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Unique functions of repetitive transcriptomes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 285:115-88. [PMID: 21035099 DOI: 10.1016/b978-0-12-381047-2.00003-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Repetitive sequences occupy a huge fraction of essentially every eukaryotic genome. Repetitive sequences cover more than 50% of mammalian genomic DNAs, whereas gene exons and protein-coding sequences occupy only ~3% and 1%, respectively. Numerous genomic repeats include genes themselves. They generally encode "selfish" proteins necessary for the proliferation of transposable elements (TEs) in the host genome. The major part of evolutionary "older" TEs accumulated mutations over time and fails to encode functional proteins. However, repeats have important functions also on the RNA level. Repetitive transcripts may serve as multifunctional RNAs by participating in the antisense regulation of gene activity and by competing with the host-encoded transcripts for cellular factors. In addition, genomic repeats include regulatory sequences like promoters, enhancers, splice sites, polyadenylation signals, and insulators, which actively reshape cellular transcriptomes. TE expression is tightly controlled by the host cells, and some mechanisms of this regulation were recently decoded. Finally, capacity of TEs to proliferate in the host genome led to the development of multiple biotechnological applications.
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Abstract
CD4 T cells play critical roles in mediating adaptive immunity to a variety of pathogens. They are also involved in autoimmunity, asthma, and allergic responses as well as in tumor immunity. During TCR activation in a particular cytokine milieu, naive CD4 T cells may differentiate into one of several lineages of T helper (Th) cells, including Th1, Th2, Th17, and iTreg, as defined by their pattern of cytokine production and function. In this review, we summarize the discovery, functions, and relationships among Th cells; the cytokine and signaling requirements for their development; the networks of transcription factors involved in their differentiation; the epigenetic regulation of their key cytokines and transcription factors; and human diseases involving defective CD4 T cell differentiation.
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Affiliation(s)
- Jinfang Zhu
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-1892
| | - Hidehiro Yamane
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-1892
| | - William E. Paul
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-1892
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Abstract
How does a juvenile insect transform into an adult? This question, which sums up the wonder of insect metamorphosis, has fascinated mankind since ancient times. Modern physiology has established the endocrine basis regulating these transformations, which mainly depend on two hormone types: ecdysteroids, which promote molts, and juvenile hormones, which repress the transformation into the adult stage. The interplay of these two hormones regulates the genes involved in juvenile and adult programs and the shift from one to the other. microRNAs (miRNAs) are small noncoding RNAs, which participate in many biological processes, and we wondered whether they might be also involved in insect metamorphosis. In insects, Dicer-1 ribonuclease transforms miRNA precursors into mature miRNAs. Thus, using systemic RNA interference (RNAi) to silence the expression of Dicer-1 in the hemimetabolan insect Blattella germanica, we depleted miRNA contents in the last instar nymph. This practically inhibited metamorphosis after the next molt, as the resulting specimens showed nymphoid features and were able to molt again. The experiments show that miRNAs play a key role in hemimetabolan metamorphosis, perhaps regulating genes that are juvenile hormone targets.
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154
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Grelier G, Voirin N, Ay AS, Cox DG, Chabaud S, Treilleux I, Léon-Goddard S, Rimokh R, Mikaelian I, Venoux C, Puisieux A, Lasset C, Moyret-Lalle C. Prognostic value of Dicer expression in human breast cancers and association with the mesenchymal phenotype. Br J Cancer 2009; 101:673-83. [PMID: 19672267 PMCID: PMC2736830 DOI: 10.1038/sj.bjc.6605193] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 06/21/2009] [Accepted: 06/30/2009] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Dicer, a ribonuclease, is the key enzyme required for the biogenesis of microRNAs and small interfering RNAs and is essential for both mammalian development and cell differentiation. Recent evidence indicates that Dicer may also be involved in tumourigenesis. However, no studies have examined the clinical significance of Dicer at both the RNA and the protein levels in breast cancer. METHODS In this study, the biological and prognostic value of Dicer expression was assessed in breast cancer cell lines, breast cancer progression cellular models, and in two well-characterised sets of breast carcinoma samples obtained from patients with long-term follow-up using tissue microarrays and quantitative reverse transcription-PCR. RESULTS We have found that Dicer protein expression is significantly associated with hormone receptor status and cancer subtype in breast tumours (ER P=0.008; PR P=0.019; cancer subtype P=0.023, luminal A P=0.0174). Dicer mRNA expression appeared to have an independent prognostic impact in metastatic disease (hazard ratio=3.36, P=0.0032). In the breast cancer cell lines, lower Dicer expression was found in cells harbouring a mesenchymal phenotype and in metastatic bone derivatives of a breast cancer cell line. These findings suggest that the downregulation of Dicer expression may be related to the metastatic spread of tumours. CONCLUSION Assessment of Dicer expression may facilitate prediction of distant metastases for patients suffering from breast cancer.
