940231 DOI: 10.1371/journal.ppat.1006977] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/08/2018] [Accepted: 03/16/2018] [Indexed: 12/20/2022] Open
Abstract
During immature capsid assembly, HIV-1 genome packaging is initiated when Gag first associates with unspliced HIV-1 RNA by a poorly understood process. Previously, we defined a pathway of sequential intracellular HIV-1 capsid assembly intermediates; here we sought to identify the intermediate in which HIV-1 Gag first associates with unspliced HIV-1 RNA. In provirus-expressing cells, unspliced HIV-1 RNA was not found in the soluble fraction of the cytosol, but instead was largely in complexes ≥30S. We did not detect unspliced HIV-1 RNA associated with Gag in the first assembly intermediate, which consists of soluble Gag. Instead, the earliest assembly intermediate in which we detected Gag associated with unspliced HIV-1 RNA was the second assembly intermediate (~80S intermediate), which is derived from a host RNA granule containing two cellular facilitators of assembly, ABCE1 and the RNA granule protein DDX6. At steady-state, this RNA-granule-derived ~80S complex was the smallest assembly intermediate that contained Gag associated with unspliced viral RNA, regardless of whether lysates contained intact or disrupted ribosomes, or expressed WT or assembly-defective Gag. A similar complex was identified in HIV-1-infected T cells. RNA-granule-derived assembly intermediates were detected in situ as sites of Gag colocalization with ABCE1 and DDX6; moreover these granules were far more numerous and smaller than well-studied RNA granules termed P bodies. Finally, we identified two steps that lead to association of assembling Gag with unspliced HIV-1 RNA. Independent of viral-RNA-binding, Gag associates with a broad class of RNA granules that largely lacks unspliced viral RNA (step 1). If a viral-RNA-binding domain is present, Gag further localizes to a subset of these granules that contains unspliced viral RNA (step 2). Thus, our data raise the possibility that HIV-1 packaging is initiated not by soluble Gag, but by Gag targeted to a subset of host RNA granules containing unspliced HIV-1 RNA.
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Affiliation(s)
- Brook C. Barajas
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Motoko Tanaka
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Bridget A. Robinson
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Daryl J. Phuong
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Kasana Chutiraka
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Jonathan C. Reed
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Jaisri R. Lingappa
- Department of Global Health, University of Washington, Seattle, WA, United States of America
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25
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De Franco S, O'Connell MR, Vandevenne M. Engineering RNA-Binding Proteins by Modular Assembly of RanBP2-Type Zinc Fingers. Methods Mol Biol 2018; 1867:57-74. [PMID: 30155815 DOI: 10.1007/978-1-4939-8799-3_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Deciphering the function of the nonprotein-coding portion of genomes represents one of the major challenges that molecular biology is facing today. Numerous classes of RNAs have been discovered over the last past decade and appear to play important regulatory roles in gene expression and disease. The ability to study and manipulate these RNAs relies on the development of programmable RNA-binding molecules such as RNA-binding proteins. Most RNA-binding proteins have modular architectures and combine different RNA-binding domains that provide binding affinity toward a specific RNA sequence and/or structure. Herein, we describe a general strategy to design single-stranded RNA-binding proteins using RanBP2-type zinc-finger (ZF) domains that can recognize a given RNA sequence with high affinity and specificity.
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Affiliation(s)
- Simona De Franco
- Center for Protein Engineering, University of Liège, Liège, Belgium
| | - Mitchell R O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, USA
- Center for RNA Biology, University of Rochester, Rochester, NY, USA
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26
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Azizi H, Dumas C, Papadopoulou B. The Pumilio-domain protein PUF6 contributes to SIDER2 retroposon-mediated mRNA decay in Leishmania. RNA (NEW YORK, N.Y.) 2017; 23:1874-1885. [PMID: 28877997 PMCID: PMC5689007 DOI: 10.1261/rna.062950.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
Leishmania and other trypanosomatid protozoa lack control at the level of transcription initiation and regulate gene expression exclusively post-transcriptionally. We have reported previously that Leishmania harbors a unique class of short interspersed degenerate retroposons (SIDERs) that are predominantly located within 3'UTRs and play a major role in post-transcriptional control. We have shown that members of the SIDER2 subfamily initiate mRNA decay through endonucleolytic cleavage within the second conserved 79-nt signature sequence of SIDER2 retroposons. Here, we have developed an optimized MS2 coat protein tethering system to capture trans-acting factor(s) regulating SIDER2-mediated mRNA decay. Tethering of the MS2 coat protein to a reporter RNA harboring two MS2 stem-loop aptamers and the cognate SIDER2-containing 3'UTR in combination with immunoprecipitation and mass spectrometry analysis led to the identification of RNA-binding proteins with known functions in mRNA decay. Among the candidate SIDER2-interacting proteins that were individually tethered to a SIDER2 reporter RNA, the Pumilio-domain protein PUF6 was shown to enhance degradation and reduce transcript half-life. Furthermore, we showed that PUF6 binds to SIDER2 sequences that include the regulatory 79-nt signature motif, hence contributing to the mRNA decay process. Consistent with a role of PUF6 in SIDER2-mediated decay, genetic inactivation of PUF6 resulted in increased accumulation and higher stability of endogenous SIDER2-bearing transcripts. Overall, these studies provide new insights into regulated mRNA decay pathways in Leishmania controlled by SIDER2 retroposons and propose a broader role for PUF proteins in mRNA decay within the eukaryotic kingdom.
