201
|
Otsuka M, Jing Q, Georgel P, New L, Chen J, Mols J, Kang YJ, Jiang Z, Du X, Cook R, Das SC, Pattnaik AK, Beutler B, Han J. Hypersusceptibility to vesicular stomatitis virus infection in Dicer1-deficient mice is due to impaired miR24 and miR93 expression. Immunity 2007; 27:123-34. [PMID: 17613256 DOI: 10.1016/j.immuni.2007.05.014] [Citation(s) in RCA: 274] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 04/10/2007] [Accepted: 05/07/2007] [Indexed: 01/24/2023]
Abstract
Dicer is essential for plant, Caenorhabditis elegans, and Drosophila antiviral responses because of its role in generating small interfering RNA (siRNA) from viral genomes. We show that because of impaired miRNA production, mice with a variant Dicer1 allele (Dicer1(d/d)) were more susceptible to vesicular stomatitis virus (VSV) infection. We did not detect VSV genome-derived siRNA in wild-type cells or any alteration of interferon-mediated antiviral responses by Dicer1 deficiency. Rather, we found that host miR24 and miR93 could target viral large protein (L protein) and phosphoprotein (P protein) genes, and a lack of miR24 and miR93 was responsible for increased VSV replication in Dicer1(d/d) cells. Our data suggest that host miRNA can play a role in host interactions with viruses.
Collapse
Affiliation(s)
- Motoyuki Otsuka
- Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
202
|
Baulcombe DC. Short silencing RNA: the dark matter of genetics? COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:13-20. [PMID: 17381275 DOI: 10.1101/sqb.2006.71.052] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Plants and animals have single-stranded silencing RNAs (sRNAs) of 21-25 nucleotides in length that are derived from a double-stranded (ds)RNA precursor by Dicer (DCL) processing. These RNAs are the guide RNA for nucleases of the AGO class that cleave targeted RNA in a nucleotide sequence-specific manner. The cleaved RNAs are then degraded further or they are the template for an RNA-dependent RNA polymerase (RDR) that generates a dsRNA. In this paper, I discuss the possibility that this RDR-generated dsRNA initiates a cascade in which there are multiple rounds of secondary sRNA production. I propose that these secondary sRNAs feature in mechanisms that can either buffer mRNA populations against change or, in certain circumstances, mediate extensive changes in mRNA populations. The RNA cascades may also have RNA-mediated epigenetic characteristics in addition to the DNA and chromatin transcriptional silencing potential that has been previously linked with RNA silencing.
Collapse
|
203
|
Patel DJ, Ma JB, Yuan YR, Ye K, Pei Y, Kuryavyi V, Malinina L, Meister G, Tuschl T. Structural biology of RNA silencing and its functional implications. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:81-93. [PMID: 17381284 PMCID: PMC4689314 DOI: 10.1101/sqb.2006.71.053] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We outline structure-function contributions from our laboratories on protein-RNA recognition events that monitor siRNA length, 5 -phosphate and 2-nucleotide 3 overhangs, as well as the architecture of Argonaute, its externally bound siRNA complex, and Argonaute-based models involving guide-strand-mediated mRNA binding, cleavage, and release.
Collapse
Affiliation(s)
- D J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
204
|
Yu Z, Li Z, Jolicoeur N, Zhang L, Fortin Y, Wang E, Wu M, Shen SH. Aberrant allele frequencies of the SNPs located in microRNA target sites are potentially associated with human cancers. Nucleic Acids Res 2007; 35:4535-41. [PMID: 17584784 PMCID: PMC1935019 DOI: 10.1093/nar/gkm480] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of noncoding small RNAs that regulate gene expression by base pairing with target mRNAs at the 3′-terminal untranslated regions (3′-UTRs), leading to mRNA cleavage or translational repression. Single-nucleotide polymorphisms (SNPs) located at miRNA-binding sites (miRNA-binding SNPs) are likely to affect the expression of the miRNA target and may contribute to the susceptibility of humans to common diseases. We herein performed a genome-wide analysis of SNPs located in the miRNA-binding sites of the 3′-UTR of various human genes. We found that miRNA-binding SNPs are negatively selected in respect to SNP distribution between the miRNA-binding ‘seed’ sequence and the entire 3′-UTR sequence. Furthermore, we comprehensively defined the expression of each miRNA-binding SNP in cancers versus normal tissues through mining EST databases. Interestingly, we found that some miRNA-binding SNPs exhibit significant different allele frequencies between the human cancer EST libraries and the dbSNP database. More importantly, using human cancer specimens against the dbSNP database for case-control association studies, we found that twelve miRNA-binding SNPs indeed display an aberrant allele frequency in human cancers. Hence, SNPs located in miRNA-binding sites affect miRNA target expression and function, and are potentially associated with cancers.
Collapse
Affiliation(s)
- Zhenbao Yu
- Health Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, Canada, H4P 2R2 and Department of Medicine, McGill University, Montréal, Québec, Canada, H3G 1A4
| | - Zhen Li
- Health Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, Canada, H4P 2R2 and Department of Medicine, McGill University, Montréal, Québec, Canada, H3G 1A4
| | - Normand Jolicoeur
- Health Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, Canada, H4P 2R2 and Department of Medicine, McGill University, Montréal, Québec, Canada, H3G 1A4
| | - Linhua Zhang
- Health Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, Canada, H4P 2R2 and Department of Medicine, McGill University, Montréal, Québec, Canada, H3G 1A4
| | - Yves Fortin
- Health Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, Canada, H4P 2R2 and Department of Medicine, McGill University, Montréal, Québec, Canada, H3G 1A4
| | - Edwin Wang
- Health Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, Canada, H4P 2R2 and Department of Medicine, McGill University, Montréal, Québec, Canada, H3G 1A4
| | - Meiqun Wu
- Health Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, Canada, H4P 2R2 and Department of Medicine, McGill University, Montréal, Québec, Canada, H3G 1A4
| | - Shi-Hsiang Shen
- Health Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montréal, Québec, Canada, H4P 2R2 and Department of Medicine, McGill University, Montréal, Québec, Canada, H3G 1A4
- *To whom correspondence should be addressed. +514 496 6318+514 496 6319 Correspondence may also be addressed to Zhenbao Yu. +514 496 6377+514 496 6319
| |
Collapse
|
205
|
Sklan EH, Glenn JS. The Power of silence: application of small interfering RNAs to gastrointestinal diseases. Gastroenterology 2007; 132:2291-5. [PMID: 17570202 DOI: 10.1053/j.gastro.2007.04.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Ella H Sklan
- Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Palo Alto, California 94305-5187, USA
| | | |
Collapse
|
206
|
Zhao T, Li G, Mi S, Li S, Hannon GJ, Wang XJ, Qi Y. A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev 2007; 21:1190-203. [PMID: 17470535 PMCID: PMC1865491 DOI: 10.1101/gad.1543507] [Citation(s) in RCA: 290] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Endogenous small RNAs function in RNA interference (RNAi) pathways to control gene expression through mRNA cleavage, translational repression, or chromatin modification. Plants and animals contain many microRNAs (miRNAs) that play vital roles in development, including helping to specify cell type and tissue identity. To date, no miRNAs have been reported in unicellular organisms. Here we show that Chlamydomonas reinhardtii, a unicellular green alga, encodes many miRNAs. We also show that a Chlamydomonas miRNA can direct the cleavage of its target mRNA in vivo and in vitro. We further show that the expression of some miRNAs/Candidates increases or decreases during Chlamydomonas gametogenesis. In addition to miRNAs, Chlamydomonas harbors other types of small RNAs including phased small interfering RNAs (siRNAs) that are reminiscent of plant trans-acting siRNAs, as well as siRNAs originating from protein-coding genes and transposons. Our findings suggest that the miRNA pathway and some siRNA pathways are ancient mechanisms of gene regulation that evolved prior to the emergence of multicellularity.
Collapse
Affiliation(s)
- Tao Zhao
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
| | - Guanglin Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shijun Mi
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
| | - Shan Li
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
| | - Gregory J. Hannon
- Cold Spring Harbor Laboratory, Watson School of Biological Sciences and Howard Hughes Medical Institute, Cold Spring Harbor, New York 11724, USA
| | - Xiu-Jie Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- E-MAIL ; FAX 86-10-64873428
| | - Yijun Qi
- National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
- Corresponding author.E-mail ; FAX 86-10-80727873
| |
Collapse
|
207
|
Morita S, Horii T, Kimura M, Goto Y, Ochiya T, Hatada I. One Argonaute family member, Eif2c2 (Ago2), is essential for development and appears not to be involved in DNA methylation. Genomics 2007; 89:687-96. [PMID: 17418524 DOI: 10.1016/j.ygeno.2007.01.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 10/23/2006] [Accepted: 01/10/2007] [Indexed: 11/18/2022]
Abstract
To elucidate the epigenetic role of RNAi in mammals, we disrupted the gene for Eif2c2 (Ago2), which works as the sole slicer of RNAi in the Argonaute family. In mice, disruption of Eif2c2 leads to embryonic lethality early in development after the implantation stage. This phenotype is completely different from that in a previous report, but somewhat similar to the disruption of Dicer1, another important component of RNAi. We also show that Eif2c2 is not required for the maintenance of DNA methylation in imprinted genes, centromeric repeats, and Xist. This suggests that developmental defects in the Eif2c2-deficient mouse are caused not at the transcriptional level, but rather at the posttranscriptional level through the miRNA-protein complex.