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Affiliation(s)
- G Grelier
- Université de Lyon, Université Lyon 1, ISPB, Lyon, F-69003, France
- Inserm, U590, Lyon, F-69008, France
- Centre Léon Bérard, Lyon, F-69008, France
| | - N Voirin
- Université de Lyon, Université Lyon 1, Faculté Grange Blanche, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Lyon, F-69373, France
- Hospices Civils de Lyon, Hôpital Edouard Herriot, Service d’Hygiène, Epidémiologie et Prévention, Lyon, F-69437, France
| | - A-S Ay
- Université de Lyon, Université Lyon 1, ISPB, Lyon, F-69003, France
- Inserm, U590, Lyon, F-69008, France
- Centre Léon Bérard, Lyon, F-69008, France
| | - D G Cox
- Inserm, U590, Lyon, F-69008, France
| | - S Chabaud
- Centre Léon Bérard, Département de Santé Publique, Lyon, F-69008, France
| | - I Treilleux
- Centre Léon Bérard, Service d’Anatomopathologie, Lyon, F-69008, France
| | - S Léon-Goddard
- Centre Léon Bérard, Service d’Anatomopathologie, Lyon, F-69008, France
| | - R Rimokh
- Inserm, U590, Lyon, F-69008, France
- Centre Léon Bérard, Lyon, F-69008, France
| | - I Mikaelian
- Université de Lyon, université Lyon 1, Faculté Grange Blanche, CNRS, UMR5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69008, France
| | - C Venoux
- Université de Lyon, université Lyon 1, Faculté Grange Blanche, CNRS, UMR5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69008, France
| | - A Puisieux
- Université de Lyon, Université Lyon 1, ISPB, Lyon, F-69003, France
- Inserm, U590, Lyon, F-69008, France
- Centre Léon Bérard, Lyon, F-69008, France
| | - C Lasset
- Université de Lyon, Université Lyon 1, Faculté Grange Blanche, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Lyon, F-69373, France
- Centre Léon Bérard, Département de Santé Publique, Lyon, F-69008, France
| | - C Moyret-Lalle
- Université de Lyon, Université Lyon 1, ISPB, Lyon, F-69003, France
- Inserm, U590, Lyon, F-69008, France
- Centre Léon Bérard, Lyon, F-69008, France
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155
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Flores-jasso CF, Arenas-huertero C, Reyes JL, Contreras-cubas C, Covarrubias A, Vaca L. First step in pre-miRNAs processing by human Dicer. Acta Pharmacol Sin 2009; 30:1177-85. [PMID: 19654583 DOI: 10.1038/aps.2009.108] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AIM To investigate the strand preference of the initial cleavage of human pre-miRNAs by human Dicer in vitro. METHODS We used a series of in vitro transcribed pre-miRNAs that were radioactively labeled at their 5' or 3' ends in cleavage reactions with recombinant human Dicer or HeLa cytoplasmic S100 extracts. Pre-miRNAs samples were purified by denaturing and native PAGE and only the stem-loop structures were used in the experiments. Products of cleavage reactions were resolved by denaturing PAGE, and scanned by phosphor-imaging. RESULTS Recombinant hDicer performs a biased first-cleavage in the pre-let-7b and hsa-pre-miR-17 3' strand. This result is recapitulated in HeLa S100 cytoplasmic extracts. CONCLUSION The differential first-nick is observed in cleavage reactions only when stem-loops are substrates for hDicer.
