51
|
Ozata DM, Gainetdinov I, Zoch A, O'Carroll D, Zamore PD. PIWI-interacting RNAs: small RNAs with big functions. Nat Rev Genet 2019; 20:89-108. [PMID: 30446728 DOI: 10.1038/s41576-018-0073-3] [Citation(s) in RCA: 666] [Impact Index Per Article: 133.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) of 21-35 nucleotides in length silence transposable elements, regulate gene expression and fight viral infection. piRNAs guide PIWI proteins to cleave target RNA, promote heterochromatin assembly and methylate DNA. The architecture of the piRNA pathway allows it both to provide adaptive, sequence-based immunity to rapidly evolving viruses and transposons and to regulate conserved host genes. piRNAs silence transposons in the germ line of most animals, whereas somatic piRNA functions have been lost, gained and lost again across evolution. Moreover, most piRNA pathway proteins are deeply conserved, but different animals employ remarkably divergent strategies to produce piRNA precursor transcripts. Here, we discuss how a common piRNA pathway allows animals to recognize diverse targets, ranging from selfish genetic elements to genes essential for gametogenesis.
Collapse
Affiliation(s)
- Deniz M Ozata
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ildar Gainetdinov
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ansgar Zoch
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Dónal O'Carroll
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Wellcome Centre for Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | - Phillip D Zamore
- RNA Therapeutics Institute and Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA, USA.
| |
Collapse
|
52
|
Sheu‐Gruttadauria J, Xiao Y, Gebert LFR, MacRae IJ. Beyond the seed: structural basis for supplementary microRNA targeting by human Argonaute2. EMBO J 2019; 38:e101153. [PMID: 31268608 PMCID: PMC6600645 DOI: 10.15252/embj.2018101153] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/27/2019] [Accepted: 04/08/2019] [Indexed: 11/09/2022] Open
Abstract
microRNAs (miRNAs) guide Argonaute proteins to mRNAs targeted for repression. Target recognition occurs primarily through the miRNA seed region, composed of guide (g) nucleotides g2-g8. However, nucleotides beyond the seed are also important for some known miRNA-target interactions. Here, we report the structure of human Argonaute2 (Ago2) engaged with a target RNA recognized through both miRNA seed and supplementary (g13-g16) regions. Ago2 creates a "supplementary chamber" that accommodates up to five miRNA-target base pairs. Seed and supplementary chambers are adjacent to each other and can be bridged by an unstructured target loop of 1-15 nucleotides. Opening of the supplementary chamber may be constrained by tension in the miRNA 3' tail, as increases in miRNA length stabilize supplementary interactions. Contrary to previous reports, we demonstrate that optimal supplementary interactions can increase target affinity > 20-fold. These results provide a mechanism for extended miRNA targeting, suggest a function for 3' isomiRs in tuning miRNA targeting specificity, and indicate that supplementary interactions may contribute more to target recognition than is widely appreciated.
Collapse
Affiliation(s)
- Jessica Sheu‐Gruttadauria
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCAUSA
- Present address:
Department of Cellular and Molecular PharmacologyHoward Hughes Medical InstituteUniversity of California, San FranciscoSan FranciscoCAUSA
| | - Yao Xiao
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCAUSA
| | - Luca FR Gebert
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCAUSA
| | - Ian J MacRae
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCAUSA
| |
Collapse
|
53
|
Chernikov IV, Vlassov VV, Chernolovskaya EL. Current Development of siRNA Bioconjugates: From Research to the Clinic. Front Pharmacol 2019; 10:444. [PMID: 31105570 PMCID: PMC6498891 DOI: 10.3389/fphar.2019.00444] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/08/2019] [Indexed: 12/12/2022] Open
Abstract
Small interfering RNAs (siRNAs) acting via RNA interference mechanisms are able to recognize a homologous mRNA sequence in the cell and induce its degradation. The main problems in the development of siRNA-based drugs for therapeutic use are the low efficiency of siRNA delivery to target cells and the degradation of siRNAs by nucleases in biological fluids. Various approaches have been proposed to solve the problem of siRNA delivery in vivo (e.g., viruses, cationic lipids, polymers, nanoparticles), but all have limitations for therapeutic use. One of the most promising approaches to solve the problem of siRNA delivery to target cells is bioconjugation; i.e., the covalent connection of siRNAs with biogenic molecules (lipophilic molecules, antibodies, aptamers, ligands, peptides, or polymers). Bioconjugates are "ideal nanoparticles" since they do not need a positive charge to form complexes, are less toxic, and are less effectively recognized by components of the immune system because of their small size. This review is focused on strategies and principles for constructing siRNA bioconjugates for in vivo use.
Collapse
Affiliation(s)
- Ivan V Chernikov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena L Chernolovskaya
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| |
Collapse
|
54
|
Abstract
Small silencing RNAs have provided powerful reverse genetics tools and have opened new areas of research. This introduction describes the use of RNAi to suppress expression of individual genes for loss-of-function analysis. It also summarizes methods for measuring specific and global changes in small RNA expression, as well as methods to inhibit the function of individual endogenous small RNA species such as miRNAs.
Collapse
|
55
|
Abstract
Small RNAs govern almost every biological process in eukaryotes associating with the Argonaute (AGO) proteins to form the RNA-induced silencing complex (mRISC). AGO proteins constitute the core of RISCs with different members having variety of protein-binding partners and biochemical properties. This review focuses on the AGO subfamily of the AGOs that are ubiquitously expressed and are associated with small RNAs. The structure, function and role of the AGO proteins in the cell is discussed in detail.
Collapse
Affiliation(s)
- Saife Niaz
- Department of Biotechnology, University of Kashmir, Srinagar 190006, Jammu and Kashmir, India
| |
Collapse
|
56
|
Duchaine TF, Fabian MR. Mechanistic Insights into MicroRNA-Mediated Gene Silencing. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032771. [PMID: 29959194 DOI: 10.1101/cshperspect.a032771] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) posttranscriptionally regulate gene expression by repressing protein synthesis and exert a broad influence over development, physiology, adaptation, and disease. Over the past two decades, great strides have been made toward elucidating how miRNAs go about shutting down messenger RNA (mRNA) translation and promoting mRNA decay.
Collapse
Affiliation(s)
- Thomas F Duchaine
- Department of Biochemistry & Goodman Cancer Research Centre, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Marc R Fabian
- Department of Oncology, McGill University, Montreal, Quebec H3G 1Y6, Canada.,Lady Davis Institute, Jewish General Hospital, Montreal, Quebec H3T 1E2, Canada
| |
Collapse
|
57
|
Lockhart J, Canfield J, Mong EF, VanWye J, Totary-Jain H. Nucleotide Modification Alters MicroRNA-Dependent Silencing of MicroRNA Switches. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:339-350. [PMID: 30665183 PMCID: PMC6350232 DOI: 10.1016/j.omtn.2018.12.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/12/2018] [Accepted: 12/12/2018] [Indexed: 02/08/2023]
Abstract
mRNA therapeutics hold great promise for the treatment of human diseases. While incorporating naturally occurring modified nucleotides during synthesis has greatly increased their potency and safety, challenges in selective expression have hindered clinical applications. MicroRNA (miRNA)-regulated in vitro-transcribed mRNAs, called miRNA switches, have been used to control the expression of exogenous mRNA in a cell-selective manner. However, the effect of nucleotide modifications on miRNA-dependent silencing has not been examined. Here we show that the incorporation of pseudouridine, N1-methylpseudourdine, or pseudouridine and 5-methylcytidine, which increases translation, tends to decrease the regulation of miRNA switches. Moreover, pseudouridine and 5-methylcytidine modification enables one miRNA target site at the 3′ UTR to be as effective as four target sites. We also demonstrate that the effects of pseudouridine, pseudouridine and 5-methylcytidine, and N1-methylpseudourdine modification are miRNA switch specific and do not correlate with the proportion of modified nucleotides in the miRNA target site. Furthermore, modified miRNA switches containing seed-complementary target sites are poorly regulated by miRNA. We also show that placing the miRNA target site in the 5′ UTR of the miRNA switch abolishes the effect of nucleotide modification on miRNA-dependent silencing. This work provides insights into the influence of nucleotide modifications on miRNA-dependent silencing and informs the design of optimal miRNA switches.
Collapse
Affiliation(s)
- John Lockhart
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - John Canfield
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Ezinne Francess Mong
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Jeffrey VanWye
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Hana Totary-Jain
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| |
Collapse
|
58
|
Lisitskaya L, Aravin AA, Kulbachinskiy A. DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins. Nat Commun 2018; 9:5165. [PMID: 30514832 PMCID: PMC6279821 DOI: 10.1038/s41467-018-07449-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 10/26/2018] [Indexed: 12/14/2022] Open
Abstract
Recognition and repression of RNA targets by Argonaute proteins guided by small RNAs is the essence of RNA interference in eukaryotes. Argonaute proteins with diverse structures are also found in many bacterial and archaeal genomes. Recent studies revealed that, similarly to their eukaryotic counterparts, prokaryotic Argonautes (pAgos) may function in cell defense against foreign genetic elements but, in contrast, preferably act on DNA targets. Many crucial details of the pAgo action, and the roles of a plethora of pAgos with non-conventional architecture remain unknown. Here, we review available structural and biochemical data on pAgos and discuss their possible functions in host defense and other genetic processes in prokaryotic cells. In this review, Aravin and colleagues examine bacterial and archaeal Argonaute proteins, discuss their diverse architectures and their possible roles in host defense, proposing additional functions for Argonaute proteins in prokaryotic cells.