Collapse
Affiliation(s)
- Sumiyo Morita
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15 Showa-machi, Maebashi 371-8512, Japan
| | | | | | | | | | | |
Collapse
|
208
|
Gonzalez-Alegre P. Therapeutic RNA interference for neurodegenerative diseases: From promise to progress. Pharmacol Ther 2007; 114:34-55. [PMID: 17316816 DOI: 10.1016/j.pharmthera.2007.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 12/28/2006] [Indexed: 12/22/2022]
Abstract
RNA interference (RNAi) has emerged as a powerful tool to manipulate gene expression in the laboratory. Due to its remarkable discriminating properties, individual genes, or even alleles can be targeted with exquisite specificity in cultured cells or living animals. Among its many potential biomedical applications, silencing of disease-linked genes stands out as a promising therapeutic strategy for many incurable disorders. Neurodegenerative diseases represent one of the more attractive targets for the development of therapeutic RNAi. In this group of diseases, the progressive loss of neurons leads to the gradual appearance of disabling neurological symptoms and premature death. Currently available therapies aim to improve the symptoms but not to halt the process of neurodegeneration. The increasing prevalence and economic burden of some of these diseases, such as Alzheimer's disease (AD) or Parkinson's disease (PD), has boosted the efforts invested in the development of interventions, such as RNAi, aimed at altering their natural course. This review will summarize where we stand in the therapeutic application of RNAi for neurodegenerative diseases. The basic principles of RNAi will be reviewed, focusing on features important for its therapeutic manipulation. Subsequently, a stepwise strategy for the development of therapeutic RNAi will be presented. Finally, the different preclinical trials of therapeutic RNAi completed in disease models will be summarized, stressing the experimental questions that need to be addressed before planning application in human disease.
Collapse
Affiliation(s)
- Pedro Gonzalez-Alegre
- Department of Neurology, 2-RCP, Carver College of Medicine at The University of Iowa, Iowa City, IA 52242, United States.
| |
Collapse
|
209
|
Abstract
Repair of a defect in the human skin is a highly orchestrated physiological process involving numerous factors that act in a temporally resolved synergistic manner to re-establish barrier function by regenerating new skin. The inducible expression and repression of genes represents a key component of this regenerative process. MicroRNAs (miRNAs) are approximately 22-nucleotide-long endogenously expressed non-coding RNAs that regulate the expression of gene products by inhibition of translation and/or transcription in animals. miRNAs play a key role in skin morphogenesis and in regulating angiogenesis. The vascular endothelial growth factor signaling path seems to be under repressor control by miRNAs. Mature miRNA-dependent mechanisms impair angiogenesis in vivo. It is critically important to recognize that the understanding of cutaneous wound healing is incomplete without appreciating the functional significance of wound-induced miRNA. Ongoing work in our laboratory has led to the observation that the cutaneous wound healing process involves changes in the expression of specific miRNA at specific phases of wound healing. We hypothesize that dysregulation of specific miRNA is critical in derailing the healing sequence in chronic problem wounds. If tested positive, this hypothesis is likely to lead to completely novel diagnostic and therapeutic strategies for the treatment of problem wounds.
Collapse
Affiliation(s)
- Shani Shilo
- Laboratory of Molecular Medicine, Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University Medical Center, Columbus, Ohio, USA
| | | | | | | |
Collapse
|
210
|
Choudhary S, Lee HC, Maiti M, He Q, Cheng P, Liu Q, Liu Y. A double-stranded-RNA response program important for RNA interference efficiency. Mol Cell Biol 2007; 27:3995-4005. [PMID: 17371837 PMCID: PMC1900031 DOI: 10.1128/mcb.00186-07] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
When recognized by the RNA interference (RNAi) pathway, double-stranded RNA (dsRNA) produced in eukaryotic cells results in posttranscriptional gene silencing. In addition, dsRNA can trigger the interferon response as part of the immune response in vertebrates. In this study, we show that dsRNA, but not short interfering RNA (siRNA), induces the expression of qde-2 (an Argonaute gene) and dcl-2 (a Dicer gene), two central components of the RNAi pathway in the filamentous fungus Neurospora crassa. The induction of QDE-2 by dsRNA is required for normal gene silencing, indicating that this is a regulatory mechanism that allows the optimal function of the RNAi pathway. In addition, we demonstrate that Dicer proteins (DCLs) regulate QDE-2 posttranscriptionally, suggesting a role for DCLs or siRNA in QDE-2 accumulation. Finally, a genome-wide search revealed that additional RNAi components and homologs of antiviral and interferon-stimulated genes are also dsRNA-activated genes in Neurospora. Together, our results suggest that the activation of the RNAi components is part of a broad ancient host defense response against viral and transposon infections.
Collapse
Affiliation(s)
- Swati Choudhary
- Department of Physiology, Room ND13.214A, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9040, USA
| | | | | | | | | | | | | |
Collapse
|
211
|
Maiti M, Lee HC, Liu Y. QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands. Genes Dev 2007; 21:590-600. [PMID: 17311884 PMCID: PMC1820900 DOI: 10.1101/gad.1497607] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Single-stranded small interfering RNA (siRNA) guides the cleavage of homologous mRNA by Argonaute proteins, the catalytic core of the RNA-induced silencing complex (RISC), in the conserved RNA interference (RNAi) pathway. The separation of the siRNA duplex into single strands is essential for the activation of RISC. Previous biochemical studies have suggested that Argonaute proteins cleave and remove the passenger strand of siRNA duplex from RISC, but the in vivo importance of this process and the mechanism for the removal of the nicked passenger strand are not known. Here, we show that in the filamentous fungus Neurospora, the Argonaute homolog QDE-2 and its slicer function are required for the generation of single-stranded siRNA and gene silencing in vivo. Biochemical purification of QDE-2 led to the identification of QIP, a QDE-2-interacting protein, with an exonuclease domain. The disruption of qip in Neurospora impaired gene silencing and siRNA accumulated, mostly in nicked duplex form. Furthermore, our results suggest that QIP acts as an exonuclease that cleaves and removes the nicked passenger strand from siRNA duplex in a QDE-2-dependent manner. Together, these results suggest that both the cleavage and removal of the passenger strand from the siRNA duplex are important steps in RNAi pathways.
Collapse
Affiliation(s)
- Mekhala Maiti
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Heng-Chi Lee
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Corresponding author.E-MAIL ; FAX (214) 645-6049
| |
Collapse
|
212
|
Rana TM. Illuminating the silence: understanding the structure and function of small RNAs. Nat Rev Mol Cell Biol 2007; 8:23-36. [PMID: 17183358 DOI: 10.1038/nrm2085] [Citation(s) in RCA: 722] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA interference (RNAi) is triggered by double-stranded RNA helices that have been introduced exogenously into cells as small interfering (si)RNAs or that have been produced endogenously from small non-coding RNAs known as microRNAs (miRNAs). RNAi has become a standard experimental tool and its therapeutic potential is being aggressively harnessed. Understanding the structure and function of small RNAs, such as siRNAs and miRNAs, that trigger RNAi has shed light on the RNAi machinery. In particular, it has highlighted the assembly and function of the RNA-induced silencing complex (RISC), and has provided guidelines to efficiently silence genes for biological research and therapeutic applications of RNAi.
Collapse
Affiliation(s)
- Tariq M Rana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
| |
Collapse
|
213
|
Makarova JA, Kramerov DA. Small nucleolar RNA genes. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
214
|
Cheng TL, Chang WT. Construction of simple and efficient DNA vector-based short hairpin RNA expression systems for specific gene silencing in mammalian cells. Methods Mol Biol 2007; 408:223-241. [PMID: 18314586 DOI: 10.1007/978-1-59745-547-3_13] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
RNA interference (RNAi) is an evolutionarily conserved mechanism of posttranscriptional gene silencing induced by introducing the double-stranded RNAs (dsRNAs) into cells. Recent progress in RNAi-based gene-silencing techniques has revolutionarily advanced in studies of the functional genomics and molecular therapeutics. Among the widely used dsRNAs including exogenously synthetic and endogenously expressed small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs), the shRNAs are more efficient than siRNAs on the induction of gene silencing and currently have evolved as an extremely powerful and the most popular gene silencing reagent. The DNA vector-based shRNA-expression systems provide not only a simple and effective way in inhibiting gene activities in either inheritable or inducible manner, but also a cost-effective tool in constructing the expression vectors. To fully explore the DNA vector-based shRNA-expression systems in RNAi-mediated gene-silencing techniques, four distinct RNA polymerase III (Pol III)-controlled type III promoter-based expression vectors are constructed including pHsH1, pHsU6, pMmH1, and pMmU6, which contain either the RNase P RNA H1 (H1) or small nuclear RNA U6 (U6) promoter from human and mouse. Moreover, to improve the constructing and screening efficiency for the shRNA-expression recombinant clones, these four DNA vectors are further reconstructed by inserting a stuffer of puromycin resistance gene (PuroR) between restriction enzyme ClaI and HindIII sites, which makes the preparation of vectors easy and simple for cloning the shRNA-expression sequences. Because of the ease, speed, and cost efficiency, these four improved DNA vector-based shRNA-expression vectors provide a simple, convenient, and efficient gene-silencing system for analyzing specific gene functions in mammalian cells. Herein, the simple and practical procedures for the construction of DNA vector-based expression vectors, potential and rational design rules for the selection of effective RNAi-targeting sequences, efficient and cost-effective cloning strategies for the construction of shRNA-expression cassettes, and effective and functional activity assays for the evaluation of expressed shRNAs are described.