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156
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Rao DD, Vorhies JS, Senzer N, Nemunaitis J. siRNA vs. shRNA: similarities and differences. Adv Drug Deliv Rev 2009; 61:746-59. [PMID: 19389436 DOI: 10.1016/j.addr.2009.04.004] [Citation(s) in RCA: 405] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 04/13/2009] [Indexed: 12/11/2022]
Abstract
RNA interference (RNAi) is a natural process through which expression of a targeted gene can be knocked down with high specificity and selectivity. Using available technology and bioinformatics investigators will soon be able to identify relevant bio molecular tumor network hubs as potential key targets for knockdown approaches. Methods of mediating the RNAi effect involve small interfering RNA (siRNA), short hairpin RNA (shRNA) and bi-functional shRNA. The simplicity of siRNA manufacturing and transient nature of the effect per dose are optimally suited for certain medical disorders (i.e. viral injections). However, using the endogenous processing machinery, optimized shRNA constructs allow for high potency and sustainable effects using low copy numbers resulting in less off-target effects, particularly if embedded in a miRNA scaffold. Bi-functional design may further enhance potency and safety of RNAi-based therapeutics. Remaining challenges include tumor selective delivery vehicles and more complete evaluation of the scope and scale of off-target effects. This review will compare siRNA, shRNA and bi-functional shRNA.
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157
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Zhang HM, Su Y, Guo S, Yuan J, Lim T, Liu J, Guo P, Yang D. Targeted delivery of anti-coxsackievirus siRNAs using ligand-conjugated packaging RNAs. Antiviral Res 2009; 83:307-16. [PMID: 19616030 PMCID: PMC3909712 DOI: 10.1016/j.antiviral.2009.07.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 07/02/2009] [Accepted: 07/08/2009] [Indexed: 11/22/2022]
Abstract
Coxsackievirus B3 (CVB3) is a common pathogen of myocarditis. We previously synthesized a siRNA targeting the CVB3 protease 2A (siRNA/2A) gene and achieved reduction of CVB3 replication by 92% in vitro. However, like other drugs under development, CVB3 siRNA faces a major challenge of targeted delivery. In this study, we investigated a novel approach to deliver CVB3 siRNAs to a specific cell population (e.g. HeLa cells containing folate receptor) using receptor ligand (folate)-linked packaging RNA (pRNA) from bacterial phage phi29. pRNA monomers can spontaneously form dimers and multimers under optimal conditions by base-pairing between their stem loops. By covalently linking a fluorescence-tag to folate, we delivered the conjugate specifically to HeLa cells without the need of transfection. We further demonstrated that pRNA covalently conjugated to siRNA/2A achieved an equivalent antiviral effect to that of the siRNA/2A alone. Finally, the drug targeted delivery was further evaluated by using pRNA monomers or dimers, which carried both the siRNA/2A and folate ligand and demonstrated that both of them strongly inhibited CVB3 replication. These data indicate that pRNA as a siRNA carrier can specifically deliver the drug to target cells via its ligand and specific receptor interaction and inhibit virus replication effectively.
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Affiliation(s)
- Huifang M Zhang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Canada
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158
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Mcintyre GJ, Groneman JL, Yu YH, Jaramillo A, Shen S, Applegate TL. 96 shRNAs designed for maximal coverage of HIV-1 variants. Retrovirology 2009; 6:55. [PMID: 19497094 PMCID: PMC2698899 DOI: 10.1186/1742-4690-6-55] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 06/04/2009] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The RNA interference (RNAi) pathway is a mechanism of gene-suppression with potential gene therapy applications for treating viral disease such as HIV-1. The most suitable inducer of RNAi for this application is short hairpin RNA (shRNA) although it is limited to suppressing a single target. A successful anti-HIV-1 therapy will require combinations of multiple highly active, highly conserved shRNAs to adequately counter the emergence of resistant strains. RESULTS We calculated the percentage conservations of 8, 846 unique 19 nucleotide HIV-1 targets amongst 37, 949 HIV-1 gene sequence fragments containing 24.8 million 19 mers. We developed a novel method of determining conservation in 'profile' sets of 5 overlapping 19 mer sequences (covering 23 nucleotides in total) to ensure that the intended conservation of each shRNA would be unaffected by possible variations in shRNA processing. Ninety six of the top ranking targets from 22 regions were selected based on conservation profiles, predicted activities, targets and specific nucleotide inclusion/exclusion criteria. We constructed 53 shRNAs with 20 bp stems and 43 shRNAs with 21 bp stems which we tested and ranked using fluorescent reporter and HIV-1 expression assays. Average suppressive activities ranged from 71 - 75%, with 65 hairpins classed as highly active (> 75% activity). Overall we found little difference in activities from minor changes in stem length (20 cf. 21), or between neighboring targets differing by a single nucleotide in start position. However, there were several exceptions which suggest that all sequences, irrespective of similarities in target site or design, may be useful candidates. We encountered technical limitations with GFP reporter assays when the target domain was long and or when the distance between the target site and fusion junction was large. Assay performance was improved by dividing large targets into several shorter domains. CONCLUSION In summary, our novel selection process resulted in a large panel of highly active shRNAs spanning the HIV-1 genome, representing excellent candidates for use in multiple shRNA gene therapies. Our core selection method ensuring maximal conservation in the processed product(s) is also widely applicable to other shRNA applications.