Collapse
Affiliation(s)
- Lidiya Lisitskaya
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia
| | - Alexei A Aravin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| |
Collapse
|
59
|
Calcino AD, Fernandez-Valverde SL, Taft RJ, Degnan BM. Diverse RNA interference strategies in early-branching metazoans. BMC Evol Biol 2018; 18:160. [PMID: 30382896 PMCID: PMC6211395 DOI: 10.1186/s12862-018-1274-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Micro RNAs (miRNAs) and piwi interacting RNAs (piRNAs), along with the more ancient eukaryotic endogenous small interfering RNAs (endo-siRNAs) constitute the principal components of the RNA interference (RNAi) repertoire of most animals. RNAi in non-bilaterians - sponges, ctenophores, placozoans and cnidarians - appears to be more diverse than that of bilaterians, and includes structurally variable miRNAs in sponges, an enormous number of piRNAs in cnidarians and the absence of miRNAs in ctenophores and placozoans. RESULTS Here we identify thousands of endo-siRNAs and piRNAs from the sponge Amphimedon queenslandica, the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis using a computational approach that clusters mapped small RNA sequences and annotates each cluster based on the read length and relative abundance of the constituent reads. This approach was validated on 11 small RNA libraries in Drosophila melanogaster, demonstrating the successful annotation of RNAi-associated loci with properties consistent with previous reports. In the non-bilaterians we uncover seven new miRNAs from Amphimedon and four from Nematostella as well as sub-populations of candidate cis-natural antisense transcript (cis-NAT) endo-siRNAs. We confirmed the absence of miRNAs in Mnemiopsis but detected an abundance of endo-siRNAs in this ctenophore. Analysis of putative piRNA structure suggests that conserved localised secondary structures in primary transcripts may be important for the production of mature piRNAs in Amphimedon and Nematostella, as is also the case for endo-siRNAs. CONCLUSION Together, these findings suggest that the last common ancestor of extant animals did not have the entrained RNAi system that typifies bilaterians. Instead it appears that bilaterians, cnidarians, ctenophores and sponges express unique repertoires and combinations of miRNAs, piRNAs and endo-siRNAs.
Collapse
Affiliation(s)
- Andrew D Calcino
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Integrative Zoology, University of Vienna, Althanstraße 1, 4A-1090, Vienna, Austria
| | - Selene L Fernandez-Valverde
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: CONACYT, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio). CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia.,Illumina Inc, San Diego, California, 92122, USA
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
| |
Collapse
|
60
|
Cai Y, Wan J. Competing Endogenous RNA Regulations in Neurodegenerative Disorders: Current Challenges and Emerging Insights. Front Mol Neurosci 2018; 11:370. [PMID: 30344479 PMCID: PMC6182084 DOI: 10.3389/fnmol.2018.00370] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/18/2018] [Indexed: 12/14/2022] Open
Abstract
The past decade has witnessed exciting breakthroughs that have contributed to the richness and complexity of a burgeoning modern RNA world, and one particular breakthrough-the competing endogenous RNA (ceRNA) hypothesis-has been described as the "Rosetta Stone" for decoding the RNA language used in regulating RNA crosstalk and modulating biological functions. The proposed far-reaching mechanism unites diverse RNA species and provides new insights into previously unrecognized RNA-RNA interactions and RNA regulatory networks that perhaps determine gene expression in an organized, hierarchical manner. The recently uncovered ceRNA regulatory loops and networks have emphasized the power of ceRNA regulation in a wide range of developmental stages and pathological contexts, such as in tumorigenesis and neurodegenerative disorders. Although the ceRNA hypothesis drastically enhanced our understanding of RNA biology, shortly after the hypothesis was proposed, disputes arose in relation mainly to minor discrepancies in the reported effects of ceRNA regulation under physiological conditions, and this resulted in ceRNA regulation becoming an extensively studied and fast-growing research field. Here, we focus on the evidence supporting ceRNA regulation in neurodegenerative disorders and address three critical points related to the ceRNA regulatory mechanism: the microRNA (miRNA) and ceRNA hierarchies in cross-regulations; the balance between destabilization and stable binding in ceRNA-miRNA interactions; and the true extent to which ceRNA regulatory mechanisms are involved in both health and disease, and the experimental shortcomings in current ceRNA studies.
Collapse
Affiliation(s)
- Yifei Cai
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China
| | - Jun Wan
- Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University - The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| |
Collapse
|
61
|
Fuchs Wightman F, Giono LE, Fededa JP, de la Mata M. Target RNAs Strike Back on MicroRNAs. Front Genet 2018; 9:435. [PMID: 30333855 PMCID: PMC6175985 DOI: 10.3389/fgene.2018.00435] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/13/2018] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs are extensively studied regulatory non-coding small RNAs that silence animal genes throughout most biological processes, typically doing so by binding to partially complementary sequences within target RNAs. A plethora of studies has described detailed mechanisms for microRNA biogenesis and function, as well as their temporal and spatial regulation during development. By inducing translational repression and/or degradation of their target RNAs, microRNAs can contribute to achieve highly specific cell- or tissue-specific gene expression, while their aberrant expression can lead to disease. Yet an unresolved aspect of microRNA biology is how such small RNA molecules are themselves cleared from the cell, especially under circumstances where fast microRNA turnover or specific degradation of individual microRNAs is required. In recent years, it was unexpectedly found that binding of specific target RNAs to microRNAs with extensive complementarity can reverse the outcome, triggering degradation of the bound microRNAs. This emerging pathway, named TDMD for Target RNA-Directed MicroRNA Degradation, leads to microRNA 3'-end tailing by the addition of A/U non-templated nucleotides, trimming or shortening from the 3' end, and highly specific microRNA loss, providing a new layer of microRNA regulation. Originally described in flies and known to be triggered by viral RNAs, novel endogenous instances of TDMD have been uncovered and are now starting to be understood. Here, we review our current knowledge of this pathway and its potential role in the control and diversification of microRNA expression patterns.
Collapse
Affiliation(s)
- Federico Fuchs Wightman
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Luciana E Giono
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| | - Juan Pablo Fededa
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Manuel de la Mata
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Buenos Aires, Argentina
| |
Collapse
|
62
|
Luo F, Xie Y, Wang Z, Huang J, Tan Q, Sun X, Li F, Li C, Liu M, Zhang D, Xu M, Su N, Ni Z, Jiang W, Chang J, Chen H, Chen S, Xu X, Deng C, Wang Z, Du X, Chen L. Adeno-Associated Virus-Mediated RNAi against Mutant Alleles Attenuates Abnormal Calvarial Phenotypes in an Apert Syndrome Mouse Model. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 13:291-302. [PMID: 30321816 PMCID: PMC6197781 DOI: 10.1016/j.omtn.2018.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/19/2018] [Accepted: 09/19/2018] [Indexed: 12/01/2022]
Abstract
Apert syndrome (AS), the most severe form of craniosynostosis, is caused by missense mutations including Pro253Arg(P253R) of fibroblast growth factor receptor 2 (FGFR2), which leads to enhanced FGF/FGFR2-signaling activity. Surgical correction of the deformed skull is the typical treatment for AS. Because of constant maldevelopment of sutures, the corrective surgery is often executed several times, resulting in increased patient challenge and complications. Biological therapies targeting the signaling of mutant FGFR2 allele, in combination with surgery, may bring better outcome. Here we screened and found a small interfering RNA (siRNA) specifically targeting the Fgfr2-P253R allele, and we revealed that it inhibited osteoblastic differentiation and matrix mineralization by reducing the signaling of ERK1/2 and P38 in cultured primary calvarial cells and calvarial explants from Apert mice (Fgfr2+/P253R). Furthermore, AAV9 carrying short hairpin RNA (shRNA) (AAV9-Fgfr2-shRNA) against mutant Fgfr2 was delivered to the skulls of AS mice. Results demonstrate that AAV9-Fgfr2-shRNA attenuated the premature closure of coronal suture and the decreased calvarial bone volume of AS mice. Our study provides a novel practical biological approach, which will, in combination with other therapies, including surgeries, help treat patients with AS while providing experimental clues for the biological therapies of other genetic skeletal diseases.
Collapse
Affiliation(s)
- Fengtao Luo
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Yangli Xie
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Zuqiang Wang
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Junlan Huang
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Qiaoyan Tan
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Xianding Sun
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Fangfang Li
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Can Li
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Mi Liu
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Dali Zhang
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Meng Xu
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Nan Su
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Zhenhong Ni
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Wanling Jiang
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Jinhong Chang
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Hangang Chen
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Shuai Chen
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China
| | - Xiaoling Xu
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chuxia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Zhugang Wang
- State Key Laboratory of Medical Genomics, Research Center for Experimental Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaolan Du
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China.
| | - Lin Chen
- Laboratory for the Rehabilitation of Traumatic Injuries, Center of Bone Metabolism and Repair, State Key Laboratory of Trauma, Burns and Combined Injury, Trauma Center, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing 400042, China.
| |
Collapse
|
63
|
Lin CJ, Hu F, Dubruille R, Vedanayagam J, Wen J, Smibert P, Loppin B, Lai EC. The hpRNA/RNAi Pathway Is Essential to Resolve Intragenomic Conflict in the Drosophila Male Germline. Dev Cell 2018; 46:316-326.e5. [PMID: 30086302 DOI: 10.1016/j.devcel.2018.07.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/13/2018] [Accepted: 07/02/2018] [Indexed: 11/27/2022]
Abstract
Intragenomic conflicts are fueled by rapidly evolving selfish genetic elements, which induce selective pressures to innovate opposing repressive mechanisms. This is patently manifest in sex-ratio (SR) meiotic drive systems, in which distorter and suppressor factors bias and restore equal transmission of X and Y sperm. Here, we reveal that multiple SR suppressors in Drosophila simulans (Nmy and Tmy) encode related hairpin RNAs (hpRNAs), which generate endo-siRNAs that repress the paralogous distorters Dox and MDox. All components in this drive network are recently evolved and largely testis restricted. To connect SR hpRNA function to the RNAi pathway, we generated D. simulans null mutants of Dcr-2 and AGO2. Strikingly, these core RNAi knockouts massively derepress Dox and MDox and are in fact completely male sterile and exhibit highly defective spermatogenesis. Altogether, our data reveal how the adaptive capacity of hpRNAs is critically deployed to restrict selfish gonadal genetic systems that can exterminate a species.