Collapse
Affiliation(s)
- Tsung-Lin Cheng
- National Cheng Kung University Medical College, Tainan, Taiwan
| | | |
Collapse
|
215
|
Abstract
RNA interference (RNAi) is an adaptive defense mechanism through which double stranded RNAs silence cognate genes in a sequence-specific manner. It has been employed widely as a powerful tool in functional genomics studies, target validation and therapeutic product development. Similarly, the application of small interfering RNA (siRNA) to the silencing of the disease-causing genes involved in cardiovascular diseases has made great progress. In this overview, we attempt to provide a brief outline of the current understanding of the mechanism of RNAi and its potential application to the cardiovascular system, with particular emphasis on its ability to identify the pathophysiological function of genes related to several important cardiovascular disorders. The prospects of RNAi-based therapeutics, as well as the advantages and potential problems, are also discussed.
Collapse
Affiliation(s)
- Yu Tang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | | | | |
Collapse
|
216
|
Yigit E, Batista PJ, Bei Y, Pang KM, Chen CCG, Tolia NH, Joshua-Tor L, Mitani S, Simard MJ, Mello CC. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell 2006; 127:747-57. [PMID: 17110334 DOI: 10.1016/j.cell.2006.09.033] [Citation(s) in RCA: 463] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Revised: 08/30/2006] [Accepted: 09/28/2006] [Indexed: 11/15/2022]
Abstract
Argonaute (AGO) proteins interact with small RNAs to mediate gene silencing. C. elegans contains 27 AGO genes, raising the question of what roles these genes play in RNAi and related gene-silencing pathways. Here we describe 31 deletion alleles representing all of the previously uncharacterized AGO genes. Analysis of single- and multiple-AGO mutant strains reveals functions in several pathways, including (1) chromosome segregation, (2) fertility, and (3) at least two separate steps in the RNAi pathway. We show that RDE-1 interacts with trigger-derived sense and antisense RNAs to initiate RNAi, while several other AGO proteins interact with amplified siRNAs to mediate downstream silencing. Overexpression of downstream AGOs enhances silencing, suggesting that these proteins are limiting for RNAi. Interestingly, these AGO proteins lack key residues required for mRNA cleavage. Our findings support a two-step model for RNAi, in which functionally and structurally distinct AGOs act sequentially to direct gene silencing.
Collapse
Affiliation(s)
- Erbay Yigit
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
217
|
Wang YT, Yang WJ, Li CL, Doudeva LG, Yuan HS. Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases. Nucleic Acids Res 2006; 35:584-94. [PMID: 17175542 PMCID: PMC1802626 DOI: 10.1093/nar/gkl621] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 08/08/2006] [Accepted: 08/08/2006] [Indexed: 12/03/2022] Open
Abstract
Nonspecific endonucleases hydrolyze DNA without sequence specificity but with sequence preference, however the structural basis for cleavage preference remains elusive. We show here that the nonspecific endonuclease ColE7 cleaves DNA with a preference for making nicks after (at 3'O-side) thymine bases but the periplasmic nuclease Vvn cleaves DNA more evenly with little sequence preference. The crystal structure of the 'preferred complex' of the nuclease domain of ColE7 bound to an 18 bp DNA with a thymine before the scissile phosphate had a more distorted DNA phosphate backbone than the backbones in the non-preferred complexes, so that the scissile phosphate was compositionally closer to the endonuclease active site resulting in more efficient DNA cleavage. On the other hand, in the crystal structure of Vvn in complex with a 16 bp DNA, the DNA phosphate backbone was similar and not distorted in comparison with that of a previously reported complex of Vvn with a different DNA sequence. Taken together these results suggest a general structural basis for the sequence-dependent DNA cleavage catalyzed by nonspecific endonucleases, indicating that nonspecific nucleases could induce DNA to deform to distinctive levels depending on the local sequence leading to different cleavage rates along the DNA chain.
Collapse
Affiliation(s)
- Yi-Ting Wang
- Institute of Molecular Biology, Academia SinicaTaipei, Taiwan 11529, Republic of China
- Institute of Biochemistry, National Yang-Ming UniversityTaipei, Taiwan, Republic of China
| | - Wei-Jen Yang
- Institute of Molecular Biology, Academia SinicaTaipei, Taiwan 11529, Republic of China
| | - Chia-Lung Li
- Institute of Molecular Biology, Academia SinicaTaipei, Taiwan 11529, Republic of China
| | - Lyudmila G. Doudeva
- Institute of Molecular Biology, Academia SinicaTaipei, Taiwan 11529, Republic of China
| | - Hanna S. Yuan
- Institute of Molecular Biology, Academia SinicaTaipei, Taiwan 11529, Republic of China
| |
Collapse
|
218
|
Yu Z, Jian Z, Shen SH, Purisima E, Wang E. Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic Acids Res 2006; 35:152-64. [PMID: 17158157 PMCID: PMC1802562 DOI: 10.1093/nar/gkl1032] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding small RNAs of ∼22 nt that regulate the gene expression by base pairing with target mRNAs, leading to mRNA cleavage or translational repression. It is currently estimated that miRNAs account for ∼1% of predicted genes in higher eukaryotic genomes and that up to 30% of genes might be regulated by miRNAs. However, only very few miRNAs have been functionally characterized and the general functions of miRNAs are not globally studied. In this study, we systematically analyzed the expression patterns of miRNA targets using several public microarray profiles. We found that the expression levels of miRNA targets are lower in all mouse and Drosophila tissues than in the embryos. We also found miRNAs more preferentially target ubiquitously expressed genes than tissue-specifically expressed genes. These results support the current suggestion that miRNAs are likely to be largely involved in embryo development and maintaining of tissue identity.
Collapse
Affiliation(s)
- Zhenbao Yu
- To whom correspondence should be addressed. Tel: +514 496 6377; Fax: +514 496 6319;
| | - Zhaofeng Jian
- Computational Chemistry & Biology Group, Biotechnology Research Institute, National Research Council CanadaMontreal, Quebec, H4P 2R2, Canada
| | | | - Enrico Purisima
- Computational Chemistry & Biology Group, Biotechnology Research Institute, National Research Council CanadaMontreal, Quebec, H4P 2R2, Canada
| | - Edwin Wang
- Computational Chemistry & Biology Group, Biotechnology Research Institute, National Research Council CanadaMontreal, Quebec, H4P 2R2, Canada
- To whom correspondence should be addressed. Tel: +514 496 6377; Fax: +514 496 6319;
| |
Collapse
|
219
|
Shi H, Tschudi C, Ullu E. An unusual Dicer-like1 protein fuels the RNA interference pathway in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2006; 12:2063-72. [PMID: 17053086 PMCID: PMC1664728 DOI: 10.1261/rna.246906] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
RNA interference (RNAi) is an evolutionarily conserved gene-silencing pathway that is triggered by double-stranded RNA (dsRNA). Central to this pathway are two ribonucleases: Dicer, a multidomain RNase III family enzyme that initiates RNAi by generating small interfering RNAs (siRNAs), and Argonaute or Slicer, an RNase H signature enzyme that affects cleavage of mRNA. Previous studies in the early diverging protozoan Trypanosoma brucei have established a key role for Argonaute 1 in RNAi. However, the identity of Dicer has not been resolved. Here, we report the identification and functional characterization of a T. brucei Dicer-like enzyme (TbDcl1). Using genetic and biochemical approaches, we provide evidence that TbDcl1 is required for the generation of siRNA-size molecules and for RNAi. Whereas Dicer and Dicer-like proteins are endowed with two adjacent RNase III domains at the carboxyl terminus (RNase IIIa and RNase IIIb), the arrangement of these two domains is unusual in TbDcl1. RNase IIIa is close to the amino terminus, and RNase IIIb is located approximately in the center of the molecule. This domain organization is specific to trypanosomatids and further illustrates the variable structures of protozoan Dicer-like proteins as compared to fungal and metazoan Dicer.