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Affiliation(s)
- Glen John Mcintyre
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Jennifer Lynne Groneman
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Yi-Hsin Yu
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Angel Jaramillo
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Sylvie Shen
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
| | - Tanya Lynn Applegate
- Johnson and Johnson Research Pty Ltd, Level 4 Biomedical Building, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW, 1430, Australia
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159
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He Z, Kokkinaki M, Pant D, Gallicano GI, Dym M. Small RNA molecules in the regulation of spermatogenesis. Reproduction 2009; 137:901-11. [DOI: 10.1530/rep-08-0494] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Small RNA molecules (small RNAs), including small interfering RNAs (siRNAs), microRNAs (miRNAs), and piwi-interacting RNAs (piRNAs), have recently emerged as important regulators of gene expression at the post-transcriptional or translation level. Significant progress has recently been made utilizing small RNAs in elucidating the molecular mechanisms regulating spermatogenesis. Spermatogenesis is a complex process that involves the division and eventual differentiation of spermatogonial stem cells into mature spermatozoa. The process of spermatogenesis is composed of several phases: mitotic proliferation of spermatogonia to produce spermatocytes; two meiotic divisions of spermatocytes to generate haploid round spermatids; and spermiogenesis, the final phase that involves the maturation of early-round spermatids into elongated mature spermatids. A number of miRNAs are expressed abundantly in male germ cells throughout spermatogenesis, while piRNAs are only present in pachytene spermatocytes and round spermatids. In this review, we first address the synthesis, mechanisms of action, and functions of siRNA, miRNA, and piRNA, and then we focus on the recent advancements in defining the small RNAs in the regulation of spermatogenesis. Concerns pertaining to the use of siRNAs in exploring spermatogenesis mechanisms and open questions in miRNAs and piRNAs in this field are highlighted. The potential applications of small RNAs to male contraception and treatment for male infertility and testicular cancer are also discussed.
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160
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Kurscheid S, Lew-Tabor AE, Rodriguez Valle M, Bruyeres AG, Doogan VJ, Munderloh UG, Guerrero FD, Barrero RA, Bellgard MI. Evidence of a tick RNAi pathway by comparative genomics and reverse genetics screen of targets with known loss-of-function phenotypes in Drosophila. BMC Mol Biol 2009; 10:26. [PMID: 19323841 PMCID: PMC2676286 DOI: 10.1186/1471-2199-10-26] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 03/26/2009] [Indexed: 11/13/2022] Open
Abstract
Background The Arthropods are a diverse group of organisms including Chelicerata (ticks, mites, spiders), Crustacea (crabs, shrimps), and Insecta (flies, mosquitoes, beetles, silkworm). The cattle tick, Rhipicephalus (Boophilus) microplus, is an economically significant ectoparasite of cattle affecting cattle industries world wide. With the availability of sequence reads from the first Chelicerate genome project (the Ixodes scapularis tick) and extensive R. microplus ESTs, we investigated evidence for putative RNAi proteins and studied RNA interference in tick cell cultures and adult female ticks targeting Drosophila homologues with known cell viability phenotype. Results We screened 13,643 R. microplus ESTs and I. scapularis genome reads to identify RNAi related proteins in ticks. Our analysis identified 31 RNAi proteins including a putative tick Dicer, RISC associated (Ago-2 and FMRp), RNA dependent RNA polymerase (EGO-1) and 23 homologues implicated in dsRNA uptake and processing. We selected 10 R. microplus ESTs with >80% similarity to D. melanogaster proteins associated with cell viability for RNAi functional screens in both BME26 R. microplus embryonic cells and female ticks in vivo. Only genes associated with proteasomes had an effect on cell viability in vitro. In vivo RNAi showed that 9 genes had significant effects either causing lethality or impairing egg laying. Conclusion We have identified key RNAi-related proteins in ticks and along with our loss-of-function studies support a functional RNAi pathway in R. microplus. Our preliminary studies indicate that tick RNAi pathways may differ from that of other Arthropods such as insects.