Collapse
Affiliation(s)
- Ching-Jung Lin
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA; Weill Graduate School of Medical Sciences, Weill Cornell Medical College, New York, NY 10065, USA
| | - Fuqu Hu
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Raphaelle Dubruille
- Laboratoire de Biométrie et Biologie Evolutive - UMR5558, Université Claude Bernard Lyon I, 16, rue R. Dubois - Bât. G. Mendel, 69622 Villeurbanne Cedex, France
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Jiayu Wen
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Peter Smibert
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Benjamin Loppin
- Laboratoire de Biométrie et Biologie Evolutive - UMR5558, Université Claude Bernard Lyon I, 16, rue R. Dubois - Bât. G. Mendel, 69622 Villeurbanne Cedex, France
| | - Eric C Lai
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA.
| |
Collapse
|
64
|
Modepalli V, Fridrich A, Agron M, Moran Y. The methyltransferase HEN1 is required in Nematostella vectensis for microRNA and piRNA stability as well as larval metamorphosis. PLoS Genet 2018; 14:e1007590. [PMID: 30118479 PMCID: PMC6114907 DOI: 10.1371/journal.pgen.1007590] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 08/29/2018] [Accepted: 07/25/2018] [Indexed: 11/18/2022] Open
Abstract
Small non-coding RNAs (sRNAs) such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs) regulate the levels of endogenous, viral and transposable element RNA in plants (excluding piRNAs) and animals. These pathways are explored mainly in bilaterian animals, such as vertebrates, arthropods and nematodes, where siRNAs and piRNAs, but not miRNAs bind their targets with a perfect match and mediate the cleavage of the target RNA. Methylation of the 3′ ends of piRNAs and siRNAs by the methyltransferase HEN1 protects these sRNAs from degradation. There is a noticeable selection in bilaterian animals against miRNA-mRNA perfect matching, as it leads to the degradation of miRNAs. Cnidarians (sea anemones, corals, hydroids and jellyfish), are separated from bilaterians by more than 600 million years. As opposed to bilaterians, cnidarian miRNAs frequently bind their targets with a nearly perfect match. Knowing that an ortholog of HEN1 is widely expressed in the sea anemone Nematostella vectensis, we tested in this work whether it mediates the stabilization of its sRNAs. We show that the knockdown of HEN1 in Nematostella results in a developmental arrest. Small RNA sequencing revealed that the levels of both miRNAs and piRNAs drop dramatically in the morphant animals. Moreover, knockdown experiments of Nematostella Dicer1 and PIWI2, homologs of major bilaterian biogenesis components of miRNAs and piRNAs, respectively, resulted in developmental arrest similar to HEN1 morphants. Our findings suggest that HEN1 mediated methylation of sRNAs reflects the ancestral state, where miRNAs were also methylated. Thus, we provide the first evidence of a methylation mechanism that stabilizes miRNAs in animals, and highlight the importance of post-transcriptional regulation in non-bilaterian animals. Plants and animals use small RNAs to regulate gene expression, virus silencing and genomic integrity. These functions depend on specific binding of small RNAs to longer RNA targets. The methyltransferase HEN1 plays a crucial role in stabilizing small RNAs upon their binding to perfectly-matching targets. Lack of methylation in case of a perfect match will lead to small RNA degradation. In general, methylation of microRNAs, a class of small RNAs, is part of their biogenesis in plants, but not in bilaterian animals such as vertebrates, worms and insects, where perfectly-matching microRNA targets are rare. In contrast, in Cnidaria (sea anemones, corals and jellyfish), the sister group to Bilateria, microRNAs frequently bind their targets with a nearly perfect match. In this study, we show that in the cnidarian Nematostella vectensis methylation of microRNAs and other small RNAs is consistent and frequent throughout development and that knockdown of the cnidarian HEN1 results in a developmental arrest. Small RNA sequencing of the treated animals, reveals that small RNAs are depleted and shortened. Therefore, our findings suggest that HEN1-mediated methylation of small RNAs was present in the last common ancestor of Cnidaria and Bilateria 600 million years ago and was responsible for microRNA stabilization.
Collapse
Affiliation(s)
- Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail: (VM); (YM)
| | - Arie Fridrich
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maayan Agron
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail: (VM); (YM)
| |
Collapse
|
65
|
Kano T, Katsuragi Y, Maeda Y, Ueno Y. Synthesis and properties of 4′-C-aminoalkyl-2′-fluoro-modified RNA oligomers. Bioorg Med Chem 2018; 26:4574-4582. [DOI: 10.1016/j.bmc.2018.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 01/16/2023]
|
66
|
Tambe A, East-Seletsky A, Knott GJ, Doudna JA, O'Connell MR. RNA Binding and HEPN-Nuclease Activation Are Decoupled in CRISPR-Cas13a. Cell Rep 2018; 24:1025-1036. [PMID: 30044970 PMCID: PMC6085867 DOI: 10.1016/j.celrep.2018.06.105] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/24/2018] [Accepted: 06/27/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas13a enzymes are RNA-guided, RNA-activated RNases. Their properties have been exploited as powerful tools for RNA detection, RNA imaging, and RNA regulation. However, the relationship between target RNA binding and HEPN (higher eukaryotes and prokaryotes nucleotide binding) domain nuclease activation is poorly understood. Using sequencing experiments coupled with in vitro biochemistry, we find that Cas13a target RNA binding affinity and HEPN-nuclease activity are differentially affected by the number and the position of mismatches between the guide and the target. We identify a central binding seed for which perfect base pairing is required for target binding and a separate nuclease switch for which imperfect base pairing results in tight binding, but not HEPN-nuclease activation. These results demonstrate that the binding and cleavage activities of Cas13a are decoupled, highlighting a complex specificity landscape. Our findings underscore a need to consider the range of effects off-target recognition has on Cas13a RNA binding and cleavage behavior for RNA-targeting tool development.
Collapse
Affiliation(s)
- Akshay Tambe
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alexandra East-Seletsky
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gavin J Knott
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Mitchell R O'Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
| |
Collapse
|
67
|
Del Giudice M, Bo S, Grigolon S, Bosia C. On the role of extrinsic noise in microRNA-mediated bimodal gene expression. PLoS Comput Biol 2018; 14:e1006063. [PMID: 29664903 PMCID: PMC5922620 DOI: 10.1371/journal.pcbi.1006063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 04/27/2018] [Accepted: 02/28/2018] [Indexed: 01/01/2023] Open
Abstract
Several studies highlighted the relevance of extrinsic noise in shaping cell decision making and differentiation in molecular networks. Bimodal distributions of gene expression levels provide experimental evidence of phenotypic differentiation, where the modes of the distribution often correspond to different physiological states of the system. We theoretically address the presence of bimodal phenotypes in the context of microRNA (miRNA)-mediated regulation. MiRNAs are small noncoding RNA molecules that downregulate the expression of their target mRNAs. The nature of this interaction is titrative and induces a threshold effect: below a given target transcription rate almost no mRNAs are free and available for translation. We investigate the effect of extrinsic noise on the system by introducing a fluctuating miRNA-transcription rate. We find that the presence of extrinsic noise favours the presence of bimodal target distributions which can be observed for a wider range of parameters compared to the case with intrinsic noise only and for lower miRNA-target interaction strength. Our results suggest that combining threshold-inducing interactions with extrinsic noise provides a simple and robust mechanism for obtaining bimodal populations without requiring fine tuning. Furthermore, we characterise the protein distribution's dependence on protein half-life.
Collapse
Affiliation(s)
- Marco Del Giudice
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy
- Italian Institute for Genomic Medicine, Torino, Italy
| | - Stefano Bo
- Nordita, Royal Institute of Technology and Stockholm University, Stockholm, Sweden
| | | | - Carla Bosia
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy
- Italian Institute for Genomic Medicine, Torino, Italy
| |
Collapse
|
68
|
Klum SM, Chandradoss SD, Schirle NT, Joo C, MacRae IJ. Helix-7 in Argonaute2 shapes the microRNA seed region for rapid target recognition. EMBO J 2018; 37:75-88. [PMID: 28939659 PMCID: PMC5753032 DOI: 10.15252/embj.201796474] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 08/08/2017] [Accepted: 08/10/2017] [Indexed: 01/29/2023] Open
Abstract
Argonaute proteins use microRNAs (miRNAs) to identify mRNAs targeted for post-transcriptional repression. Biochemical assays have demonstrated that Argonaute functions by modulating the binding properties of its miRNA guide so that pairing to the seed region is exquisitely fast and accurate. However, the mechanisms used by Argonaute to reshape the binding properties of its small RNA guide remain poorly understood. Here, we identify a structural element, α-helix-7, in human Argonaute2 (Ago2) that is required for speed and fidelity in binding target RNAs. Biochemical, structural, and single-molecule data indicate that helix-7 acts as a molecular wedge that pivots to enforce rapid making and breaking of miRNA:target base pairs in the 3' half of the seed region. These activities allow Ago2 to rapidly dismiss off-targets and dynamically search for seed-matched sites at a rate approaching the limit of diffusion.
Collapse
Affiliation(s)
- Shannon M Klum
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stanley D Chandradoss
- Department of BioNanoScience, Kavli Institute of NanoScience, Delft University of Technology, Delft, The Netherlands
| | - Nicole T Schirle
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of NanoScience, Delft University of Technology, Delft, The Netherlands
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| |
Collapse
|
69
|
RNA stem structure governs coupling of dicing and gene silencing in RNA interference. Proc Natl Acad Sci U S A 2017; 114:E10349-E10358. [PMID: 29133395 PMCID: PMC5715756 DOI: 10.1073/pnas.1710298114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNAi is an RNA-induced gene-silencing pathway that is shared among various organisms. Better understanding of RNAi is urgently needed to improve our knowledge of RNA-mediated gene regulation and to advance the field of functional genomics and its application to gene therapy. We counted with high precision the number of transcripts in each cell’s nucleus and cytoplasm as a function of silencing time to investigate the role of small RNA secondary structures such as loop length and stem mismatches. We screened various structural features of small RNAs and discovered a distinct role of each structural element that contributes to gene-silencing kinetics. We provide a helpful guideline for designing small RNAs for more efficient gene silencing. PremicroRNAs (premiRNAs) possess secondary structures consisting of a loop and a stem with multiple mismatches. Despite the well-characterized RNAi pathway, how the structural features of premiRNA contribute to dicing and subsequent gene-silencing efficiency remains unclear. Using single-molecule FISH, we demonstrate that cytoplasmic mRNA, but not nuclear mRNA, is reduced during RNAi. The dicing rate and silencing efficiency both increase in a correlated manner as a function of the loop length. In contrast, mismatches in the stem drastically diminish the silencing efficiency without impacting the dicing rate. We show that this decoupling effect is not due to the loading to the RNA-induced silencing complex, RNA uptake, or cellular dicing. We postulate that the stem mismatches perturb the handover of the cleaved miRNAs from Dicer to Argonaute, leading to poor strand selection. Our results imply that the stem structures prevalent in cellular miRNAs have suboptimal silencing efficiency.