Collapse
Affiliation(s)
- Huafang Shi
- Department of Internal Medicine, Yale University Medical School, New Haven, Connecticut 06536-0812, USA
| | | | | |
Collapse
|
220
|
Cui Q, Yu Z, Pan Y, Purisima EO, Wang E. MicroRNAs preferentially target the genes with high transcriptional regulation complexity. Biochem Biophys Res Commun 2006; 352:733-8. [PMID: 17141185 DOI: 10.1016/j.bbrc.2006.11.080] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 11/15/2006] [Indexed: 01/26/2023]
Abstract
Over the past few years, microRNAs (miRNAs) have emerged as a new prominent class of gene regulatory factors that negatively regulate expression of approximately one-third of the genes in animal genomes at post-transcriptional level. However, it is still unclear why some genes are regulated by miRNAs but others are not, i.e. what principles govern miRNA regulation in animal genomes. In this study, we systematically analyzed the relationship between transcription factors (TFs) and miRNAs in gene regulation. We found that the genes with more TF-binding sites have a higher probability of being targeted by miRNAs and have more miRNA-binding sites on average. This observation reveals that the genes with higher cis-regulation complexity are more coordinately regulated by TFs at the transcriptional level and by miRNAs at the post-transcriptional level. This is a potentially novel discovery of mechanism for coordinated regulation of gene expression. Gene ontology analysis further demonstrated that such coordinated regulation is more popular in the developmental genes.
Collapse
Affiliation(s)
- Qinghua Cui
- Biotechnology Research Institute, National Research Council Canada, Montreal, Que., Canada H4P 2R2
| | | | | | | | | |
Collapse
|
221
|
Cui XS, Shen XH, Kim NH. Dicer1 expression in preimplantation mouse embryos: Involvement of Oct3/4 transcription at the blastocyst stage. Biochem Biophys Res Commun 2006; 352:231-6. [PMID: 17113034 DOI: 10.1016/j.bbrc.2006.11.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 11/03/2006] [Indexed: 12/31/2022]
Abstract
Dicer1, an RNAse III enzyme, is a key factor for the production of microRNAs involved in post-transcriptional gene silencing. To elucidate the roles of Dicer1 and the microRNA pathway in early embryo development, we initially evaluated its gene expression in mouse oocytes and embryos in vitro. The transcript levels in GV stage oocytes steadily decreased up to the 2-cell embryo stage, and expression remained stable during morulae and blastocyst formation. DICER1 protein synthesis was additionally observed in mouse oocytes and early embryos. Silencing of mRNA expression by RNA interference (siRNA) did not inhibit development up to the blastocyst stage. Real-time RT-PCR experiments confirmed the decreased expression of selected transcription factors, including POU domain, class 5, transcription factor 1 (Pou5f1), SRY-box containing gene 2 (Sox2), and Nanog homeobox (Nanog). Moreover, POU5F1 protein expression was suppressed by Dicer1 siRNA. The results suggest that Dicer1 gene expression is associated with the levels of transcription factors, Pou5f1, Sox2, and Nanog which possibly regulate differentiation processes at the blastocyst stage.
Collapse
Affiliation(s)
- Xiang-Shun Cui
- National Research Laboratory, Department of Animal Sciences, Chungbuk National University, Gaesin-dong, Cheongju, Chungbuk 361-763, Seoul, Republic of Korea
| | | | | |
Collapse
|
222
|
Kanneganti TD, Body-Malapel M, Amer A, Park JH, Whitfield J, Franchi L, Taraporewala ZF, Miller D, Patton JT, Inohara N, Núñez G. Critical role for Cryopyrin/Nalp3 in activation of caspase-1 in response to viral infection and double-stranded RNA. J Biol Chem 2006; 281:36560-8. [PMID: 17008311 DOI: 10.1074/jbc.m607594200] [Citation(s) in RCA: 528] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Viral infection induces the production of interleukin (IL)-1beta and IL-18 in macrophages through the activation of caspase-1, but the mechanism by which host cells sense viruses to induce caspase-1 activation is unknown. In this report, we have identified a signaling pathway leading to caspase-1 activation that is induced by double-stranded RNA (dsRNA) and viral infection that is mediated by Cryopyrin/Nalp3. Stimulation of macrophages with dsRNA, viral RNA, or its analog poly(I:C) induced the secretion of IL-1beta and IL-18 in a cryopyrin-dependent manner. Consistently, caspase-1 activation triggered by poly(I:C), dsRNA, and viral RNA was abrogated in macrophages lacking cryopyrin or the adaptor ASC (apoptosis-associated speck-like protein containing a caspase-activating and recruitment domain) but proceeded normally in macrophages deficient in Toll-like receptor 3 or 7. We have also shown that infection with Sendai and influenza viruses activates the cryopyrin inflammasome. Finally, cryopyrin was required for IL-1beta production in response to poly(I:C) in vivo. These results identify a mechanism mediated by cryopyrin and ASC that links dsRNA and viral infection to caspase-1 activation resulting in IL-1beta and IL-18 production.
Collapse
Affiliation(s)
- Thirumala-Devi Kanneganti
- Department of Pathology and Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
223
|
Jonstrup SP, Koch J, Kjems J. A microRNA detection system based on padlock probes and rolling circle amplification. RNA (NEW YORK, N.Y.) 2006; 12:1747-52. [PMID: 16888321 PMCID: PMC1557702 DOI: 10.1261/rna.110706] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The differential expression and the regulatory roles of microRNAs (miRNAs) are being studied intensively these years. Their minute size of only 19-24 nucleotides and strong sequence similarity among related species call for enhanced methods for reliable detection and quantification. Moreover, miRNA expression is generally restricted to a limited number of specific cells within an organism and therefore requires highly sensitive detection methods. Here we present a simple and reliable miRNA detection protocol based on padlock probes and rolling circle amplification. It can be performed without specialized equipment and is capable of measuring the content of specific miRNAs in a few nanograms of total RNA.
Collapse
Affiliation(s)
- Søren Peter Jonstrup
- Department of Molecular Biology, University of Aarhus, C.F. Møllers Allé, DK-8000 Arhus C, Denmark
| | | | | |
Collapse
|
224
|
Guo S, Huang F, Guo P. Construction of folate-conjugated pRNA of bacteriophage phi29 DNA packaging motor for delivery of chimeric siRNA to nasopharyngeal carcinoma cells. Gene Ther 2006; 13:814-20. [PMID: 16482206 PMCID: PMC2840388 DOI: 10.1038/sj.gt.3302716] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nasopharyngeal carcinoma is a poorly differentiated upper respiratory tract cancer that highly expresses human folate receptors (hFR). Binding of folate to hFR triggers endocytosis. The folate was conjugated into adenosine 5'-monophosphate (AMP) by 1,6-hexanediamine linkages. After reverse HPLC to reach 93% purity, the folate-AMP, which can only be used for transcription initiation but not for chain extension, was incorporated into the 5'-end of bacteriophage phi29 motor pRNA. A 16:1 ratio of folate-AMP to ATP in transcription resulted in more than 60% of the pRNA containing folate. A pRNA with a 5'-overhang is needed to enhance the accessibility of the 5' folate for specific receptor binding. Utilizing the engineered left/right interlocking loops, polyvalent dimeric pRNA nanoparticles were constructed using RNA nanotechnology to carry folate, a detection marker, and siRNA targeting at an antiapoptosis factor. The chimeric pRNAs were processed into ds-siRNA by Dicer. Incubation of nasopharyngeal epidermal carcinoma (KB) cells with the dimer resulted in its entry into cancer cells, and the subsequent silencing of the target gene. Such a protein-free RNA nanoparticle with undetectable antigenicity has a potential for repeated long-term administration for nasopharyngeal carcinoma as the effectiveness and specificity were confirmed by ex vivo delivery in the animal trial.
Collapse
Affiliation(s)
- S Guo
- Department of Pathobiology and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - F Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS, USA
| | - P Guo
- Department of Pathobiology and Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
225
|
Pertzev AV, Nicholson AW. Characterization of RNA sequence determinants and antideterminants of processing reactivity for a minimal substrate of Escherichia coli ribonuclease III. Nucleic Acids Res 2006; 34:3708-21. [PMID: 16896014 PMCID: PMC1540722 DOI: 10.1093/nar/gkl459] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Members of the ribonuclease III family are the primary agents of double-stranded (ds) RNA processing in prokaryotic and eukaryotic cells. Bacterial RNase III orthologs cleave their substrates in a highly site-specific manner, which is necessary for optimal RNA function or proper decay rates. The processing reactivities of Escherichia coli RNase III substrates are determined in part by the sequence content of two discrete double-helical elements, termed the distal box (db) and proximal box (pb). A minimal substrate of E.coli RNase III, μR1.1 RNA, was characterized and used to define the db and pb sequence requirements for reactivity and their involvement in cleavage site selection. The reactivities of μR1.1 RNA sequence variants were examined in assays of cleavage and binding in vitro. The ability of all examined substitutions in the db to inhibit cleavage by weakening RNase III binding indicates that the db is a positive determinant of RNase III recognition, with the canonical UA/UG sequence conferring optimal recognition. A similar analysis showed that the pb also functions as a positive recognition determinant. It also was shown that the ability of the GC or CG bp substitution at a specific position in the pb to inhibit RNase III binding is due to the purine 2-amino group, which acts as a minor groove recognition antideterminant. In contrast, a GC or CG bp at the pb position adjacent to the scissile bond can suppress cleavage without inhibiting binding, and thus act as a catalytic antideterminant. It is shown that a single pb+db ‘set’ is sufficient to specify a cleavage site, supporting the primary function of the two boxes as positive recognition determinants. The base pair sequence control of reactivity is discussed within the context of new structural information on a post-catalytic complex of a bacterial RNase III bound to the cleaved minimal substrate.