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Affiliation(s)
- Sebastian Kurscheid
- Cooperative Research Centre for Beef Genetic Technologies, Armidale, NSW, Australia.
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161
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Mtango NR, Potireddy S, Latham KE. Expression of microRNA processing machinery genes in rhesus monkey oocytes and embryos of different developmental potentials. Mol Reprod Dev 2009; 76:255-69. [PMID: 18646051 PMCID: PMC2631102 DOI: 10.1002/mrd.20950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are a class of small RNAs that silence gene expression. In animal cells, miRNAs bind to the 3' untranslated regions of specific mRNAs and inhibit their translation. The correct regulation of mRNA expression by miRNAs is believed to be important for oocyte maturation, early development and implantation. We examined the expression of 25 mRNAs involved in the microRNA processing pathway in a nonhuman primate oocyte and embryo model. We observed that mRNAs related to miRNA splicing are downregulated during oocyte maturation while those related to miRNA processing are upregulated, indicating that there may exist a temporal difference in their activities related to transcriptional activity in germinal vesicle stage oocytes. We also observed that the vast majority of mRNAs examined were insensitive to alpha-amanitin at the 8-16 cell stage. The expression data did not reveal a major impact of embryo culture, and hormonal stimulation protocol affected only a small number of mRNAs, suggesting that the components of the pathway may be accumulated in the oocyte during oogenesis and resistant to exogenous insults. In comparison to published mouse array data, we observed species differences and similarities in the temporal expression patterns of some genes, suggesting that miRNA processing may be regulated differently. These data extend our understanding of the potential roles of miRNA during primate embryogenesis.
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Affiliation(s)
- Namdori R Mtango
- The Fels Institute for Cancer Research and Molecular Biology, Temple University Medical School, Philadelphia, Pennsylvania 19140, USA
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162
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Lee TL, Pang ALY, Rennert OM, Chan WY. Genomic landscape of developing male germ cells. BIRTH DEFECTS RESEARCH. PART C, EMBRYO TODAY : REVIEWS 2009; 87:43-63. [PMID: 19306351 PMCID: PMC2939912 DOI: 10.1002/bdrc.20147] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Spermatogenesis is a highly orchestrated developmental process by which spermatogonia develop into mature spermatozoa. This process involves many testis- or male germ cell-specific gene products whose expressions are strictly regulated. In the past decade the advent of high-throughput gene expression analytical techniques has made functional genomic studies of this process, particularly in model animals such as mice and rats, feasible and practical. These studies have just begun to reveal the complexity of the genomic landscape of the developing male germ cells. Over 50% of the mouse and rat genome are expressed during testicular development. Among transcripts present in germ cells, 40% - 60% are uncharacterized. A number of genes, and consequently their associated biological pathways, are differentially expressed at different stages of spermatogenesis. Developing male germ cells present a rich repertoire of genetic processes. Tissue-specific as well as spermatogenesis stage-specific alternative splicing of genes exemplifies the complexity of genome expression. In addition to this layer of control, discoveries of abundant presence of antisense transcripts, expressed psuedogenes, non-coding RNAs (ncRNA) including long ncRNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and retrogenes all point to the presence of multiple layers of expression and functional regulation in male germ cells. It is anticipated that application of systems biology approaches will further our understanding of the regulatory mechanism of spermatogenesis.
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Affiliation(s)
- Tin-Lap Lee
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Alan Lap-Yin Pang
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Owen M. Rennert
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Wai-Yee Chan
- Section on Developmental Genomics, Laboratory of Clinical Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, Department of Pediatrics, Georgetown University College of Medicine, Washington, DC
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Cecere G, Cogoni C. Quelling targets the rDNA locus and functions in rDNA copy number control. BMC Microbiol 2009; 9:44. [PMID: 19243581 PMCID: PMC2650698 DOI: 10.1186/1471-2180-9-44] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 02/25/2009] [Indexed: 03/09/2023] Open
Abstract
Background RNA silencing occurs in a broad range of organisms. Although its ancestral function is probably related to the genome defense mechanism against repetitive selfish elements, it has been found that RNA silencing regulates different cellular processes such as gene expression and chromosomal segregation. In Neurospora crassa, a RNA silencing mechanism, called quelling, acts to repress the expression of transgenes and transposons, but until now no other cellular functions have been shown to be regulated by this mechanism. Results Here, we detected by northern blotting endogenous short interfering RNA (siRNAs) from the repetitive ribosomal DNA locus (rDNA) that are loaded onto the argonaute protein QDE-2. Moreover, we found a bidirectional transcription that can generate double strand RNA (dsRNA) molecules. Interestingly, quelling mutants have a reduced rDNA gene copy number. Conclusion Our finding could suggest a new biological function for RNA silencing in the maintenance of the integrity and stability of the Neurospora rDNA locus.