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Affiliation(s)
- Hiva Azizi
- Research Center in Infectious Diseases, CHU de Quebec Research Center-Laval University, Quebec, QC, G1V 4G2 Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec, QC, G1V 0A6 Canada
| | - Carole Dumas
- Research Center in Infectious Diseases, CHU de Quebec Research Center-Laval University, Quebec, QC, G1V 4G2 Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec, QC, G1V 0A6 Canada
| | - Barbara Papadopoulou
- Research Center in Infectious Diseases, CHU de Quebec Research Center-Laval University, Quebec, QC, G1V 4G2 Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec, QC, G1V 0A6 Canada
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27
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Azad MTA, Bhakta S, Tsukahara T. Site-directed RNA editing by adenosine deaminase acting on RNA for correction of the genetic code in gene therapy. Gene Ther 2017; 24:779-786. [PMID: 28984845 DOI: 10.1038/gt.2017.90] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/11/2022]
Abstract
Site-directed RNA editing is an important technique for correcting gene sequences and ultimately tuning protein function. In this study, we engineered the deaminase domain of adenosine deaminase acting on RNA (ADAR1) and the MS2 system to target-specific adenosines, with the goal of correcting G-to-A mutations at the RNA level. For this purpose, the ADAR1 deaminase domain was fused downstream of the RNA-binding protein MS2, which has affinity for the MS2 RNA. To direct editing to specific targets, we designed guide RNAs complementary to target RNAs. The guide RNAs directed the ADAR1 deaminase to the desired editing site, where it converted adenosine to inosine. To provide proof of principle, we used an allele of enhanced green fluorescent protein (EGFP) bearing a mutation at the 58th amino acid (TGG), encoding Trp, into an amber (TAG) or ochre (TAA) stop codon. In HEK-293 cells, our system could convert stop codons to read-through codons, thereby turning on fluorescence. We confirmed the specificity of editing at the DNA level by restriction fragment length polymorphism analysis and sequencing, and at the protein level by western blotting. The editing efficiency of this enzyme system was ~5%. We believe that this system could be used to treat genetic diseases resulting from G-to-A point mutations.
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Affiliation(s)
- Md T A Azad
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, Japan
- Department of Veterinary and Animal Sciences, Faculty of Agriculture, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - S Bhakta
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, Japan
| | - T Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology, Ishikawa, Japan
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28
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Pankert T, Jegou T, Caudron-Herger M, Rippe K. Tethering RNA to chromatin for fluorescence microscopy based analysis of nuclear organization. Methods 2017; 123:89-101. [DOI: 10.1016/j.ymeth.2017.01.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/23/2017] [Accepted: 01/30/2017] [Indexed: 12/22/2022] Open
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29
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Cook JM, Charlesworth A. Insertion of inter-domain linkers improves expression and bioactivity of Zygote arrest (Zar) fusion proteins. Protein Eng Des Sel 2017; 30:313-319. [PMID: 28130327 DOI: 10.1093/protein/gzx002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/10/2017] [Indexed: 11/12/2022] Open
Abstract
Developmentally important proteins that are crucial for fertilization and embryogenesis are synthesized through highly regulated translation of maternal mRNA. The Zygote arrest proteins, Zar1 and Zar2, are crucial for embryogenesis and have been implicated in binding mRNA and repressing mRNA translation. To investigate Zar1 and Zar2, the full-length proteins had been fused to glutathione-S-transferase (GST) or MS2 protein tags with minimal inter-domain linkers derived from multiple cloning sites; however, these fusion proteins expressed poorly and/or lacked robust function. Here, we tested the effect of inserting additional linkers between the fusion domains. Three linkers were tested, each 17 amino acids long with different physical and chemical properties: flexible hydrophilic, rigid extended or rigid helical. In the presence of any of the three linkers, GST-Zar1 and GST-Zar2 had fewer breakdown products. Moreover, in the presence of any of the linkers, MS2-Zar1 was expressed to higher levels, and in dual luciferase tethered assays, both MS2-Zar1 and MS2-Zar2 repressed luciferase translation to a greater extent. These data suggest that for Zar fusion proteins, increasing the length of linkers, regardless of their physical or chemical properties, improves stability, expression and bioactivity.