Collapse
Affiliation(s)
| | - Allen W. Nicholson
- To whom correspondence should be addressed. Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, PA 19122, USA. Tel: +1 215 204 9048; Fax: +1 215 204 1532;
| |
Collapse
|
226
|
Cesarone G, Garofalo C, Abrams MT, Igoucheva O, Alexeev V, Yoon K, Surmacz E, Wickstrom E. RNAi-mediated silencing of insulin receptor substrate 1 (IRS-1) enhances tamoxifen-induced cell death in MCF-7 breast cancer cells. J Cell Biochem 2006; 98:440-50. [PMID: 16440325 DOI: 10.1002/jcb.20817] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Insulin receptor substrate 1 (IRS-1) is a major downstream signaling protein for insulin and insulin-like growth factor I (IGF-I) receptors, conveying signals to PI-3K/Akt and ERK1/2 pathways. In breast cancer, IRS-1 overexpression has been associated with tumor development, hormone-independence and antiestrogen-resistance. In part, these effects are related to potentiation of IRS-1/PI-3K/Akt signaling. In estrogen sensitive breast cancer cell lines, tamoxifen treatment reduces IRS-1 expression and function; consequently, inhibiting IRS-1/PI-3K signaling. We tested whether anti-IRS1 siRNA could inhibit growth and survival of estrogen-sensitive MCF-7 breast cancer cells, when used alone or in combination with TAM. Our results indicated: (a) out of four tested anti-IRS1 siRNAs, two siRNAs reduced IRS-1 protein by approximately three-fold in both growing and IGF-I-stimulated cells without affecting a closely related protein, IRS-2; (b) these effects paralleled IRS1 mRNA downregulation by approximately three-fold, measured by quantitative real time-polymerase chain reaction; (c) action of anti-IRS1 siRNAs induced the apoptotic response, observed by altered mitochondrial membrane potential coupled with downregulation of NF-kappaB target Bcl-xL and reduced cell viability; (d) anti-IRS1 siRNA treatment enhanced the cytotoxic effects of TAM by approximately 20%. In summary, anti-IRS1 RNAi strategy could become a potent tool to induce breast cancer cell death, especially if combined with standard TAM therapy.
Collapse
Affiliation(s)
- Gregory Cesarone
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | | | | | | | | | | | | | | |
Collapse
|
227
|
Wannenes F, Ciafré SA, Niola F, Frajese G, Farace MG. Vector-based RNA interference against vascular endothelial growth factor-A significantly limits vascularization and growth of prostate cancer in vivo. Cancer Gene Ther 2006; 12:926-34. [PMID: 15956982 DOI: 10.1038/sj.cgt.7700862] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RNA interference technology is emerging as a very potent tool to obtain a cellular knockdown of a desired gene. In this work we used vector-based RNA interference to inhibit vascular endothelial growth factor (VEGF) expression in prostate cancer in vitro and in vivo. We demonstrated that transduction with a plasmid carrying a small interfering RNA targeting all isoforms of VEGF, dramatically impairs the expression of this growth factor in the human prostate cancer cell line PC3. As a consequence, PC3 cells loose their ability to induce one of the fundamental steps of angiogenesis, namely the formation of a tube-like network in vitro. Most importantly, our "therapeutic" vector is able to impair tumor growth rate and vascularization in vivo. We show that a single injection of naked plasmid in developing neoplastic mass significantly decreases microvessel density in an androgen-refractory prostate xenograft and is able to sustain a long-term slowing down of tumor growth. In conclusion, our results confirm the basic role of VEGF in the angiogenic development of prostate carcinoma, and suggest that the use of our vector-based RNA interference approach to inhibit angiogenesis could be an effective tool in view of future gene therapy applications for prostate cancer.
Collapse
Affiliation(s)
- Francesca Wannenes
- Department of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | | | | | | | | |
Collapse
|
228
|
Bergstrom K, Urquhart JC, Tafech A, Doyle E, Lee CH. Purification and characterization of a novel mammalian endoribonuclease. J Cell Biochem 2006; 98:519-37. [PMID: 16317762 DOI: 10.1002/jcb.20726] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Endonuclease-mediated mRNA decay appears to be a common mode of mRNA degradation in mammalian cells, but yet only a few mRNA endonucleases have been described. Here, we report the existence of a second mammalian endonuclease that is capable of cleaving c-myc mRNA within the coding region in vitro. This study describes the partial purification and biochemical characterization of this enzyme. Five major proteins of approximately 10-35 kDa size co-purified with the endonuclease activity, a finding supported by gel filtration and glycerol gradient centrifugation analysis. The enzyme is an RNA-specific endonuclease that degrades single-stranded RNA, but not double-stranded RNA, DNA or DNA-RNA duplexes. It preferentially cleaves RNA in between the pyrimidine and purine dinucleotides UA, UG, and CA, at the coding region determinant (CRD) of c-myc RNA. The enzyme generates products with a 3'hydroxyl group, and it appears to be a protein-only endonuclease. It does not possess RNase A-like activity. The enzyme is capable of cleaving RNAs other than c-myc CRD RNA in vitro. It is Mg(2+)-independent and is resistant to EDTA. The endonuclease is inactivated at and above 70 degrees C. These properties distinguished the enzyme from other previously described vertebrate endonucleases.
Collapse
Affiliation(s)
- Kirk Bergstrom
- Chemistry Program, University of Northern British Columbia, 3333 University Way, Prince George, BC V2N 4Z9, Canada
| | | | | | | | | |
Collapse
|
229
|
Abstract
RNA-mediated interference (RNAi) is a recently discovered process by which dsRNA is able to silence specific gene functions. Although initially described in plants, nematodes and Drosophila, the process is currently considered to be an evolutionarily conserved process that is present in the entire eukaryotic kingdom in which its original function was as a defense mechanism against viruses and foreign nucleic acids. Similarly to the silencing of genes by RNAi, viral functions can be also silenced by the same mechanism, through the introduction of specific dsRNA molecules into cells, where they are targeted to essential genes or directly to the viral genome in case RNA viruses, thus arresting viral replication. Since the pioneering work of Elbashir and coworkers, who identified RNAi activity in mammalian cells, many publications have described the inhibition of viruses belonging to most if not all viral families, by targeting and silencing diverse viral genes as well as cell genes that are essential for virus replication. Moreover, virus expression vectors were developed and used as vehicles with which to deliver siRNAs into cells. This review will describe the use of RNAi to inhibit virus replication directly, as well as through the silencing of the appropriate cell functions.
Collapse
Affiliation(s)
- Yehuda Stram
- Virology Division, Kimron Veterinary institute, 12, 50250, Beit-Dagan, Israel.
| | | |
Collapse
|
230
|
Bracha R, Nuchamowitz Y, Anbar M, Mirelman D. Transcriptional silencing of multiple genes in trophozoites of Entamoeba histolytica. PLoS Pathog 2006; 2:e48. [PMID: 16733544 PMCID: PMC1464398 DOI: 10.1371/journal.ppat.0020048] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 04/10/2006] [Indexed: 01/19/2023] Open
Abstract
In a previous work we described the transcriptional silencing of the amoebapore A (AP-A) gene (Ehap-a) of Entamoeba histolytica strain HM-1:IMSS. The silencing occurred following transfection with a plasmid containing a 5′ upstream region (473 bp) of Ehap-a that included a truncated segment (140 bp) of a short interspersed nuclear element (SINE1). Silencing remained in effect even after removal of the plasmid (clone G3). Neither short interfering RNA nor methylated DNA were detected, but the chromatin domain of Ehap-a in the gene-silenced trophozoites was modified. Two other similar genes (Ehap-b and one encoding a Saposin-like protein, SAPLIP 1) also became silenced. In the present work we demonstrate the silencing of a second gene of choice, one that encodes the light subunit of the Gal/GalNAc inhibitable lectin (Ehlgl1) and the other, the cysteine proteinase 5 (EhCP-5). This silencing occurred in G3 trophozoites transfected with a plasmid in which the 473 bp 5′ upstream Ehap-a fragment was directly ligated to the second gene. Transcriptional silencing occurred in both the transgene and the chromosomal gene. SINE1 sequences were essential, as was a direct connection between the Ehap-a upstream region and the beginning of the open reading frame of the second gene. Gene silencing did not occur in strain HM-1:IMSS with any of these plasmid constructs. The trophozoites with two silenced genes were virulence-attenuated as were those of clone G3. In addition, trophozoites not expressing Lgl1 and AP-A proteins had a significantly reduced ability to cap the Gal/GalNAc-lectin to the uroid region when incubated with antibodies against the heavy (170 kDa) subunit of the lectin. Lysates of trophozoites lacking cysteine proteinase 5 and AP-A proteins had 30% less cysteine proteinase activity than those of HM-1:IMSS strain or the G3 clone. Silencing of other genes in G3 amoebae could provide a model to study their various functions. In addition, double gene-silenced, virulence-attenuated trophozoites may be an important tool in vaccine development. The human intestinal parasite Entamoeba histolytica has numerous genes that code for virulence. Silencing the expression of individual genes is useful to determine their roles. In previous work the authors demonstrated the silencing of the gene coding for amoebapore, which is responsible for killing of human cells. They transfected amoebic trophozoites with a plasmid that contained DNA sequences homologous to the promoter region of the amoebapore gene, as well as a portion of a repetitive DNA element (called a short interspersed nuclear element). This construct induced a modification of the chromatin and prevented the expression of the gene. Removal of the plasmid resulted in stable, amoebapore-deficient parasites possessing low virulence. In the present work, Bracha and colleagues show silencing of additional genes following transfection of E. histolytica trophozoites already silenced in amoebapore with a plasmid containing the second gene directly ligated to the upstream region of the amoebapore gene. The DNA sequences that are essential for transferring the silencing from the plasmid to the chromosomal gene copy were identified. Additional virulence genes that the authors irreversibly silenced are those encoding a subunit of a surface lectin that mediates the adherence of the parasite to host cells, and a cysteine proteinase that plays a role in inflammation and invasion of the intestine.