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Affiliation(s)
- Germano Cecere
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Università La Sapienza, Rome, Italy.
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164
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Beauregard A, Curcio MJ, Belfort M. The take and give between retrotransposable elements and their hosts. Annu Rev Genet 2009; 42:587-617. [PMID: 18680436 DOI: 10.1146/annurev.genet.42.110807.091549] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Retrotransposons mobilize via RNA intermediates and usually carry with them the agent of their mobility, reverse transcriptase. Retrotransposons are streamlined, and therefore rely on host factors to proliferate. However, retrotransposons are exposed to cellular forces that block their paths. For this review, we have selected for our focus elements from among target-primed (TP) retrotransposons, also called non-LTR retrotransposons, and extrachromosomally-primed (EP) retrotransposons, also called LTR retrotransposons. The TP retrotransposons considered here are group II introns, LINEs and SINEs, whereas the EP elements considered are the Ty and Tf retrotransposons, with a brief comparison to retroviruses. Recurring themes for these elements, in hosts ranging from bacteria to humans, are tie-ins of the retrotransposons to RNA metabolism, DNA replication and repair, and cellular stress. Likewise, there are parallels among host-cell defenses to combat rampant retrotransposon spread. The interactions between the retrotransposon and the host, and their coevolution to balance the tension between retrotransposon proliferation and host survival, form the basis of this review.
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Affiliation(s)
- Arthur Beauregard
- New York State Department of Health, Center for Medical Sciences, Albany, New York 12208, 12201-2002, USA.
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165
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Identification of microRNA in the protist Trichomonas vaginalis. Genomics 2009; 93:487-93. [PMID: 19442639 DOI: 10.1016/j.ygeno.2009.01.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 12/31/2008] [Accepted: 01/17/2009] [Indexed: 01/11/2023]
Abstract
MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. However, miRNA has never been identified experimentally in protist. Direct cloning of 438 expressed miRNA tags by microRNA serial analysis of gene expression from the parasitic protist Trichomonas vaginalis identified nine candidate miRNAs. Bioinformatics analysis of the corresponding genomic region revealed that these miRNA candidates contain a classical stem-loop-stem structure of pre-microRNAs. Analysis of the 20 nt long mature tva-miR-001 showed that it is an intergenic miRNA located at the scaffold DS113596. Tva-miR-001 was differentially expressed in the trophozoite, pseudocyst and amoeboid stages. Based on the experimental results of the present study, we provided solid evidence that protist possesses a miRNA regulating network comparable with multicellular organisms for the first time.
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166
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Ivashuta SI, Petrick JS, Heisel SE, Zhang Y, Guo L, Reynolds TL, Rice JF, Allen E, Roberts JK. Endogenous small RNAs in grain: semi-quantification and sequence homology to human and animal genes. Food Chem Toxicol 2009; 47:353-60. [PMID: 19068223 DOI: 10.1016/j.fct.2008.11.025] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Revised: 11/05/2008] [Accepted: 11/14/2008] [Indexed: 12/29/2022]
Abstract
Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are effector molecules of RNA interference (RNAi), a highly conserved RNA-based gene suppression mechanism in plants, mammals and other eukaryotes. Endogenous RNAi-based gene suppression has been harnessed naturally and through conventional breeding to achieve desired plant phenotypes. The present study demonstrates that endogenous small RNAs, such as siRNAs and miRNAs, are abundant in soybean seeds, corn kernels, and rice grain, plant tissues that are traditionally used for food and feed. Numerous endogenous plant small RNAs were found to have perfect complementarity to human genes as well as those of other mammals. The abundance of endogenous small RNA molecules in grain from safely consumed food and feed crops such as soybean, corn, and rice and the homology of a number of these dietary small RNAs to human and animal genomes and transcriptomes establishes a history of safe consumption for dietary small RNAs.