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Affiliation(s)
- Jonathan M Cook
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80204, USA
| | - Amanda Charlesworth
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80204, USA
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30
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Wettengel J, Reautschnig P, Geisler S, Kahle PJ, Stafforst T. Harnessing human ADAR2 for RNA repair - Recoding a PINK1 mutation rescues mitophagy. Nucleic Acids Res 2017; 45:2797-2808. [PMID: 27907896 PMCID: PMC5389476 DOI: 10.1093/nar/gkw911] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 02/06/2023] Open
Abstract
Site-directed A-to-I RNA editing is a technology for re-programming genetic information at the RNA-level. We describe here the first design of genetically encodable guideRNAs that enable the re-addressing of human ADAR2 toward specific sites in user-defined mRNA targets. Up to 65% editing yield has been achieved in cell culture for the recoding of a premature Stop codon (UAG) into tryptophan (UIG). In the targeted gene, editing was very specific. We applied the technology to recode a recessive loss-of-function mutation in PINK1 (W437X) in HeLa cells and showed functional rescue of PINK1/Parkin-mediated mitophagy, which is linked to the etiology of Parkinson's disease. In contrast to other editing strategies, this approach requires no artificial protein. Our novel guideRNAs may allow for the development of a platform technology that requires only the administration or expression of a guideRNA to recode genetic information, with high potential for application in biology and medicine.
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Affiliation(s)
- Jacqueline Wettengel
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Philipp Reautschnig
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Sven Geisler
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Otfried-Müller-Strasse 27, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases, Otfried-Müller-Strasse 23, 72076 Tübingen, Germany
| | - Philipp J. Kahle
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Otfried-Müller-Strasse 27, 72076 Tübingen, Germany
- German Center for Neurodegenerative Diseases, Otfried-Müller-Strasse 23, 72076 Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
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31
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Azizi H, Müller-McNicoll M, Papadopoulou B. SIDER2 retroposon-mediated mRNA decay in Leishmania is coupled to translation. Int J Parasitol 2017; 47:305-310. [PMID: 28315363 DOI: 10.1016/j.ijpara.2017.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 02/10/2017] [Accepted: 02/13/2017] [Indexed: 12/17/2022]
Abstract
We previously reported that Short Interspersed Degenerate Retroposons of the SIDER2 subfamily predominantly located within 3' untranslated regions (UTRs) of Leishmania transcripts promote rapid turnover that is initiated by endonucleolytic cleavage. Here, we investigated whether SIDER2-mediated mRNA decay is linked to translation. We show that preventing translation initiation by inserting a hairpin structure at the 5'-end of a SIDER2-containing mRNA blocks degradation. Similarly, global inhibition of translation elongation by cycloheximide or termination by puromycin causes stabilisation of SIDER2-containing transcripts. Altogether, these findings support that the mechanism of SIDER2-mediated decay is coupled to translation, possibly through the recruitment of decay factors to elongating ribosomes.
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Affiliation(s)
- Hiva Azizi
- Research Center in Infectious Disease, CHU de Quebec Research Center, 2705 Laurier Blvd., Quebec G1V 4G2, QC, Canada; Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, Canada
| | - Michaela Müller-McNicoll
- Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Frankfurt, Germany
| | - Barbara Papadopoulou
- Research Center in Infectious Disease, CHU de Quebec Research Center, 2705 Laurier Blvd., Quebec G1V 4G2, QC, Canada; Department of Microbiology-Infectious Disease and Immunology, Faculty of Medicine, University Laval, Quebec, Canada.
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32
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Portoso M, Ragazzini R, Brenčič Ž, Moiani A, Michaud A, Vassilev I, Wassef M, Servant N, Sargueil B, Margueron R. PRC2 is dispensable for HOTAIR-mediated transcriptional repression. EMBO J 2017; 36:981-994. [PMID: 28167697 PMCID: PMC5391141 DOI: 10.15252/embj.201695335] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/23/2016] [Accepted: 01/05/2017] [Indexed: 11/09/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) play diverse roles in physiological and pathological processes. Several lncRNAs have been suggested to modulate gene expression by guiding chromatin‐modifying complexes to specific sites in the genome. However, besides the example of Xist, clear‐cut evidence demonstrating this novel mode of regulation remains sparse. Here, we focus on HOTAIR, a lncRNA that is overexpressed in several tumor types and previously proposed to play a key role in gene silencing through direct recruitment of Polycomb Repressive Complex 2 (PRC2) to defined genomic loci. Using genetic tools and a novel RNA‐tethering system, we investigated the interplay between HOTAIR and PRC2 in gene silencing. Surprisingly, we observed that forced overexpression of HOTAIR in breast cancer cells leads to subtle transcriptomic changes that appear to be independent of PRC2. Mechanistically, we found that artificial tethering of HOTAIR to chromatin causes transcriptional repression, but that this effect does not require PRC2. Instead, PRC2 recruitment appears to be a consequence of gene silencing. We propose that PRC2 binding to RNA might serve functions other than chromatin targeting.