Collapse
Affiliation(s)
- Rivka Bracha
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Nuchamowitz
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Anbar
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - David Mirelman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
231
|
Janzen CJ, van Deursen F, Shi H, Cross GA, Matthews KR, Ullu E. Expression site silencing and life-cycle progression appear normal in Argonaute1-deficient Trypanosoma brucei. Mol Biochem Parasitol 2006; 149:102-107. [PMID: 16735068 PMCID: PMC3904126 DOI: 10.1016/j.molbiopara.2006.04.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2006] [Revised: 04/01/2006] [Accepted: 04/07/2006] [Indexed: 11/19/2022]
Affiliation(s)
- Christian J. Janzen
- Laboratory of Molecular Parasitology, The Rockefeller University, Box 185, 1230 York Avenue, New York, NY 10021-6399, USA
| | - Frederick van Deursen
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
| | - Huafang Shi
- Department of Internal Medicine, Yale Medical School, BCMM 136D, 295 Congress Avenue, Box 9812, New Haven, CT, 06536-8012, USA
| | - George A.M. Cross
- Laboratory of Molecular Parasitology, The Rockefeller University, Box 185, 1230 York Avenue, New York, NY 10021-6399, USA
| | - Keith R. Matthews
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JT, UK
| | - Elisabetta Ullu
- Department of Internal Medicine, Yale Medical School, BCMM 136D, 295 Congress Avenue, Box 9812, New Haven, CT, 06536-8012, USA
- Department of Cell Biology, Yale Medical School, BCMM 136D, 295 Congress Avenue, Box 9812, New Haven, CT, 06536-8012, USA
- Corresponding author. Tel.: +203 785 3563; fax: +203 785 7329.
| |
Collapse
|
232
|
Parker GS, Eckert DM, Bass BL. RDE-4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA. RNA (NEW YORK, N.Y.) 2006; 12:807-18. [PMID: 16603715 PMCID: PMC1440910 DOI: 10.1261/rna.2338706] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA-binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not required in subsequent steps, and how RDE-4 distinguishes between long dsRNA and short siRNA is unclear. We report the first detailed analysis of RDE-4 binding, using purified recombinant RDE-4 and various truncated proteins. We find that, similar to other dsRBPs, RDE-4 is not sequence-specific. However, consistent with its in vivo roles, RDE-4 binds with higher affinity to long dsRNA. We also observe that RDE-4 is a homodimer in solution, and that the C-terminal domain of the protein is required for dimerization. Using extracts from wild-type and rde-4 mutant C. elegans, we show that the C-terminal dimerization domain is required for the production of siRNA. Our findings suggest a model for RDE-4 function during the initiation of RNAi.
Collapse
Affiliation(s)
- Greg S Parker
- Department of Biochemistry/HHMI, University of Utah, Salt Lake City 84112-5650, USA
| | | | | |
Collapse
|
233
|
Chilibeck KA, Wu T, Liang C, Schellenberg MJ, Gesner EM, Lynch JM, MacMillan AM. FRET analysis of in vivo dimerization by RNA-editing enzymes. J Biol Chem 2006; 281:16530-5. [PMID: 16618704 DOI: 10.1074/jbc.m511831200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the ADAR (adenosine deaminase that acts on RNA) enzyme family catalyze the hydrolytic deamination of adenosine to inosine within double-stranded RNAs, a poorly understood process that is critical to mammalian development. We have performed fluorescence resonance energy transfer experiments in mammalian cells transfected with fluorophore-bearing ADAR1 and ADAR2 fusion proteins to investigate the relationship between these proteins. These studies conclusively demonstrate the homodimerization of ADAR1 and ADAR2 and also show that ADAR1 and ADAR2 form heterodimers in human cells. RNase treatment of cells expressing these fusion proteins changes their localization but does not affect dimerization. Taken together these results suggest that homo- and heterodimerization are important for the activity of ADAR family members in vivo and that these associations are RNA independent.
Collapse
Affiliation(s)
- Kaari A Chilibeck
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | | | | | | | | | | | | |
Collapse
|
234
|
Margis R, Fusaro AF, Smith NA, Curtin SJ, Watson JM, Finnegan EJ, Waterhouse PM. The evolution and diversification of Dicers in plants. FEBS Lett 2006; 580:2442-50. [PMID: 16638569 DOI: 10.1016/j.febslet.2006.03.072] [Citation(s) in RCA: 188] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 03/24/2006] [Accepted: 03/28/2006] [Indexed: 12/30/2022]
Abstract
Most multicellular organisms regulate developmental transitions by microRNAs, which are generated by an enzyme, Dicer. Insects and fungi have two Dicer-like genes, and many animals have only one, yet the plant, Arabidopsis, has four. Examining the poplar and rice genomes revealed that they contain five and six Dicer-like genes, respectively. Analysis of these genes suggests that plants require a basic set of four Dicer types which were present before the divergence of mono- and dicotyledonous plants ( approximately 200 million years ago), but after the divergence of plants from green algae. A fifth type of Dicer seems to have evolved in monocots.
Collapse
Affiliation(s)
- Rogerio Margis
- CSIRO Plant Industry, P.O. Box 1600, Canberra, ACT 2601, Australia
| | | | | | | | | | | | | |
Collapse
|
235
|
Mei YP, Zhu XF, Zhou JM, Huang H, Deng R, Zeng YX. siRNA targeting LMP1-induced apoptosis in EBV-positive lymphoma cells is associated with inhibition of telomerase activity and expression. Cancer Lett 2006; 232:189-98. [PMID: 16458115 DOI: 10.1016/j.canlet.2005.02.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 02/12/2005] [Indexed: 11/22/2022]
Abstract
Epstein-Barr Virus (EBV) is closely associated with B cell malignancies. However, whether EBV appears to be absolutely required for cell proliferation and survival in lymphoma cells is still unknown. In this study, small interfering RNA (siRNA) targeting LMP1 was employed to investigate the effect of LMP1 on cell proliferation in EBV-positive lymphoblastoid B-cell line. A plasmid stable encoding 21-nt small RNA specifically and efficiently interfering LMP1 was constructed, resulting in a substantial loss of LMP1 mRNA and a significantly decreased LMP1 protein expression. Our data demonstrated that cell proliferation was completely inhibited and apoptosis was induced after knockdown of LMP1 gene in lymphoblastoid B-cell line. Also, we found that suppression of LMP1 caused downregulation of telomerase protein expression and decreased telomerase activity in lymphoma cells. In EBV-negative NPC cell line, transfection of plasmid expressing LMP1 greatly enhanced telomerase protein expression. Our results suggested that siRNA targeting LMP1 can induce apoptosis in EBV-positive lymphoma cells and is associated with inhibition of telomerase activity and expression. siRNA-directed LMP1 silencing may be of the therapeutic value for preventing and treating those EBV-associated tumors.
Collapse
Affiliation(s)
- Yu-Ping Mei
- Department of Experimental Research, State Key Laboratory of Oncology in Southern China, Cancer Center, Sun Yat-sen University, 651 DongFeng Road East, GuangZhou 510060, China
| | | | | | | | | | | |
Collapse
|
236
|
Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 2006; 20:515-24. [PMID: 16510870 DOI: 10.1101/gad.1399806] [Citation(s) in RCA: 1574] [Impact Index Per Article: 87.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The control of translation and mRNA degradation is an important part of the regulation of gene expression. It is now clear that small RNA molecules are common and effective modulators of gene expression in many eukaryotic cells. These small RNAs that control gene expression can be either endogenous or exogenous micro RNAs (miRNAs) and short interfering RNAs (siRNAs) and can affect mRNA degradation and translation, as well as chromatin structure, thereby having impacts on transcription rates. In this review, we discuss possible mechanisms by which miRNAs control translation and mRNA degradation. An emerging theme is that miRNAs, and siRNAs to some extent, target mRNAs to the general eukaryotic machinery for mRNA degradation and translation control.