Collapse
|
70
|
Burke JM, Kincaid RP, Aloisio F, Welch N, Sullivan CS. Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes. Nucleic Acids Res 2017; 45:e154. [PMID: 28973449 PMCID: PMC5622367 DOI: 10.1093/nar/gkx653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/19/2017] [Indexed: 12/03/2022] Open
Abstract
Short hairpin RNAs (shRNAs) are effective in generating stable repression of gene expression. RNA polymerase III (RNAP III) type III promoters (U6 or H1) are typically used to drive shRNA expression. While useful for some knockdown applications, the robust expression of U6/H1-driven shRNAs can induce toxicity and generate heterogeneous small RNAs with undesirable off-target effects. Additionally, typical U6/H1 promoters encompass the majority of the ∼270 base pairs (bp) of vector space required for shRNA expression. This can limit the efficacy and/or number of delivery vector options, particularly when delivery of multiple gene/shRNA combinations is required. Here, we develop a compact shRNA (cshRNA) expression system based on retroviral microRNA (miRNA) gene architecture that uses RNAP III type II promoters. We demonstrate that cshRNAs coded from as little as 100 bps of total coding space can precisely generate small interfering RNAs (siRNAs) that are active in the RNA-induced silencing complex (RISC). We provide an algorithm with a user-friendly interface to design cshRNAs for desired target genes. This cshRNA expression system reduces the coding space required for shRNA expression by >2-fold as compared to the typical U6/H1 promoters, which may facilitate therapeutic RNAi applications where delivery vector space is limiting.
Collapse
Affiliation(s)
- James M Burke
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Rodney P Kincaid
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Francesca Aloisio
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Nicole Welch
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| | - Christopher S Sullivan
- The University of Texas at Austin, Institute for Cellular and Molecular Biology, Center for Synthetic and Systems Biology, Center for Infectious Disease and Department Molecular Biosciences, 1 University Station A5000, Austin, TX 78712-0162, USA
| |
Collapse
|
71
|
Global analysis of AGO2-bound RNAs reveals that miRNAs induce cleavage of target RNAs with limited complementarity. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1148-1158. [PMID: 29031931 DOI: 10.1016/j.bbagrm.2017.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/11/2017] [Accepted: 10/04/2017] [Indexed: 01/26/2023]
Abstract
Among the four Argonaute family members in mammals, only AGO2 protein retains endonuclease activity and facilitates cleavage of target RNAs base-pairing with highly complementary guide RNAs. Despite the deeply conserved catalytic activity, only a small number of targets have been reported to extensively base pair with cognate miRNAs to be cleaved by AGO2. Here, we analyzed AGO2-bound RNAs by CrossLinking ImmunoPrecipitation (CLIP) of genetically modified cells that express epitope-tagged AGO2 from the native genomic locus. We found that HMGA2 mRNA is cleaved by AGO2 loaded with let-7 and miR-21. In contrast to the generally accepted notion, the base-pairing from the seed region to the cleavage site, rather than perfect or near perfect complementarity, was required for cleavage of the target mRNA in cells. Non-templated addition of nucleotides at the 3' end of the cleaved RNA was observed, further supporting the AGO2-mediated cleavage. Based on the observation that the limited complementarity is the minimum requirement for cleavage, we found that AGO2-mediated cleavage of targets is more common than previously thought. Our result may explain the vital role of endonuclease activity in controlling miRNA-mediated gene regulation.
Collapse
|
72
|
Fiorentino J, De Martino A. Independent channels for miRNA biosynthesis ensure efficient static and dynamic control in the regulation of the early stages of myogenesis. J Theor Biol 2017; 430:53-63. [PMID: 28689889 DOI: 10.1016/j.jtbi.2017.06.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/30/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022]
Abstract
Motivated by recent experimental work, we define and study a deterministic model of the complex miRNA-based regulatory circuit that putatively controls the early stage of myogenesis in human. We aim in particular at a quantitative understanding of (i) the roles played by the separate and independent miRNA biosynthesis channels (one involving a miRNA-decoy system regulated by an exogenous controller, the other given by transcription from a distinct genomic locus) that appear to be crucial for the differentiation program, and of (ii) how competition to bind miRNAs can efficiently control molecular levels in such an interconnected architecture. We show that optimal static control via the miRNA-decoy system constrains kinetic parameters in narrow ranges where the channels are tightly cross-linked. On the other hand, the alternative locus for miRNA transcription can ensure that the fast concentration shifts required by the differentiation program are achieved, specifically via non-linear response of the target to even modest surges in the miRNA transcription rate. While static, competition-mediated regulation can be achieved by the miRNA-decoy system alone, both channels are essential for the circuit's overall functionality, suggesting that that this type of joint control may represent a minimal optimal architecture in different contexts.
Collapse
Affiliation(s)
| | - Andrea De Martino
- Soft & Living Matter Lab, CNR-NANOTEC, Rome, Italy; Italian Institute for Genomic Medicine, Turin, Italy.
| |
Collapse
|
73
|
Developing integrated PBPK/PD coupled mechanistic pathway model (miRNA-BDNF): An approach towards system toxicology. Toxicol Lett 2017; 280:79-91. [DOI: 10.1016/j.toxlet.2017.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/30/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022]
|
74
|
Luby BM, Zheng G. Specific and Direct Amplified Detection of MicroRNA with MicroRNA:Argonaute-2 Cleavage (miRACle) Beacons. Angew Chem Int Ed Engl 2017; 56:13704-13708. [DOI: 10.1002/anie.201707366] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Benjamin M. Luby
- Princess Margaret Cancer Centre and Techna Institute; University Health Network; 101 College St. Toronto ON Canada
- Institute of Biomaterials and Biomedical Engineering; University of Toronto; Toronto Ontario Canada
| | - Gang Zheng
- Princess Margaret Cancer Centre and Techna Institute; University Health Network; 101 College St. Toronto ON Canada
- Institute of Biomaterials and Biomedical Engineering; University of Toronto; Toronto Ontario Canada
- Department of Medical Biophysics; University of Toronto; Toronto Ontario Canada
| |
Collapse
|
75
|
Luby BM, Zheng G. Specific and Direct Amplified Detection of MicroRNA with MicroRNA:Argonaute-2 Cleavage (miRACle) Beacons. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707366] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Benjamin M. Luby
- Princess Margaret Cancer Centre and Techna Institute; University Health Network; 101 College St. Toronto ON Canada
- Institute of Biomaterials and Biomedical Engineering; University of Toronto; Toronto Ontario Canada
| | - Gang Zheng
- Princess Margaret Cancer Centre and Techna Institute; University Health Network; 101 College St. Toronto ON Canada
- Institute of Biomaterials and Biomedical Engineering; University of Toronto; Toronto Ontario Canada
- Department of Medical Biophysics; University of Toronto; Toronto Ontario Canada
| |
Collapse
|
76
|
ASPsiRNA: A Resource of ASP-siRNAs Having Therapeutic Potential for Human Genetic Disorders and Algorithm for Prediction of Their Inhibitory Efficacy. G3-GENES GENOMES GENETICS 2017; 7:2931-2943. [PMID: 28696921 PMCID: PMC5592921 DOI: 10.1534/g3.117.044024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Allele-specific siRNAs (ASP-siRNAs) have emerged as promising therapeutic molecules owing to their selectivity to inhibit the mutant allele or associated single-nucleotide polymorphisms (SNPs) sparing the expression of the wild-type counterpart. Thus, a dedicated bioinformatics platform encompassing updated ASP-siRNAs and an algorithm for the prediction of their inhibitory efficacy will be helpful in tackling currently intractable genetic disorders. In the present study, we have developed the ASPsiRNA resource (http://crdd.osdd.net/servers/aspsirna/) covering three components viz (i) ASPsiDb, (ii) ASPsiPred, and (iii) analysis tools like ASP-siOffTar. ASPsiDb is a manually curated database harboring 4543 (including 422 chemically modified) ASP-siRNAs targeting 78 unique genes involved in 51 different diseases. It furnishes comprehensive information from experimental studies on ASP-siRNAs along with multidimensional genetic and clinical information for numerous mutations. ASPsiPred is a two-layered algorithm to predict efficacy of ASP-siRNAs for fully complementary mutant (Effmut) and wild-type allele (Effwild) with one mismatch by ASPsiPredSVM and ASPsiPredmatrix, respectively. In ASPsiPredSVM, 922 unique ASP-siRNAs with experimentally validated quantitative Effmut were used. During 10-fold cross-validation (10nCV) employing various sequence features on the training/testing dataset (T737), the best predictive model achieved a maximum Pearson’s correlation coefficient (PCC) of 0.71. Further, the accuracy of the classifier to predict Effmut against novel genes was assessed by leave one target out cross-validation approach (LOTOCV). ASPsiPredmatrix was constructed from rule-based studies describing the effect of single siRNA:mRNA mismatches on the efficacy at 19 different locations of siRNA. Thus, ASPsiRNA encompasses the first database, prediction algorithm, and off-target analysis tool that is expected to accelerate research in the field of RNAi-based therapeutics for human genetic diseases.