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Affiliation(s)
- Manuela Portoso
- Institut Curie, PSL Research University, Paris, France.,INSERM U934, CNRS UMR3215, Paris, France
| | - Roberta Ragazzini
- Institut Curie, PSL Research University, Paris, France.,INSERM U934, CNRS UMR3215, Paris, France
| | - Živa Brenčič
- Institut Curie, PSL Research University, Paris, France.,INSERM U934, CNRS UMR3215, Paris, France
| | - Arianna Moiani
- Institut Curie, PSL Research University, Paris, France.,INSERM U934, CNRS UMR3215, Paris, France
| | - Audrey Michaud
- Institut Curie, PSL Research University, Paris, France.,INSERM U934, CNRS UMR3215, Paris, France
| | - Ivaylo Vassilev
- Institut Curie, PSL Research University, Paris, France.,INSERM U934, CNRS UMR3215, Paris, France
| | - Michel Wassef
- Institut Curie, PSL Research University, Paris, France.,INSERM U934, CNRS UMR3215, Paris, France
| | - Nicolas Servant
- Institut Curie, PSL Research University, Paris, France.,INSERM U900, Mines ParisTech, Paris, France
| | - Bruno Sargueil
- CNRS UMR 8015, Université Paris Descartes, Paris, France
| | - Raphaël Margueron
- Institut Curie, PSL Research University, Paris, France .,INSERM U934, CNRS UMR3215, Paris, France
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33
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Abstract
Multiple mRNA processing steps, including splicing and 3' processing, take place in macromolecular complexes that contain many proteins and sometimes RNA molecules. A key challenge in the mRNA processing field has been to define the structure-function relationship of these sophisticated molecular machines. A prerequisite for addressing this challenge is to develop tools for purifying mRNA processing complexes in their native and intact forms that are suitable for functional and structural studies. Among many methods that have been developed, RNA affinity-based methods are most widely applied. In these methods, RNA molecules that are substrates to mRNA processing machineries are fused with an affinity tag, incubated with cellular extracts/lysates to allow for the assembly of mRNA processing complexes, and finally the assembled complexes are purified using RNA affinity tag. In this chapter, we will overview RNA affinity-based purification methods and describe in detail one such method, MS2-tagging, and its application in the purification of mRNA 3' processing complexes. Although these methods were originally developed for purifying mRNA processing complexes, they should be applicable to purification of other RNA-protein complexes as well.
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34
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Montiel-González MF, Vallecillo-Viejo IC, Rosenthal JJC. An efficient system for selectively altering genetic information within mRNAs. Nucleic Acids Res 2016; 44:e157. [PMID: 27557710 PMCID: PMC5137428 DOI: 10.1093/nar/gkw738] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 08/02/2016] [Accepted: 08/12/2016] [Indexed: 01/09/2023] Open
Abstract
Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encoded iteration of SDRE could target adenosines expressed in human cells, but not efficiently. Here we developed a reporter assay to quantify editing, and used it to improve our strategy. By enhancing the linkage between ADAR's catalytic domain and the guide RNA, and by introducing a mutation in the catalytic domain, the efficiency of converting a U A: G premature termination codon (PTC) to tryptophan (U G: G) was improved from ∼11 % to ∼70 %. Other PTCs were edited, but less efficiently. Numerous off-target edits were identified in the targeted mRNA, but not in randomly selected endogenous messages. Off-target edits could be eliminated by reducing the amount of guide RNA with a reduction in on-target editing. The catalytic rate of SDRE was compared with those for human ADARs on various substrates and found to be within an order of magnitude of most. These data underscore the promise of site-directed RNA editing as a therapeutic or experimental tool.