Collapse
Affiliation(s)
- Marco Antonio Valencia-Sanchez
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of Arizona, Tucson, Arizona 85721, USA
| | | | | | | |
Collapse
|
237
|
Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. Structural basis for double-stranded RNA processing by Dicer. Science 2006; 311:195-8. [PMID: 16410517 DOI: 10.1126/science.1121638] [Citation(s) in RCA: 654] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end.
Collapse
Affiliation(s)
- Ian J Macrae
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | | | | | | | | | | | | | | |
Collapse
|
238
|
Drider D, Condon C. The continuing story of endoribonuclease III. J Mol Microbiol Biotechnol 2005; 8:195-200. [PMID: 16179796 DOI: 10.1159/000086700] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Endoribonuclease III (RNase III) plays an important role in the processing of rRNA and mRNAs. It is timely to summarize the most relevant insights obtained during the last years stemming from RNase III. With this aim, the present mini-review provides a wealth of new information focusing on the distribution and architecture of RNase III, substrate recognition, cleavage mechanisms and regulation of gene expression.
Collapse
Affiliation(s)
- Djamel Drider
- Laboratoire de Microbiologie Alimentaire et Industrielle, ENITIAA, Rue de la Géraudière BP 82225, FR-44322 Nantes Cedex, France.
| | | |
Collapse
|
239
|
Hung CF, Cheng TL, Wu RH, Teng CF, Chang WT. A novel bidirectional expression system for simultaneous expression of both the protein-coding genes and short hairpin RNAs in mammalian cells. Biochem Biophys Res Commun 2005; 339:1035-42. [PMID: 16337609 DOI: 10.1016/j.bbrc.2005.11.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Accepted: 11/17/2005] [Indexed: 10/25/2022]
Abstract
RNA interference (RNAi) is an extremely powerful and widely used gene silencing approach for reverse functional genomics and molecular therapeutics. In mammals, the conserved poly(ADP-ribose) polymerase 2 (PARP-2)/RNase P bidirectional control promoter simultaneously expresses both the PARP-2 protein and RNase P RNA by RNA polymerase II- and III-dependent mechanisms, respectively. To explore this unique bidirectional control system in RNAi-mediated gene silencing strategy, we have constructed two novel bidirectional expression vectors, pbiHsH1 and pbiMmH1, which contained the PARP-2/RNase P bidirectional control promoters from human and mouse, for simultaneous expression of both the protein-coding genes and short hairpin RNAs. Analyses of the dual transcriptional activities indicated that these two bidirectional expression vectors could not only express enhanced green fluorescent protein as a functional reporter but also simultaneously transcribe shLuc for inhibiting the firefly luciferase expression. In addition, to extend its utility for the establishment of inherited stable clones, we have also reconstructed this bidirectional expression system with the blasticidin S deaminase gene, an effective dominant drug resistance selectable marker, and examined both the selection and inhibition efficiencies in drug resistance and gene expression. Moreover, we have further demonstrated that this bidirectional expression system could efficiently co-regulate the functionally important genes, such as overexpression of tumor suppressor protein p53 and inhibition of anti-apoptotic protein Bcl-2 at the same time. In summary, the bidirectional expression vectors, pbiHsH1 and pbiMmH1, should provide a simple, convenient, and efficient novel tool for manipulating the gene function in mammalian cells.
Collapse
Affiliation(s)
- Chuan-Fu Hung
- Department of Biochemistry and Molecular Biology, National Cheng Kung University Medical College, No. 1, University Road, Tainan 701, Taiwan, ROC
| | | | | | | | | |
Collapse
|
240
|
Malone CD, Anderson AM, Motl JA, Rexer CH, Chalker DL. Germ line transcripts are processed by a Dicer-like protein that is essential for developmentally programmed genome rearrangements of Tetrahymena thermophila. Mol Cell Biol 2005; 25:9151-64. [PMID: 16199890 PMCID: PMC1265777 DOI: 10.1128/mcb.25.20.9151-9164.2005] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abundant approximately 28-nucleotide RNAs that are thought to direct histone H3 lysine 9 (H3K9) methylation and promote the elimination of nearly 15 Mbp of DNA from the developing somatic genome are generated during Tetrahymena thermophila conjugation. To identify the protein(s) that generates these small RNAs, we studied three Dicer-related genes encoded within the Tetrahymena genome, two that contain both RNase III and RNA helicase motifs, Dicer 1 (DCR1) and DCR2, and a third that lacks the helicase domain, Dicer-like 1 (DCL1). DCL1 is expressed upon the initiation of conjugation, and the protein localizes to meiotic micronuclei when bidirectional germ line transcription occurs and small RNAs begin to accumulate. Cells in which we disrupted the DCL1 gene (DeltaDCL1) grew normally and initiated conjugation as wild-type cells but arrested near the end of development and eventually died, unable to resume vegetative growth. These DeltaDCL1 cells failed to generate the abundant small RNAs but instead accumulated germ line-limited transcripts. Together, our findings demonstrate that these transcripts are the precursors of the small RNAs and that DCL1 performs RNA processing within the micronucleus. Postconjugation DeltaDCL1 cells die without eliminating the germ line-limited DNA sequences from their newly formed somatic macronuclei, a result that shows that this Dicer-related gene is required for programmed DNA rearrangements. Surprisingly, DeltaDCL1 cells were not deficient in overall H3K9 methylation, but this modification was not enriched on germ line-limited sequences as it is in wild-type cells, which clearly demonstrates that these small RNAs are essential for its targeting to specific loci.
Collapse
Affiliation(s)
- Colin D Malone
- Biology Department, Washington University, St. Louis, MO 63130, USA
| | | | | | | | | |
Collapse
|
241
|
Chen ZX, Riggs AD. Maintenance and regulation of DNA methylation patterns in mammals. Biochem Cell Biol 2005; 83:438-48. [PMID: 16094447 DOI: 10.1139/o05-138] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Proper establishment and faithful maintenance of epigenetic information is crucial for the correct development of complex organisms. For mammals, it is now accepted that DNA methylation is an important mechanism for establishing stable heritable epigenetic marks. The distribution of methylation in the genome is not random, and patterns of methylated and unmethylated DNA are well regulated during normal development. The molecular mechanisms by which methylation patterns are established and maintained are complex and just beginning to be understood. In this review, we summarize recent progress in understanding the regulation of mammalian DNA methylation patterns, with an emphasis on the emerging roles of several protein and possible RNA factors. We also revisit the stochastic model of maintenance methylation and discuss its implications for epigenetic fidelity and gene regulation.
Collapse
Affiliation(s)
- Zhao-xia Chen
- Division of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | |
Collapse
|
242
|
Rand TA, Petersen S, Du F, Wang X. Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 2005; 123:621-9. [PMID: 16271385 DOI: 10.1016/j.cell.2005.10.020] [Citation(s) in RCA: 516] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2005] [Revised: 09/25/2005] [Accepted: 10/03/2005] [Indexed: 01/30/2023]
Abstract
The mRNA-cleavage step of RNA interference is mediated by an endonuclease, Argonaute2 (Ago2), within the RNA-induced silencing complex (RISC). Ago2 uses one strand of the small interfering (si) RNA duplex as a guide to find messenger RNAs containing complementary sequences and cleaves the phosphodiester backbone at a specific site measured from the guide strand's 5' end. Here, we show that both strands of siRNA get loaded onto Ago2 protein in Drosophila S2 cell extracts. The anti-guide strand behaves as a RISC substrate and is cleaved by Ago2. This cleavage event is important for the removal of the anti-guide strand from Ago2 protein and activation of RISC.
Collapse
Affiliation(s)
- Tim A Rand
- Department of Biochemistry, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
| | | | | | | |
Collapse
|
243
|
Huang J, Shi J, Molle V, Sohlberg B, Weaver D, Bibb MJ, Karoonuthaisiri N, Lih CJ, Kao CM, Buttner MJ, Cohen SN. Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor. Mol Microbiol 2005; 58:1276-87. [PMID: 16313616 DOI: 10.1111/j.1365-2958.2005.04879.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A complex programme of regulation governs gene expression during development of the morphologically and biochemically complex eubacterial genus Streptomyces. Earlier work has suggested a model in which 'higher level' pleiotropic regulators activate 'pathway-specific' regulators located within chromosomal gene clusters encoding biosynthesis of individual antibiotics. We used mutational analysis and adventitious overexpression of key Streptomyces coelicolor regulators to investigate functional interactions among them. We report here that cluster-situated regulators (CSRs) thought to be pathway-specific can also control other antibiotic biosynthetic gene clusters, and thus have pleiotropic actions. Surprisingly, we also find that CSRs exhibit growth-phase-dependent control over afsR2/afsS, a 'higher level' pleiotropic regulatory locus not located within any of the chromosomal gene clusters it targets, and further demonstrate that cross-regulation by CSRs is modulated globally and differentially during the S. coelicolor growth cycle by the RNaseIII homologue AbsB. Our results, which reveal a network of functional interactions among regulators that govern production of antibiotics and other secondary metabolites in S. coelicolor, suggest that revision of the currently prevalent view of higher-level versus pathway-specific regulation of secondary metabolism in Streptomyces species is warranted.