Collapse
|
77
|
Hilz S, Modzelewski AJ, Cohen PE, Grimson A. The roles of microRNAs and siRNAs in mammalian spermatogenesis. Development 2017; 143:3061-73. [PMID: 27578177 PMCID: PMC5047671 DOI: 10.1242/dev.136721] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
MicroRNAs and siRNAs, both of which are AGO-bound small RNAs, are essential for mammalian spermatogenesis. Although their precise germline roles remain largely uncharacterized, recent discoveries suggest that they function in mechanisms beyond microRNA-mediated post-transcriptional control, playing roles in DNA repair and transcriptional regulation within the nucleus. Here, we discuss the latest findings regarding roles for AGO proteins and their associated small RNAs in the male germline. We integrate genetic, clinical and genomics data, and draw upon findings from non-mammalian models, to examine potential roles for AGO-bound small RNAs during spermatogenesis. Finally, we evaluate the emerging and differing roles for AGOs and AGO-bound small RNAs in the male and female germlines, suggesting potential reasons for these sexual dimorphisms. Summary: This Review article summarizes the latest findings regarding roles for AGO proteins and their associated small RNAs in the male germline, with a particular focus on spermatogenesis.
Collapse
Affiliation(s)
- Stephanie Hilz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Andrew J Modzelewski
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
78
|
Darrington M, Dalmay T, Morrison NI, Chapman T. Implementing the sterile insect technique with RNA interference - a review. ENTOMOLOGIA EXPERIMENTALIS ET APPLICATA 2017; 164:155-175. [PMID: 29200471 PMCID: PMC5697603 DOI: 10.1111/eea.12575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/06/2017] [Indexed: 05/22/2023]
Abstract
We review RNA interference (RNAi) of insect pests and its potential for implementing sterile insect technique (SIT)-related control. The molecular mechanisms that support RNAi in pest species are reviewed in detail, drawing on literature from a range of species including Drosophila melanogaster Meigen and Homo sapiens L. The underlying genes that enable RNAi are generally conserved across taxa, although variance exists in both their form and function. RNAi represents a plausible, non-GM system for targeting populations of insects for control purposes, if RNAi effector molecules can be delivered environmentally (eRNAi). We consider studies of eRNAi from across several insect orders and review to what extent taxonomy, genetics, and differing methods of double-stranded (ds) RNA synthesis and delivery can influence the efficiency of gene knockdown. Several factors, including the secondary structure of the target mRNA and the specific nucleotide sequence of dsRNA effector molecules, can affect the potency of eRNAi. However, taxonomic relationships between insects cannot be used to reliably forecast the efficiency of an eRNAi response. The mechanisms by which insects acquire dsRNA from their environment require further research, but the evidence to date suggests that endocytosis and transport channels both play key roles. Delivery of RNA molecules packaged in intermediary carriers such as bacteria or nanoparticles may facilitate their entry into and through the gut, and enable the evasion of host defence systems, such as toxic pH, that would otherwise attenuate the potential for RNAi.
Collapse
Affiliation(s)
- Michael Darrington
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNorfolkNR4 7TJUK
| | - Tamas Dalmay
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNorfolkNR4 7TJUK
| | | | - Tracey Chapman
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNorfolkNR4 7TJUK
| |
Collapse
|
79
|
Structural Foundations of RNA Silencing by Argonaute. J Mol Biol 2017; 429:2619-2639. [PMID: 28757069 DOI: 10.1016/j.jmb.2017.07.018] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/19/2022]
Abstract
Nearly every cell in the human body contains a set of programmable gene-silencing proteins named Argonaute. Argonaute proteins mediate gene regulation by small RNAs and thereby contribute to cellular homeostasis during diverse physiological process, such as stem cell maintenance, fertilization, and heart development. Over the last decade, remarkable progress has been made toward understanding Argonaute proteins, small RNAs, and their roles in eukaryotic biology. Here, we review current understanding of Argonaute proteins from a structural prospective and discuss unanswered questions surrounding this fascinating class of enzymes.
Collapse
|
80
|
Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| |
Collapse
|
81
|
Trubetskoy VS, Griffin JB, Nicholas AL, Nord EM, Xu Z, Peterson RM, Wooddell CI, Rozema DB, Wakefield DH, Lewis DL, Kanner SB. Phosphorylation-specific status of RNAi triggers in pharmacokinetic and biodistribution analyses. Nucleic Acids Res 2017; 45:1469-1478. [PMID: 28180327 PMCID: PMC5388421 DOI: 10.1093/nar/gkw828] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 01/23/2023] Open
Abstract
The RNA interference (RNAi)-based therapeutic ARC-520 for chronic hepatitis B virus (HBV) infection consists of a melittin-derived peptide conjugated to N-acetylgalactosamine for hepatocyte targeting and endosomal escape, and cholesterol-conjugated RNAi triggers, which together result in HBV gene silencing. To characterize the kinetics of RNAi trigger delivery and 5΄-phosphorylation of guide strands correlating with gene knockdown, we employed a peptide-nucleic acid (PNA) hybridization assay. A fluorescent sense strand PNA probe binding to RNAi duplex guide strands was coupled with anion exchange high performance liquid chromatography to quantitate guide strands and metabolites. Compared to PCR- or ELISA-based methods, this assay enables separate quantitation of non-phosphorylated full-length guide strands from 5΄-phosphorylated forms that may associate with RNA-induced silencing complexes (RISC). Biodistribution studies in mice indicated that ARC-520 guide strands predominantly accumulated in liver. 5΄-phosphorylation of guide strands was observed within 5 min after ARC-520 injection, and was detected for at least 4 weeks corresponding to the duration of HBV mRNA silencing. Guide strands detected in RISC by AGO2 immuno-isolation represented 16% of total 5΄-phosphorylated guide strands in liver, correlating with a 2.7 log10 reduction of HBsAg. The PNA method enables pharmacokinetic analysis of RNAi triggers, elucidates potential metabolic processing events and defines pharmacokinetic-pharmacodynamic relationships.
Collapse
MESH Headings
- Animals
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Female
- Gene Knockdown Techniques
- Hepatitis B Surface Antigens/blood
- Hepatitis B Surface Antigens/genetics
- Hepatitis B virus/genetics
- Hepatitis B virus/metabolism
- Hepatitis B, Chronic/metabolism
- Hepatitis B, Chronic/therapy
- Hepatitis B, Chronic/virology
- Humans
- Kinetics
- Liver/metabolism
- Liver/virology
- Mice
- Mice, Inbred ICR
- Mice, Inbred NOD
- Mice, SCID
- Mice, Transgenic
- Peptide Nucleic Acids/genetics
- Peptide Nucleic Acids/metabolism
- Phosphorylation
- RNA Interference
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Induced Silencing Complex/genetics
- RNA-Induced Silencing Complex/metabolism
- Tissue Distribution
Collapse
Affiliation(s)
| | - Jacob B. Griffin
- Department of Biology, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Anthony L. Nicholas
- Department of Chemistry, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Eric M. Nord
- Department of Chemistry, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Zhao Xu
- Department of Biology, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Ryan M. Peterson
- Department of Biology, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | | | - David B. Rozema
- Department of Chemistry, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | - Darren H. Wakefield
- Department of Chemistry, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| | | | - Steven B. Kanner
- Department of Biology, Arrowhead Pharmaceuticals, Inc., Madison, WI 53711, USA
| |
Collapse
|
82
|
Abstract
RNA is involved in the regulation of multiple cellular processes, often by forming sequence-specific base pairs with cellular RNA or DNA targets that must be identified among the large number of nucleic acids in a cell. Several RNA-based regulatory systems in eukaryotes, bacteria and archaea, including microRNAs (miRNAs), small interfering RNAs (siRNAs), CRISPR RNAs (crRNAs) and small RNAs (sRNAs) that are dependent on the RNA chaperone protein Hfq, achieve specificity using similar strategies. Central to their function is the presentation of short 'seed sequences' within a ribonucleoprotein complex to facilitate the search for and recognition of targets.
Collapse
|
83
|
Bisaria N, Jarmoskaite I, Herschlag D. Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing. Cell Syst 2017; 4:21-29. [PMID: 28125791 PMCID: PMC5308874 DOI: 10.1016/j.cels.2016.12.010] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/15/2016] [Accepted: 12/09/2016] [Indexed: 12/26/2022]
Abstract
RNA-guided nucleases (RGNs) provide sequence-specific gene regulation through base-pairing interactions between a small RNA guide and target RNA or DNA. RGN systems, which include CRISPR-Cas9 and RNA interference (RNAi), hold tremendous promise as programmable tools for engineering and therapeutic purposes. However, pervasive targeting of sequences that closely resemble the intended target has remained a major challenge, limiting the reliability and interpretation of RGN activity and the range of possible applications. Efforts to reduce off-target activity and enhance RGN specificity have led to a collection of empirically derived rules, which often paradoxically include decreased binding affinity of the RNA-guided nuclease to its target. We consider the kinetics of these reactions and show that basic kinetic properties can explain the specificities observed in the literature and the changes in these specificities in engineered systems. The kinetic models described provide a foundation for understanding RGN targeting and a necessary conceptual framework for their rational engineering.
Collapse
Affiliation(s)
- Namita Bisaria
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Inga Jarmoskaite
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
84
|
Del Vecchio D, Abdallah H, Qian Y, Collins JJ. A Blueprint for a Synthetic Genetic Feedback Controller to Reprogram Cell Fate. Cell Syst 2017; 4:109-120.e11. [PMID: 28065574 DOI: 10.1016/j.cels.2016.12.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/18/2016] [Accepted: 12/01/2016] [Indexed: 01/07/2023]
Abstract
To artificially reprogram cell fate, experimentalists manipulate the gene regulatory networks (GRNs) that maintain a cell's phenotype. In practice, reprogramming is often performed by constant overexpression of specific transcription factors (TFs). This process can be unreliable and inefficient. Here, we address this problem by introducing a new approach to reprogramming based on mathematical analysis. We demonstrate that reprogramming GRNs using constant overexpression may not succeed in general. Instead, we propose an alternative reprogramming strategy: a synthetic genetic feedback controller that dynamically steers the concentration of a GRN's key TFs to any desired value. The controller works by adjusting TF expression based on the discrepancy between desired and actual TF concentrations. Theory predicts that this reprogramming strategy is guaranteed to succeed, and its performance is independent of the GRN's structure and parameters, provided that feedback gain is sufficiently high. As a case study, we apply the controller to a model of induced pluripotency in stem cells.