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Affiliation(s)
| | - Isabel C Vallecillo-Viejo
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00901, USA
- Department of Pharmacology, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA
| | - Joshua J C Rosenthal
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00901, USA
- The Marine Biological Laboratory, University of Chicago, Woods Hole, MA 02543, USA
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35
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Xiao X, Hung ME, Leonard JN, Hall CK. Adding energy minimization strategy to peptide-design algorithm enables better search for RNA-binding peptides: Redesigned λ N peptide binds boxB RNA. J Comput Chem 2016; 37:2423-35. [PMID: 27487990 PMCID: PMC5314887 DOI: 10.1002/jcc.24466] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 04/20/2016] [Accepted: 07/13/2016] [Indexed: 11/10/2022]
Abstract
Our previously developed peptide-design algorithm was improved by adding an energy minimization strategy which allows the amino acid sidechains to move in a broad configuration space during sequence evolution. In this work, the new algorithm was used to generate a library of 21-mer peptides which could substitute for λ N peptide in binding to boxB RNA. Six potential peptides were obtained from the algorithm, all of which exhibited good binding capability with boxB RNA. Atomistic molecular dynamics simulations were then conducted to examine the ability of the λ N peptide and three best evolved peptides, viz. Pept01, Pept26, and Pept28, to bind to boxB RNA. Simulation results demonstrated that our evolved peptides are better at binding to boxB RNA than the λ N peptide. Sequence searches using the old (without energy minimization strategy) and new (with energy minimization strategy) algorithms confirm that the new algorithm is more effective at finding good RNA-binding peptides than the old algorithm. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Xingqing Xiao
- Chemical and Biomolecular Engineering Department, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Michelle E Hung
- Chemical and Biological Engineering Department, and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, 60208
| | - Joshua N Leonard
- Chemical and Biological Engineering Department, and Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois, 60208
| | - Carol K Hall
- Chemical and Biomolecular Engineering Department, North Carolina State University, Raleigh, North Carolina, 27695-7905.
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36
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Jazurek M, Ciesiolka A, Starega-Roslan J, Bilinska K, Krzyzosiak WJ. Identifying proteins that bind to specific RNAs - focus on simple repeat expansion diseases. Nucleic Acids Res 2016; 44:9050-9070. [PMID: 27625393 PMCID: PMC5100574 DOI: 10.1093/nar/gkw803] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/01/2016] [Indexed: 12/11/2022] Open
Abstract
RNA–protein complexes play a central role in the regulation of fundamental cellular processes, such as mRNA splicing, localization, translation and degradation. The misregulation of these interactions can cause a variety of human diseases, including cancer and neurodegenerative disorders. Recently, many strategies have been developed to comprehensively analyze these complex and highly dynamic RNA–protein networks. Extensive efforts have been made to purify in vivo-assembled RNA–protein complexes. In this review, we focused on commonly used RNA-centric approaches that involve mass spectrometry, which are powerful tools for identifying proteins bound to a given RNA. We present various RNA capture strategies that primarily depend on whether the RNA of interest is modified. Moreover, we briefly discuss the advantages and limitations of in vitro and in vivo approaches. Furthermore, we describe recent advances in quantitative proteomics as well as the methods that are most commonly used to validate robust mass spectrometry data. Finally, we present approaches that have successfully identified expanded repeat-binding proteins, which present abnormal RNA–protein interactions that result in the development of many neurological diseases.
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Affiliation(s)
- Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Julia Starega-Roslan
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Katarzyna Bilinska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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37
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Guo C, Xue Y, Yang G, Yin S, Shi W, Cheng Y, Yan X, Fan S, Zhang H, Zeng F. Nanog RNA-binding proteins YBX1 and ILF3 affect pluripotency of embryonic stem cells. Cell Biol Int 2016; 40:847-60. [PMID: 26289635 DOI: 10.1002/cbin.10539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/15/2015] [Indexed: 02/05/2023]
Abstract
Nanog is a well-known transcription factor that plays a fundamental role in stem cell self-renewal and the maintenance of their pluripotent cell identity. There remains a large data gap with respect to the spectrum of the key pluripotency transcription factors' interaction partners. Limited information is available concerning Nanog-associated RNA-binding proteins (RBPs), and the intrinsic protein-RNA interactions characteristic of the regulatory activities of Nanog. Herein, we used an improved affinity protocol to purify Nanog-interacting RBPs from mouse embryonic stem cells (ESCs), and 49 RBPs of Nanog were identified. Among them, the interaction of YBX1 and ILF3 with Nanog mRNA was further confirmed by in vitro assays, such as Western blot, RNA immunoprecipitation (RIP), and ex vivo methods, such as immunofluorescence staining and fluorescent in situ hybridization (FISH), MS2 in vivo biotin-tagged RNA affinity purification (MS2-BioTRAP). Interestingly, RNAi studies revealed that YBX1 and ILF3 positively affected the expression of Nanog and other pluripotency-related genes. Particularly, downregulation of YBX1 or ILF3 resulted in high expression of mesoderm markers. Thus, a reduction in the expression of YBX1 and ILF3 controls the expression of pluripotency-related genes in ESCs, suggesting their roles in further regulation of the pluripotent state of ESCs.