Collapse
Affiliation(s)
- Jianqiang Huang
- Department of Genetics, MC 5120, Stanford University, Stanford, CA 94305, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
244
|
Pellino JL, Jaskiewicz L, Filipowicz W, Sontheimer EJ. ATP modulates siRNA interactions with an endogenous human Dicer complex. RNA (NEW YORK, N.Y.) 2005; 11:1719-24. [PMID: 16177131 PMCID: PMC1370858 DOI: 10.1261/rna.2102805] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Short interfering RNA (siRNA) binding by Dicer is important for RNA interference in Drosophila, but human Dicer (hDcr) has been reported to lack siRNA binding activity. We used native gel electrophoresis to characterize the siRNA-binding activity of endogenous hDcr-containing complexes in extracts from human cells. We identified a complex (D) that contains hDcr, as demonstrated by antibody supershift. Complex D appears to contain double-stranded siRNAs, and requires structural features of authentic siRNAs. Glycerol gradient sedimentation indicates that Complex D is ~250 kDa, slightly larger than hDcr alone. In addition, we found that purified recombinant hDcr (rhDcr) alone has siRNA binding activity. Complex D migrates more slowly than the rhDcr/siRNA complex in a native gel, suggesting that it contains at least one additional factor. hDcr directly contacts siRNAs within Complex D, as indicated by crosslinking. The endogenous complex is significantly enhanced by ATP, unlike the siRNA-binding activity of purified rhDcr, suggesting the existence of additional factors that can enforce the ATP dependence of endogenous hDcr/siRNA interactions. Complex D could impinge upon the RISC assembly pathway in humans, similar to an analogous complex in Drosophila.
Collapse
Affiliation(s)
- Janice L Pellino
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208-3500, USA
| | | | | | | |
Collapse
|
245
|
Silva JM, Li MZ, Chang K, Ge W, Golding MC, Rickles RJ, Siolas D, Hu G, Paddison PJ, Schlabach MR, Sheth N, Bradshaw J, Burchard J, Kulkarni A, Cavet G, Sachidanandam R, McCombie WR, Cleary MA, Elledge SJ, Hannon GJ. Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 2005; 37:1281-8. [PMID: 16200065 DOI: 10.1038/ng1650] [Citation(s) in RCA: 474] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Accepted: 08/18/2005] [Indexed: 12/16/2022]
Abstract
Loss-of-function phenotypes often hold the key to understanding the connections and biological functions of biochemical pathways. We and others previously constructed libraries of short hairpin RNAs that allow systematic analysis of RNA interference-induced phenotypes in mammalian cells. Here we report the construction and validation of second-generation short hairpin RNA expression libraries designed using an increased knowledge of RNA interference biochemistry. These constructs include silencing triggers designed to mimic a natural microRNA primary transcript, and each target sequence was selected on the basis of thermodynamic criteria for optimal small RNA performance. Biochemical and phenotypic assays indicate that the new libraries are substantially improved over first-generation reagents. We generated large-scale-arrayed, sequence-verified libraries comprising more than 140,000 second-generation short hairpin RNA expression plasmids, covering a substantial fraction of all predicted genes in the human and mouse genomes. These libraries are available to the scientific community.
Collapse
Affiliation(s)
- Jose M Silva
- Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
246
|
Nordström K. Plasmid R1--replication and its control. Plasmid 2005; 55:1-26. [PMID: 16199086 DOI: 10.1016/j.plasmid.2005.07.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2005] [Revised: 07/04/2005] [Accepted: 07/12/2005] [Indexed: 11/25/2022]
Abstract
Plasmid R1 is a low-copy-number plasmid belonging to the IncFII group. The genetics, biochemistry, molecular biology, and physiology of R1 replication and its control are summarised and discussed in the present communication. Replication of R1 starts at a unique origin, oriR1, and proceeds unidirectionally according to the Theta mode. Plasmid R1 replicates during the entire cell cycle and the R1 copies in the cell are members of a pool from which a plasmid copy at random is selected for replication. However, there is an eclipse period during which a newly replicated copy does not belong to this pool. Replication of R1 is controlled by an antisense RNA, CopA, that is unstable and formed constitutively; hence, its concentration is a measure of the concentration of the plasmid. CopA-RNA interacts with its complementary target, CopT-RNA, that is located upstream of the RepA message on the repA-mRNA. CopA-RNA post-transcriptionally inhibits translation of the repA-mRNA. CopA- and CopT-RNA interact in a bimolecular reaction which results in an inverse proportionality between the relative rate of replication (replications per plasmid copy and cell cycle) and the copy number; the number of replications per cell and cell cycle, n, is independent of the actual copy number in the individual cells, the so-called +n mode of control. Single base-pair substitutions in the copA/copT region of the plasmid genome may result in mutants that are compatible with the wild type. Loss of CopA activity results in (uncontrolled) so-called runaway replication, which is lethal to the host but useful for the production of proteins from cloned genes. Plasmid R1 also has an ancillary control system, CopB, that derepresses the synthesis of repA-mRNA in cells that happen to contain lower than normal number of copies. Plasmid R1, as other plasmids, form clusters in the cell and plasmid replication is assumed to take place in the centre of the cells; this requires traffic from the cluster to the replication factories and back to the clusters. The clusters are plasmid-specific and presumably based on sequence homology.
Collapse
Affiliation(s)
- Kurt Nordström
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, P.O. Box 596, S-751 24 Uppsala, Sweden.
| |
Collapse
|
247
|
Kavi HH, Fernandez HR, Xie W, Birchler JA. RNA silencing inDrosophila. FEBS Lett 2005; 579:5940-9. [PMID: 16198344 DOI: 10.1016/j.febslet.2005.08.069] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 08/26/2005] [Accepted: 08/28/2005] [Indexed: 11/18/2022]
Abstract
Knowledge of the role of RNA in affecting gene expression has expanded in the past several years. Small RNAs serve as homology guides to target messenger RNAs for destruction at the post-transcriptional level in the experimental technique known as RNA interference and in the silencing of some transgenes. These small RNAs are also involved in sequence-specific targeting of chromatin modifications for transcriptional silencing of transgenes, transposable elements, heterochromatin and some cases of Polycomb-mediated gene silencing. RNA silencing processes in Drosophila are described.
Collapse
Affiliation(s)
- Harsh H Kavi
- Division of Biological Sciences, University of Missouri, 117 Tucker Hall, Columbia, MO 65211, USA
| | | | | | | |
Collapse
|
248
|
Affiliation(s)
- Peter A Beal
- University of Utah, Department of Chemistry, Salt Lake City, Utah 84112, USA.
| |
Collapse
|
249
|
Filipowicz W, Jaskiewicz L, Kolb FA, Pillai RS. Post-transcriptional gene silencing by siRNAs and miRNAs. Curr Opin Struct Biol 2005; 15:331-41. [PMID: 15925505 DOI: 10.1016/j.sbi.2005.05.006] [Citation(s) in RCA: 383] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Revised: 02/09/2005] [Accepted: 05/06/2005] [Indexed: 12/12/2022]
Abstract
Recent years have seen a rapid increase in our understanding of how double-stranded RNA (dsRNA) and 21- to 25-nucleotide small RNAs, microRNAs (miRNAs) and small interfering RNAs (siRNAs), control gene expression in eukaryotes. This RNA-mediated regulation generally results in sequence-specific inhibition of gene expression; this can occur at levels as different as chromatin modification and silencing, translational repression and mRNA degradation. Many details of the biogenesis and function of miRNAs and siRNAs, and of the effector complexes with which they associate have been elucidated. The first structural information on protein components of the RNA interference (RNAi) and miRNA machineries is emerging, and provides some insight into the mechanism of RNA-silencing reactions.
Collapse
Affiliation(s)
- Witold Filipowicz
- Friedrich Miescher Institute for Biomedical Research, PO Box 2543, 4002 Basel, Switzerland.
| | | | | | | |
Collapse
|
250
|
Abstract
The vertebrate genome contains hundreds of small non-coding 'microRNAs' that have been implicated in controlling the expression of potentially thousands of target genes. Presently, only a handful of these targets have been characterized. Recent reports of microRNA 'sensors', microRNA microarrays and the creation of vertebrates that lack all microRNA activity will aid in determining the roles played by microRNAs, and the genes that they regulate, during vertebrate development.
Collapse
Affiliation(s)
- Brian D Harfe
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, PO Box 100266, Gainesville, FL 32610, USA.
| |
Collapse
|