Collapse
Affiliation(s)
- Domitilla Del Vecchio
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA; Synthetic Biology Center, MIT, Cambridge, MA 02139, USA.
| | - Hussein Abdallah
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Yili Qian
- Department of Mechanical Engineering, MIT, Cambridge, MA 02139, USA
| | - James J Collins
- Synthetic Biology Center, MIT, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| |
Collapse
|
85
|
Willkomm S, Zander A, Grohmann D, Restle T. Mechanistic Insights into Archaeal and Human Argonaute Substrate Binding and Cleavage Properties. PLoS One 2016; 11:e0164695. [PMID: 27741323 PMCID: PMC5065165 DOI: 10.1371/journal.pone.0164695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/29/2016] [Indexed: 12/17/2022] Open
Abstract
Argonaute (Ago) proteins from all three domains of life are key players in processes that specifically regulate cellular nucleic acid levels. Some of these Ago proteins, among them human Argonaute2 (hAgo2) and Ago from the archaeal organism Methanocaldococcus jannaschii (MjAgo), are able to cleave nucleic acid target strands that are recognised via an Ago-associated complementary guide strand. Here we present an in-depth kinetic side-by-side analysis of hAgo2 and MjAgo guide and target substrate binding as well as target strand cleavage, which enabled us to disclose similarities and differences in the mechanistic pathways as a function of the chemical nature of the substrate. Testing all possible guide-target combinations (i.e. RNA/RNA, RNA/DNA, DNA/RNA and DNA/DNA) with both Ago variants we demonstrate that the molecular mechanism of substrate association is highly conserved among archaeal-eukaryotic Argonautes. Furthermore, we show that hAgo2 binds RNA and DNA guide strands in the same fashion. On the other hand, despite striking homology between the two Ago variants, MjAgo cannot orientate guide RNA substrates in a way that allows interaction with the target DNA in a cleavage-compatible orientation.
Collapse
Affiliation(s)
- Sarah Willkomm
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Lübeck, 23538, Germany
| | - Adrian Zander
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology- Archaea Centre, University of Regensburg, Regensburg, 93053, Germany
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology- Archaea Centre, University of Regensburg, Regensburg, 93053, Germany
| | - Tobias Restle
- Institute of Molecular Medicine, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Lübeck, 23538, Germany
| |
Collapse
|
86
|
Zhu L, Jiang H, Sheong FK, Cui X, Wang Y, Gao X, Huang X. Understanding the core of RNA interference: The dynamic aspects of Argonaute-mediated processes. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 128:39-46. [PMID: 27697475 DOI: 10.1016/j.pbiomolbio.2016.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 09/04/2016] [Accepted: 09/26/2016] [Indexed: 12/14/2022]
Abstract
At the core of RNA interference, the Argonaute proteins (Ago) load and utilize small guide nucleic acids to silence mRNAs or cleave foreign nucleic acids in a sequence specific manner. In recent years, based on extensive structural studies of Ago and its interaction with the nucleic acids, considerable progress has been made to reveal the dynamic aspects of various Ago-mediated processes. Here we review these novel insights into the guide-strand loading, duplex unwinding, and effects of seed mismatch, with a focus on two representative Agos, the human Ago 2 (hAgo2) and the bacterial Thermus thermophilus Ago (TtAgo). In particular, comprehensive molecular simulation studies revealed that although sharing similar overall structures, the two Agos have vastly different conformational landscapes and guide-strand loading mechanisms because of the distinct rigidity of their L1-PAZ hinge. Given the central role of the PAZ motions in regulating the exposure of the nucleic acid binding channel, these findings exemplify the importance of protein motions in distinguishing the overlapping, yet distinct, mechanisms of Ago-mediated processes in different organisms.
Collapse
Affiliation(s)
- Lizhe Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hanlun Jiang
- Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Fu Kit Sheong
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefeng Cui
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, 23955, Saudi Arabia
| | - Yanli Wang
- Laboratory of Non-Coding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, 23955, Saudi Arabia
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; Bioengineering Graduate Program, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
| |
Collapse
|
87
|
Tian XJ, Zhang H, Zhang J, Xing J. Reciprocal regulation between mRNA and microRNA enables a bistable switch that directs cell fate decisions. FEBS Lett 2016; 590:3443-3455. [PMID: 27578189 DOI: 10.1002/1873-3468.12379] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/21/2016] [Accepted: 08/22/2016] [Indexed: 12/14/2022]
Abstract
Micro RNAs (miRNAs) serve as crucial post-transcriptional regulators in a variety of essential cell fate decisions. However, the contribution of mRNA-miRNA mutual regulation to bistability is not fully understood. In the present study, we built a set of mathematical models of mRNA-miRNA interactions and systematically analyzed the sensitivity of the response curves under various conditions. Our findings indicate that mRNA-miRNA reciprocal regulation could manifest ultrasensitivity to subserve the generation of bistability when equipped with a positive feedback loop. We also find that the region of bistability is expanded by a stronger competing endogenous mRNA. Interestingly, bistability can be generated without a feedback loop if multiple miRNA binding sites exist on a target mRNA. Thus, we demonstrate the importance of simple mRNA-miRNA reciprocal regulation in cell fate decisions.
Collapse
Affiliation(s)
- Xiao-Jun Tian
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA.
| | - Hang Zhang
- Genetics, Bioinformatics and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Jingyu Zhang
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Jianhua Xing
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA. .,Computational Science Research Center, Beijing, China.
| |
Collapse
|
88
|
Che Harun NF, Takemoto H, Nomoto T, Tomoda K, Matsui M, Nishiyama N. Artificial Control of Gene Silencing Activity Based on siRNA Conjugation with Polymeric Molecule Having Coil-Globule Transition Behavior. Bioconjug Chem 2016; 27:1961-4. [PMID: 27506383 DOI: 10.1021/acs.bioconjchem.6b00322] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A new strategy for controlling gene silencing activity of siRNA in the cell was developed in the present study. siRNA was linearly conjugated with PNIPAAm, where coil-globule transition of the conjugated PNIPAAm allows thermoresponsive exposure of the vicinal siRNA molecule; a coil form of PNIPAAm (T < LCST) inhibits siRNA interaction with gene silencing-related proteins due to the steric hindrance effect, while a globule form of PNIPAAm (T > LCST) allows a ready access of siRNA to gene silencing pathway. As a result, at T > LCST, PNIPAAm-siRNA elicited effective association of siRNA with a gene silencing-related protein of Ago2, while siRNA recruitment into the gene silencing pathway was significantly suppressed at T < LCST. Ultimately, gene silencing efficacy of PNIPAAm-siRNA was close to unconjugated siRNA at T > LCST (∼80%), while it was dramatically decreased to ∼20% at T < LCST, suggesting that coil-globule transition of the conjugated polymer can control the bioactivity of the vicinal siRNA molecule.
Collapse
Affiliation(s)
- Noor Faizah Che Harun
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , R1-11, 4259, Nagatsuta, Midori-Ku, Yokohama, Kanagawa 226-8503, Japan
| | - Hiroyasu Takemoto
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , R1-11, 4259, Nagatsuta, Midori-Ku, Yokohama, Kanagawa 226-8503, Japan
| | - Takahiro Nomoto
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , R1-11, 4259, Nagatsuta, Midori-Ku, Yokohama, Kanagawa 226-8503, Japan
| | - Keishiro Tomoda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , R1-11, 4259, Nagatsuta, Midori-Ku, Yokohama, Kanagawa 226-8503, Japan
| | - Makoto Matsui
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , R1-11, 4259, Nagatsuta, Midori-Ku, Yokohama, Kanagawa 226-8503, Japan
| | - Nobuhiro Nishiyama
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , R1-11, 4259, Nagatsuta, Midori-Ku, Yokohama, Kanagawa 226-8503, Japan
| |
Collapse
|
89
|
Tang W, Tu S, Lee HC, Weng Z, Mello CC. The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans. Cell 2016; 164:974-84. [PMID: 26919432 DOI: 10.1016/j.cell.2016.02.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 11/14/2015] [Accepted: 02/03/2016] [Indexed: 02/05/2023]
Abstract
Piwi-interacting RNAs (piRNAs) engage Piwi proteins to suppress transposons and are essential for fertility in diverse organisms. An interesting feature of piRNAs is that, while piRNA lengths are stereotypical within a species, they can differ widely between species. For example, piRNAs are mainly 29 and 30 nucleotides in humans, 24 to 30 nucleotides in D. melanogaster, and uniformly 21 nucleotides in C. elegans. However, how piRNA length is determined and whether length impacts function remains unknown. Here, we show that C. elegans deficient for PARN-1, a conserved RNase, accumulate untrimmed piRNAs with 3' extensions. Surprisingly, these longer piRNAs are stable and associate with the Piwi protein PRG-1 but fail to robustly recruit downstream silencing factors. Our findings identify PARN-1 as a key regulator of piRNA length in C. elegans and suggest that length is regulated to promote efficient transcriptome surveillance.