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Affiliation(s)
- Chuanliang Guo
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Yan Xue
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Guanheng Yang
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Shang Yin
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wansheng Shi
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Cheng
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoshuang Yan
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China
| | - Shuyue Fan
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huijun Zhang
- Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fanyi Zeng
- Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Medical Science, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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38
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Chen YCA, Stuwe E, Luo Y, Ninova M, Le Thomas A, Rozhavskaya E, Li S, Vempati S, Laver JD, Patel DJ, Smibert CA, Lipshitz HD, Toth KF, Aravin AA. Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors. Mol Cell 2016; 63:97-109. [PMID: 27292797 DOI: 10.1016/j.molcel.2016.05.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 04/04/2016] [Accepted: 05/06/2016] [Indexed: 10/21/2022]
Abstract
Small non-coding RNAs called piRNAs serve as guides for an adaptable immune system that represses transposable elements in germ cells of Metazoa. In Drosophila the RDC complex, composed of Rhino, Deadlock and Cutoff (Cuff) bind chromatin of dual-strand piRNA clusters, special genomic regions, which encode piRNA precursors. The RDC complex is required for transcription of piRNA precursors, though the mechanism by which it licenses transcription remained unknown. Here, we show that Cuff prevents premature termination of RNA polymerase II. Cuff prevents cleavage of nascent RNA at poly(A) sites by interfering with recruitment of the cleavage and polyadenylation specificity factor (CPSF) complex. Cuff also protects processed transcripts from degradation by the exonuclease Rat1. Our work reveals a conceptually different mechanism of transcriptional enhancement. In contrast to other factors that regulate termination by binding to specific signals on nascent RNA, the RDC complex inhibits termination in a chromatin-dependent and sequence-independent manner.
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Affiliation(s)
- Yung-Chia Ariel Chen
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Evelyn Stuwe
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA.,Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Yicheng Luo
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Maria Ninova
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Adrien Le Thomas
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Ekaterina Rozhavskaya
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Sisi Li
- Memorial Sloan-Kettering Cancer Center, Structural Biology Program, 1275 York Avenue, New York, NY, 10021 USA
| | - Sivani Vempati
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - John D Laver
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Dinshaw J Patel
- Memorial Sloan-Kettering Cancer Center, Structural Biology Program, 1275 York Avenue, New York, NY, 10021 USA
| | - Craig A Smibert
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8.,Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Katalin Fejes Toth
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology, 147-75, 1200 E. California Blvd., Pasadena, CA 91125, USA
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39
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Hung ME, Leonard JN. A platform for actively loading cargo RNA to elucidate limiting steps in EV-mediated delivery. J Extracell Vesicles 2016; 5:31027. [PMID: 27189348 PMCID: PMC4870355 DOI: 10.3402/jev.v5.31027] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 04/07/2016] [Accepted: 04/19/2016] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs) mediate intercellular communication through transfer of RNA and protein between cells. Thus, understanding how cargo molecules are loaded and delivered by EVs is of central importance for elucidating the biological roles of EVs and developing EV-based therapeutics. While some motifs modulating the loading of biomolecular cargo into EVs have been elucidated, the general rules governing cargo loading and delivery remain poorly understood. To investigate how general biophysical properties impact loading and delivery of RNA by EVs, we developed a platform for actively loading engineered cargo RNAs into EVs. In our system, the MS2 bacteriophage coat protein was fused to EV-associated proteins, and the cognate MS2 stem loop was engineered into cargo RNAs. Using this Targeted and Modular EV Loading (TAMEL) approach, we identified a configuration that substantially enhanced cargo RNA loading (up to 6-fold) into EVs. When applied to vesicles expressing the vesicular stomatitis virus glycoprotein (VSVG) – gesicles – we observed a 40-fold enrichment in cargo RNA loading. While active loading of mRNA-length (>1.5 kb) cargo molecules was possible, active loading was much more efficient for smaller (~0.5 kb) RNA molecules. We next leveraged the TAMEL platform to elucidate the limiting steps in EV-mediated delivery of mRNA and protein to prostate cancer cells, as a model system. Overall, most cargo was rapidly degraded in recipient cells, despite high EV-loading efficiencies and substantial EV uptake by recipient cells. While gesicles were efficiently internalized via a VSVG-mediated mechanism, most cargo molecules were rapidly degraded. Thus, in this model system, inefficient endosomal fusion or escape likely represents a limiting barrier to EV-mediated transfer. Altogether, the TAMEL platform enabled a comparative analysis elucidating a key opportunity for enhancing EV-mediated delivery to prostate cancer cells, and this technology should be of general utility for investigations and applications of EV-mediated transfer in other systems.