Collapse
Affiliation(s)
- Wen Tang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shikui Tu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Heng-Chi Lee
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute.
| |
Collapse
|
90
|
ElHefnawi M, Kim T, Kamar MA, Min S, Hassan NM, El-Ahwany E, Kim H, Zada S, Amer M, Windisch MP. In Silico Design and Experimental Validation of siRNAs Targeting Conserved Regions of Multiple Hepatitis C Virus Genotypes. PLoS One 2016; 11:e0159211. [PMID: 27441640 PMCID: PMC4956106 DOI: 10.1371/journal.pone.0159211] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 06/28/2016] [Indexed: 12/16/2022] Open
Abstract
RNA interference (RNAi) is a post-transcriptional gene silencing mechanism that mediates the sequence-specific degradation of targeted RNA and thus provides a tremendous opportunity for development of oligonucleotide-based drugs. Here, we report on the design and validation of small interfering RNAs (siRNAs) targeting highly conserved regions of the hepatitis C virus (HCV) genome. To aim for therapeutic applications by optimizing the RNAi efficacy and reducing potential side effects, we considered different factors such as target RNA variations, thermodynamics and accessibility of the siRNA and target RNA, and off-target effects. This aim was achieved using an in silico design and selection protocol complemented by an automated MysiRNA-Designer pipeline. The protocol included the design and filtration of siRNAs targeting highly conserved and accessible regions within the HCV internal ribosome entry site, and adjacent core sequences of the viral genome with high-ranking efficacy scores. Off-target analysis excluded siRNAs with potential binding to human mRNAs. Under this strict selection process, two siRNAs (HCV353 and HCV258) were selected based on their predicted high specificity and potency. These siRNAs were tested for antiviral efficacy in HCV genotype 1 and 2 replicon cell lines. Both in silico-designed siRNAs efficiently inhibited HCV RNA replication, even at low concentrations and for short exposure times (24h); they also exceeded the antiviral potencies of reference siRNAs targeting HCV. Furthermore, HCV353 and HCV258 siRNAs also inhibited replication of patient-derived HCV genotype 4 isolates in infected Huh-7 cells. Prolonged treatment of HCV replicon cells with HCV353 did not result in the appearance of escape mutant viruses. Taken together, these results reveal the accuracy and strength of our integrated siRNA design and selection protocols. These protocols could be used to design highly potent and specific RNAi-based therapeutic oligonucleotide interventions.
Collapse
Affiliation(s)
- Mahmoud ElHefnawi
- Informatics and Systems Department, Biomedical Informatics and Chemo-Informatics Group, Centre of Excellence for Advanced Sciences (CEAS), Division of Engineering Research, National Research Centre, Cairo, Egypt
- Centre for Informatics, Nile University, Shiekh Zayed City, Egypt
- Yousef-Jameel Science and Technology Research Centre, American University in Cairo, New Cairo, Egypt
- * E-mail: (MEH); (MPW)
| | - TaeKyu Kim
- Hepatitis Research Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Mona A. Kamar
- Yousef-Jameel Science and Technology Research Centre, American University in Cairo, New Cairo, Egypt
| | - Saehong Min
- Hepatitis Research Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Nafisa M. Hassan
- Yousef-Jameel Science and Technology Research Centre, American University in Cairo, New Cairo, Egypt
| | - Eman El-Ahwany
- Biology Department, American University in Cairo, New Cairo, Egypt
- Immunology Department, Theodor Bilharz Research Institute, Giza, Egypt
| | - Heeyoung Kim
- Hepatitis Research Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Suher Zada
- Yousef-Jameel Science and Technology Research Centre, American University in Cairo, New Cairo, Egypt
- Biology Department, American University in Cairo, New Cairo, Egypt
| | - Marwa Amer
- Biology Department, American University in Cairo, New Cairo, Egypt
- Faculty of Biotechnology, Misr University for Science and Technology, 6 of October City, Egypt
| | - Marc P. Windisch
- Hepatitis Research Laboratory, Institut Pasteur Korea, 696 Sampyung-dong, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea
- * E-mail: (MEH); (MPW)
| |
Collapse
|
91
|
Miyoshi T, Ito K, Murakami R, Uchiumi T. Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute. Nat Commun 2016; 7:11846. [PMID: 27325485 PMCID: PMC4919518 DOI: 10.1038/ncomms11846] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 05/05/2016] [Indexed: 01/05/2023] Open
Abstract
Argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. However, little is known about the Argonaute protein that recognizes guide RNA/target DNA. Here, we determine the 2 Å crystal structure of Rhodobacter sphaeroides Argonaute (RsAgo) in a complex with 18-nucleotide guide RNA and its complementary target DNA. The heteroduplex maintains Watson-Crick base-pairing even in the 3'-region of the guide RNA between the N-terminal and PIWI domains, suggesting a recognition mode by RsAgo for stable interaction with the target strand. In addition, the MID/PIWI interface of RsAgo has a system that specifically recognizes the 5' base-U of the guide RNA, and the duplex-recognition loop of the PAZ domain is important for the DNA silencing activity. Furthermore, we show that Argonaute discriminates the nucleic acid type (RNA/DNA) by recognition of the duplex structure of the seed region.
Collapse
Affiliation(s)
- Tomohiro Miyoshi
- Center for Transdisciplinary Research, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Kosuke Ito
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Ryo Murakami
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| | - Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181, Japan
| |
Collapse
|
92
|
Lai X, Wolkenhauer O, Vera J. Understanding microRNA-mediated gene regulatory networks through mathematical modelling. Nucleic Acids Res 2016; 44:6019-35. [PMID: 27317695 PMCID: PMC5291278 DOI: 10.1093/nar/gkw550] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 06/06/2016] [Indexed: 12/19/2022] Open
Abstract
The discovery of microRNAs (miRNAs) has added a new player to the regulation of gene expression. With the increasing number of molecular species involved in gene regulatory networks, it is hard to obtain an intuitive understanding of network dynamics. Mathematical modelling can help dissecting the role of miRNAs in gene regulatory networks, and we shall here review the most recent developments that utilise different mathematical modelling approaches to provide quantitative insights into the function of miRNAs in the regulation of gene expression. Key miRNA regulation features that have been elucidated via modelling include: (i) the role of miRNA-mediated feedback and feedforward loops in fine-tuning of gene expression; (ii) the miRNA–target interaction properties determining the effectiveness of miRNA-mediated gene repression; and (iii) the competition for shared miRNAs leading to the cross-regulation of genes. However, there is still lack of mechanistic understanding of many other properties of miRNA regulation like unconventional miRNA–target interactions, miRNA regulation at different sub-cellular locations and functional miRNA variant, which will need future modelling efforts to deal with. This review provides an overview of recent developments and challenges in this field.
Collapse
Affiliation(s)
- Xin Lai
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, 91054, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, 18051, Germany Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, 7600, South Africa
| | - Julio Vera
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, 91054, Germany
| |
Collapse
|
93
|
Nakanishi K. Anatomy of RISC: how do small RNAs and chaperones activate Argonaute proteins? WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:637-60. [PMID: 27184117 PMCID: PMC5084781 DOI: 10.1002/wrna.1356] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 12/19/2022]
Abstract
RNA silencing is a eukaryote‐specific phenomenon in which microRNAs and small interfering RNAs degrade messenger RNAs containing a complementary sequence. To this end, these small RNAs need to be loaded onto an Argonaute protein (AGO protein) to form the effector complex referred to as RNA‐induced silencing complex (RISC). RISC assembly undergoes multiple and sequential steps with the aid of Hsc70/Hsp90 chaperone machinery. The molecular mechanisms for this assembly process remain unclear, despite their significance for the development of gene silencing techniques and RNA interference‐based therapeutics. This review dissects the currently available structures of AGO proteins and proposes models and hypotheses for RISC assembly, covering the conformation of unloaded AGO proteins, the chaperone‐assisted duplex loading, and the slicer‐dependent and slicer‐independent duplex separation. The differences in the properties of RISC between prokaryotes and eukaryotes will also be clarified. WIREs RNA 2016, 7:637–660. doi: 10.1002/wrna.1356 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Kotaro Nakanishi
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
94
|
Probing the Limits to MicroRNA-Mediated Control of Gene Expression. PLoS Comput Biol 2016; 12:e1004715. [PMID: 26812364 PMCID: PMC4727922 DOI: 10.1371/journal.pcbi.1004715] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/20/2015] [Indexed: 12/14/2022] Open
Abstract
According to the ‘ceRNA hypothesis’, microRNAs (miRNAs) may act as mediators of an effective positive interaction between long coding or non-coding RNA molecules, carrying significant potential implications for a variety of biological processes. Here, inspired by recent work providing a quantitative description of small regulatory elements as information-conveying channels, we characterize the effectiveness of miRNA-mediated regulation in terms of the optimal information flow achievable between modulator (transcription factors) and target nodes (long RNAs). Our findings show that, while a sufficiently large degree of target derepression is needed to activate miRNA-mediated transmission, (a) in case of differential mechanisms of complex processing and/or transcriptional capabilities, regulation by a post-transcriptional miRNA-channel can outperform that achieved through direct transcriptional control; moreover, (b) in the presence of large populations of weakly interacting miRNA molecules the extra noise coming from titration disappears, allowing the miRNA-channel to process information as effectively as the direct channel. These observations establish the limits of miRNA-mediated post-transcriptional cross-talk and suggest that, besides providing a degree of noise buffering, this type of control may be effectively employed in cells both as a failsafe mechanism and as a preferential fine tuner of gene expression, pointing to the specific situations in which each of these functionalities is maximized. The discovery of RNA interference has revolutionized the decades’ old view of RNAs as mere intermediaries between DNA and proteins in the gene expression workflow. MicroRNAs (or miRNAs), in particular, have been shown to be able to both stabilize the protein output by buffering transcriptional noise and to create an effective positive interaction between the levels of their target RNAs through a simple competition mechanism known as ‘ceRNA effect’. With miRNAs commonly targeting multiple species of RNAs, the potential implication is that RNAs could regulate each other through extended miRNA-mediated interaction networks. Such cross-talk is certainly active in many specific cases (like cell differentiation), but it’s unclear whether the degree of regulation of gene expression achievable through post-transcriptional miRNA-mediated coupling can effectively overcome the one obtained through other mechanisms, e.g. by direct transcriptional control via DNA-binding factors. This work quantifies the maximal post-transcriptional regulatory power achievable by miRNA-mediated cross-talk, characterizing the circumstances in which indirect control outperforms direct one. The emerging scenario suggests that, in addition to its widely recognized noise-buffering role, miRNA-mediated control may indeed act as a master regulator of gene expression.