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Affiliation(s)
- Michelle E Hung
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, USA;
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40
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Lampasona AA, Czaplinski K. RNA voyeurism: A coming of age story. Methods 2016; 98:10-17. [DOI: 10.1016/j.ymeth.2015.11.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 10/22/2022] Open
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41
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Generation of Recombinant Polioviruses Harboring RNA Affinity Tags in the 5' and 3' Noncoding Regions of Genomic RNAs. Viruses 2016; 8:v8020039. [PMID: 26861382 PMCID: PMC4776194 DOI: 10.3390/v8020039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 01/18/2016] [Accepted: 01/21/2016] [Indexed: 12/30/2022] Open
Abstract
Despite being intensely studied for more than 50 years, a complete understanding of the enterovirus replication cycle remains elusive. Specifically, only a handful of cellular proteins have been shown to be involved in the RNA replication cycle of these viruses. In an effort to isolate and identify additional cellular proteins that function in enteroviral RNA replication, we have generated multiple recombinant polioviruses containing RNA affinity tags within the 3' or 5' noncoding region of the genome. These recombinant viruses retained RNA affinity sequences within the genome while remaining viable and infectious over multiple passages in cell culture. Further characterization of these viruses demonstrated that viral protein production and growth kinetics were unchanged or only slightly altered relative to wild type poliovirus. However, attempts to isolate these genetically-tagged viral genomes from infected cells have been hindered by high levels of co-purification of nonspecific proteins and the limited matrix-binding efficiency of RNA affinity sequences. Regardless, these recombinant viruses represent a step toward more thorough characterization of enterovirus ribonucleoprotein complexes involved in RNA replication.
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42
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Isolation of Endogenously Assembled RNA-Protein Complexes Using Affinity Purification Based on Streptavidin Aptamer S1. Int J Mol Sci 2015; 16:22456-72. [PMID: 26389898 PMCID: PMC4613318 DOI: 10.3390/ijms160922456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/05/2015] [Accepted: 08/05/2015] [Indexed: 12/26/2022] Open
Abstract
Efficient isolation of endogenously assembled viral RNA-protein complexes is essential for understanding virus replication mechanisms. We have developed an affinity purification strategy based on an RNA affinity tag that allows large-scale preparation of native viral RNA-binding proteins (RBPs). The streptavidin-binding aptamer S1 sequence was inserted into the 3' end of dengue virus (DENV) 5'-3' UTR RNA, and the DENV RNA UTR fused to the S1 RNA aptamer was expressed in living mammalian cells. This allowed endogenous viral ribonucleoprotein (RNP) assembly and isolation of RNPs from whole cell extract, through binding the S1 aptamer to streptavidin magnetic beads. Several novel host DENV RBPs were subsequently identified by liquid chromatography with tandem mass spectrometry (LC-MS/MS), including RPS8, which we further implicate in DENV replication. We proposed efficient S1 aptamer-based isolation of viral assembled RNPs from living mammalian cells will be generally applicable to the purification of high- and low-affinity RBPs and RNPs under endogenous conditions.
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43
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Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00652-15. [PMID: 26112785 PMCID: PMC4481283 DOI: 10.1128/genomea.00652-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We report here the draft genome sequences of marine RNA phages EC and MB assembled from metagenomic sequencing of organisms in San Francisco wastewater. These phages showed moderate translated amino acid identity to other enterobacteria phages and appear to constitute novel members of the Leviviridae family.
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44
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Andries O, Kitada T, Bodner K, Sanders NN, Weiss R. Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review. Expert Rev Vaccines 2015; 14:313-31. [DOI: 10.1586/14760584.2015.997714] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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45
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Widom JR, Dhakal S, Heinicke LA, Walter NG. Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Arch Toxicol 2014; 88:1965-85. [PMID: 25212907 PMCID: PMC4615698 DOI: 10.1007/s00204-014-1357-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 08/28/2014] [Indexed: 12/22/2022]
Abstract
Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy.
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Affiliation(s)
- Julia R Widom
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI, 48109-1055, USA
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46
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Gelderman G, Sivakumar A, Lipp S, Contreras L. Adaptation of Tri-molecular fluorescence complementation allows assaying of regulatory Csr RNA-protein interactions in bacteria. Biotechnol Bioeng 2014; 112:365-75. [PMID: 25080893 DOI: 10.1002/bit.25351] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 07/15/2014] [Accepted: 07/18/2014] [Indexed: 12/18/2022]
Abstract
sRNAs play a significant role in controlling and regulating cellular metabolism. One of the more interesting aspects of certain sRNAs is their ability to make global changes in the cell by interacting with regulatory proteins. In this work, we demonstrate the use of an in vivo Tri-molecular Fluorescence Complementation assay to detect and visualize the central regulatory sRNA-protein interaction of the Carbon Storage Regulatory system in E. coli. The Carbon Storage Regulator consists primarily of an RNA binding protein, CsrA, that alters the activity of mRNA targets and of an sRNA, CsrB, that modulates the activity of CsrA. We describe the construction of a fluorescence complementation system that detects the interactions between CsrB and CsrA. Additionally, we demonstrate that the intensity of the fluorescence of this system is able to detect changes in the affinity of the CsrB-CsrA interaction, as caused by mutations in the protein sequence of CsrA. While previous methods have adopted this technique to study mRNA or RNA localization, this is the first attempt to use this technique to study the sRNA-protein interaction directly in bacteria. This method presents a potentially powerful tool to study complex bacterial RNA protein interactions in vivo.