Collapse
|
95
|
Recombinant hTRBP and hPACT Modulate hAgo2-Catalyzed siRNA-Mediated Target RNA Cleavage In Vitro. PLoS One 2016; 11:e0146814. [PMID: 26784517 PMCID: PMC4718636 DOI: 10.1371/journal.pone.0146814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/21/2015] [Indexed: 11/19/2022] Open
Abstract
The human TAR RNA-binding protein (hTRBP) and protein activator of protein kinase R (hPACT) are important players in RNA interference (RNAi). Together with hArgonaute2 (hAgo2) and hDicer they have been reported to form the RISC-loading complex (RLC). Among other functions, hTRBP was suggested to assist the loading of hAgo2 with small interfering RNAs (siRNAs) within the RLC. Although several studies have been conducted to evaluate the specific functions of hTRBP and hPACT in RNAi, exact mechanisms and modes of action are still unknown. Here, we present a biochemical study further evaluating the role of hTRBP and hPACT in hAgo2-loading. We found that both proteins enhance hAgo2-mediated RNA cleavage significantly; even a hAgo2 mutant impaired in siRNA binding shows full cleavage activity in the presence of hTRBP or hPACT. Pre-steady state binding studies reveal that the assembly of wildtype-hAgo2 (wt-hAgo2) and siRNAs remains largely unaffected, whereas the binding of mutant hAgo2-PAZ9 to siRNA is restored by adding either hTRBP or hPACT. We conclude that both proteins assist in positioning the siRNA within hAgo2 to ensure optimal binding and cleavage. Overall, our data indicate that hTRBP and hPACT are part of a regulative system of RNAi that is important for efficient target RNA cleavage.
Collapse
|
96
|
Sarett SM, Nelson CE, Duvall CL. Technologies for controlled, local delivery of siRNA. J Control Release 2015; 218:94-113. [PMID: 26476177 PMCID: PMC4665980 DOI: 10.1016/j.jconrel.2015.09.066] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/25/2015] [Accepted: 09/29/2015] [Indexed: 12/24/2022]
Abstract
The discovery of RNAi in the late 1990s unlocked a new realm of therapeutic possibilities by enabling potent and specific silencing of theoretically any desired genetic target. Better elucidation of the mechanism of action, the impact of chemical modifications that stabilize and reduce nonspecific effects of siRNA molecules, and the key design considerations for effective delivery systems has spurred progress toward developing clinically-successful siRNA therapies. A logical aim for initial siRNA translation is local therapies, as delivering siRNA directly to its site of action helps to ensure that a sufficient dose reaches the target tissue, lessens the potential for off-target side effects, and circumvents the substantial systemic delivery barriers. While locally injected or topically applied siRNA has progressed into numerous clinical trials, an enormous opportunity exists to develop sustained-release, local delivery systems that enable both spatial and temporal control of gene silencing. This review focuses on material platforms that establish both localized and controlled gene silencing, with emphasis on the systems that show most promise for clinical translation.
Collapse
Affiliation(s)
- Samantha M Sarett
- Vanderbilt University Department of Biomedical Engineering, United States
| | | | - Craig L Duvall
- Vanderbilt University Department of Biomedical Engineering, United States.
| |
Collapse
|
97
|
Dornseifer S, Willkomm S, Far RKK, Liebschwager J, Beltsiou F, Frank K, Laufer SD, Martinetz T, Sczakiel G, Claussen JC, Restle T. RNAi revised--target mRNA-dependent enhancement of gene silencing. Nucleic Acids Res 2015; 43:10623-32. [PMID: 26578554 PMCID: PMC4678823 DOI: 10.1093/nar/gkv1200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/26/2015] [Indexed: 01/11/2023] Open
Abstract
The discovery of RNA interference (RNAi) gave rise to the development of new nucleic acid-based technologies as powerful investigational tools and potential therapeutics. Mechanistic key details of RNAi in humans need to be deciphered yet, before such approaches take root in biomedicine and molecular therapy. We developed and validated an in silico-based model of siRNA-mediated RNAi in human cells in order to link in vitro-derived pre-steady state kinetic data with a quantitative and time-resolved understanding of RNAi on the cellular level. The observation that product release by Argonaute 2 is accelerated in the presence of an excess of target RNA in vitro inspired us to suggest an associative mechanism for the RNA slicer reaction where incoming target mRNAs actively promote dissociation of cleaved mRNA fragments. This novel associative model is compatible with high multiple turnover rates of RNAi-based gene silencing in living cells and accounts for target mRNA concentration-dependent enhancement of the RNAi machinery.
Collapse
Affiliation(s)
- Simon Dornseifer
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Sarah Willkomm
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | | | - Janine Liebschwager
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Foteini Beltsiou
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Kirsten Frank
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Sandra D Laufer
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Thomas Martinetz
- Institute for Neuro- and Bioinformatics, University of Lübeck, 23538 Lübeck, Germany
| | - Georg Sczakiel
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | | | - Tobias Restle
- Institute of Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| |
Collapse
|
98
|
Yao C, Sasaki HM, Ueda T, Tomari Y, Tadakuma H. Single-Molecule Analysis of the Target Cleavage Reaction by the Drosophila RNAi Enzyme Complex. Mol Cell 2015; 59:125-32. [PMID: 26140368 DOI: 10.1016/j.molcel.2015.05.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/02/2015] [Accepted: 05/04/2015] [Indexed: 10/23/2022]
Abstract
Small interfering RNAs (siRNAs) direct cleavage of complementary target RNAs via an RNA-induced silencing complex (RISC) that contains Argonatute2 protein at its core. However, what happens after target cleavage remains unclear. Here we analyzed the cleavage reaction by Drosophila Argonaute2-RISC using single-molecule imaging and revealed a series of intermediate states in target recognition, cleavage, and product release. Our data suggest that, after cleavage, RISC generally releases the 5' cleavage fragment from the guide 3' supplementary region first and then the 3' fragment from the seed region, highlighting the reinforcement of the seed pairing in RISC. However, this order can be reversed by extreme stabilization of the 3' supplementary region or mismatches in the seed region. Therefore, the release order of the two cleavage fragments is influenced by the stability in each region, in contrast to the unidirectional base pairing propagation from the seed to the 3' supplementary region upon target recognition.
Collapse
Affiliation(s)
- Chunyan Yao
- Graduate School of Frontier Science, The University of Tokyo, Chiba 277-8562, Japan; Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Hiroshi M Sasaki
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Takuya Ueda
- Graduate School of Frontier Science, The University of Tokyo, Chiba 277-8562, Japan
| | - Yukihide Tomari
- Graduate School of Frontier Science, The University of Tokyo, Chiba 277-8562, Japan; Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan.
| | - Hisashi Tadakuma
- Graduate School of Frontier Science, The University of Tokyo, Chiba 277-8562, Japan; Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan.
| |
Collapse
|
99
|
Yi F, Chen J, Yu J. Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet. BMC PLANT BIOLOGY 2015; 15:241. [PMID: 26444665 PMCID: PMC4594888 DOI: 10.1186/s12870-015-0632-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/30/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND mRNA degradation plays an important role in the determination of mRNA abundance and can quickly regulate gene expression. The production of uncapped mRNAs, an important mechanism of mRNA degradation, can be initiated by decapping enzymes, endonucleases or small RNAs such as microRNAs (miRNAs). Little is known, however, about the role of uncapped mRNAs in plants under environmental stress. RESULTS Using a novel approach called parallel analysis of RNA ends (PARE), we performed a global study of uncapped mRNAs under drought stress in foxtail millet (Setaria italica [L.] P. Beauv.). When both gene degradation (PARE) and gene transcription (RNA-sequencing) data were considered, four types of mRNA decay patterns were identified under drought stress. In addition, 385 miRNA-target interactions were identified in the PARE data using PAREsnip. The PARE analysis also suggested that two miRNA hairpin processing mechanisms--loop-last and loop-first processing--operate in foxtail millet, with both miR319 and miR156 gene families undergoing precise processing via the unusual loop-first mechanism. Finally, we found 11 C4 photosynthesis-related enzymes encoded by drought-responsive genes. CONCLUSIONS We performed a global analysis of mRNA degradation under drought stress and uncovered diverse drought-response mechanisms in foxtail millet. This information will deepen our understanding of mRNA expression under stressful environmental conditions in gramineous plants. In addition, PARE analysis identified many miRNA targets and revealed miRNA-precursor processing modes in foxtail millet.
Collapse
Affiliation(s)
- Fei Yi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Jingjuan Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
100
|
Chen B, Ma R, Ma G, Guo X, Tong X, Tang G, Kang L. Haemocyanin is essential for embryonic development and survival in the migratory locust. INSECT MOLECULAR BIOLOGY 2015; 24:517-527. [PMID: 26010377 DOI: 10.1111/imb.12177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Haemocyanins are commonly known as copper-containing oxygen carriers within the haemolymph of arthropods, and have been found in many orders of insects. However, it remains unresolved why haemocyanins persist in insects that possess elaborate tracheal systems for oxygen diffusion to cells. Here we identified haemocyanins in the migratory locust Locusta migratoria that consists of two distinct subunits, Hc1 and Hc2. Genomic sequence analysis indicated that Hc1 and Hc2 have four and three gene copies, respectively, which may have evolved via gene duplication followed by divergent evolution of introns. The two subunits exhibit abundant and embryonic-specific expression at the mRNA and protein level; their expression peaks in the mid-term embryo and is not detectable in the late nymphal and adult stages. A larger proportion of the haemocyanins is present in the yolk compared with that in the embryo. Immunostaining shows that haemocyanins in the embryo are mainly expressed in the epidermis. Knockdown of Hc1 and Hc2 results in significant embryonic developmental delay and abnormality as well as reduced egg hatchability, ie the proportion of hatched eggs. These results reveal a previously unappreciated and fundamental role for haemocyanins in embryonic development and survival in insects, probably involving the exchange of molecules (eg O2 ) between the embryo and its environment.
Collapse
Affiliation(s)
- B Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - R Ma
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - G Ma
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Department of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - X Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - X Tong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - G Tang
- Department of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - L Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|