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Affiliation(s)
- Grant Gelderman
- The University of Texas at Austin, McKetta Department of Chemical Engineering 200 E. Dean Keeton St. Stop C0400 Austin, Texas, USA 78712
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47
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Depletion of the Trypanosome Pumilio domain protein PUF2 or of some other essential proteins causes transcriptome changes related to coding region length. EUKARYOTIC CELL 2014; 13:664-74. [PMID: 24681684 DOI: 10.1128/ec.00018-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Pumilio domain RNA-binding proteins are known mainly as posttranscriptional repressors of gene expression that reduce mRNA translation and stability. Trypanosoma brucei has 11 PUF proteins. We show here that PUF2 is in the cytosol, with roughly the same number of molecules per cell as there are mRNAs. Although PUF2 exhibits a low level of in vivo RNA binding, it is not associated with polysomes. PUF2 also decreased reporter mRNA levels in a tethering assay, consistent with a repressive role. Depletion of PUF2 inhibited growth of bloodstream-form trypanosomes, causing selective loss of mRNAs with long open reading frames and increases in mRNAs with shorter open reading frames. Reexamination of published RNASeq data revealed the same trend in cells depleted of some other proteins. We speculate that these length effects could be caused by inhibition of the elongation phase of transcription or by an influence of translation status or polysomal conformation on mRNA decay.
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48
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Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chem Rev 2014; 114:3224-65. [PMID: 24417544 PMCID: PMC3968247 DOI: 10.1021/cr400496q] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Sethuramasundaram Pitchiaya
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Laurie A. Heinicke
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Thomas C. Custer
- Program in Chemical Biology, University of Michigan,
Ann Arbor, MI 48109-1055, USA
| | - Nils G. Walter
- Single Molecule Analysis in Real-Time (SMART)
Center, University of Michigan, Ann Arbor, MI 48109-1055, USA
- Single Molecule Analysis Group, Department of
Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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49
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Wedeles CJ, Wu MZ, Claycomb JM. Protection of germline gene expression by the C. elegans Argonaute CSR-1. Dev Cell 2014; 27:664-71. [PMID: 24360783 DOI: 10.1016/j.devcel.2013.11.016] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/10/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022]
Abstract
In Caenorhabditis elegans, the Piwi-interacting small RNA (piRNA)-mediated germline surveillance system encodes more than 30,000 unique 21-nucleotide piRNAs, which silence a variety of foreign nucleic acids. What mechanisms allow endogenous germline-expressed transcripts to evade silencing by the piRNA pathway? One likely candidate in a protective mechanism is the Argonaute CSR-1, which interacts with 22G-small RNAs that are antisense to nearly all germline-expressed genes. Here, we use an in vivo RNA tethering assay to demonstrate that the recruitment of CSR-1 to a transcript licenses expression of the transcript, protecting it from piRNA-mediated silencing. Licensing occurs mainly at the level of transcription, as we observe changes in pre-mRNA levels consistent with transcriptional activation when CSR-1 is tethered. Furthermore, the recruitment of CSR-1 to a previously silenced locus transcriptionally activates its expression. Together, these results demonstrate a rare positive role for an endogenous Argonaute pathway in heritably licensing and protecting germline transcripts.
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50
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Tacheny A, Dieu M, Arnould T, Renard P. Mass spectrometry-based identification of proteins interacting with nucleic acids. J Proteomics 2013; 94:89-109. [PMID: 24060998 DOI: 10.1016/j.jprot.2013.09.011] [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] [Received: 05/27/2013] [Revised: 08/19/2013] [Accepted: 09/13/2013] [Indexed: 01/02/2023]
Abstract
The identification of the regulatory proteins that control DNA transcription as well as RNA stability and translation represents a key step in the comprehension of gene expression regulation. Those proteins can be purified by DNA- or RNA-affinity chromatography, followed by identification by mass spectrometry. Although very simple in the concept, this represents a real technological challenge due to the low abundance of regulatory proteins compared to the highly abundant proteins binding to nucleic acids in a nonsequence-specific manner. Here we review the different strategies that have been set up to reach this purpose, discussing the key parameters that should be considered to increase the chances of success. Typically, two categories of biological questions can be distinguished: the identification of proteins that specifically interact with a precisely defined binding site, mostly addressed by quantitative mass spectrometry, and the identification in a non-comparative manner of the protein complexes recruited by a poorly characterized long regulatory region of nucleic acids. Finally, beside the numerous studies devoted to in vitro-assembled nucleic acid-protein complexes, the scarce data reported on proteomic analyses of in vivo-assembled complexes are described, with a special emphasis on the associated challenges.
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Affiliation(s)
- A Tacheny
- Laboratory of Biochemistry and Cell Biology (URBC), NAmur Research Institute for LIfe Sciences (NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
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