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Affiliation(s)
- Sergey I Ivashuta
- Monsanto Company, 800N. Lindbergh Blvd., Mail Code O3F, St. Louis, MO 63167, USA
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167
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Jin L, Kryukov K, Suzuki Y, Imanishi T, Ikeo K, Gojobori T. The evolutionary study of small RNA-directed gene silencing pathways by investigating RNase III enzymes. Gene 2009; 435:1-8. [PMID: 19393176 DOI: 10.1016/j.gene.2008.12.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Revised: 11/29/2008] [Accepted: 12/23/2008] [Indexed: 11/28/2022]
Abstract
The RNA-mediated gene silencing pathways are evolutionarily conserved processes. They highlight a fundamental role of short RNAs in eukaryotic gene regulation and antiviral defense. Recently three distinct small RNA-directed silencing pathways are observed, such as the destruction of mRNA via siRNA, inhibition of mRNA translation via miRNA, and epigenetic gene silencing via siRNA. It was also found that in these pathways, the members of ribonuclease III family play important roles in diverse RNA maturation and decay. Here we investigated the evolution of RNase III nucleases, Dicer as representative, to further figure out the evolutionary relationship of these three gene silencing pathways. With the advantage of using genomic sequences as the subject in homolog search, in un-annotated genomic regions, we were able to detect possible candidates for 3 functional domains and genes of dicer and drosha. Moreover, we found that prokaryotes including eubacteria and archaea lack completely the PAZ domain of Dicer. These results show the taxonomic-dependent evolution of the RNA-mediated gene silencing pathways.
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Affiliation(s)
- Lihua Jin
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan
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168
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Abstract
Dicer is central to the RNA interference (RNAi) pathway, because it is required for processing of double-stranded RNA (dsRNA) precursors into small RNA effector molecules. In principle, any long dsRNA could serve as a substrate for Dicer. The X inactive specific transcript (Xist) is an untranslated RNA that is required for dosage compensation in mammals. It coats and silences 1 of the 2 X chromosomes in female cells and initiates a chromosomewide change in chromatin structure that includes the recruitment of Polycomb proteins, but it is largely unknown how Xist RNA mediates these processes. To investigate a potential link between the RNAi pathway and X inactivation, we generated and analyzed Dicer-deficient embryonic stem (ES) cells. In the absence of Dicer, coating by Xist RNA, initiation of silencing, and recruitment of Polycomb proteins occur normally. Dicer ablation had modest effects on the steady-state levels of spliced Xist RNA. Together our data indicate that the RNAi machinery is not essential for the initiation of X inactivation.
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169
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Zhou H, Yang L, Li H, Li L, Chen J. Residues that affect human Argonaute2 concentration in cytoplasmic processing bodies. Biochem Biophys Res Commun 2008; 378:620-4. [PMID: 19061863 DOI: 10.1016/j.bbrc.2008.11.098] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 11/19/2008] [Indexed: 10/21/2022]
Abstract
Sequence-specific gene silencing triggered by double-stranded RNA is a fundamental gene regulatory mechanism present in almost all eukaryotes. Argonaute2 (Ago2) is the central protein component of RNA-induced silencing complex (RISC), and resides in cytoplasmic processing bodies (P-bodies). In the present study, we demonstrated one human mutant Ago2 protein containing 6 point mutations (G32W, F128L, R196Q, P458S, T741A, S752G) failed to accumulate in P-bodies. Analysis of the different Ago2 revertants indicates the S752 as a key amino acid for P-body localization of Ago2. The S752 is evolutionary conserved in the Piwi domain of Ago2 homologs from worms, insects, plants and mammals. We further showed the single point mutation S752G interfering the interaction between Ago2 and Dcp1a, a key component of P-bodies.
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Affiliation(s)
- Huamin Zhou
- The Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, 422 South Siming Road, Xiamen, Fujian 361005, China
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170
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A Drosophila pasha mutant distinguishes the canonical microRNA and mirtron pathways. Mol Cell Biol 2008; 29:861-70. [PMID: 19047376 DOI: 10.1128/mcb.01524-08] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Canonical primary microRNA (miRNA) transcripts and mirtrons are proposed to transit distinct nuclear pathways en route to generating mature approximately 22 nucleotide regulatory RNAs. We generated a null allele of Drosophila pasha, which encodes a double-stranded RNA-binding protein partner of the RNase III enzyme Drosha. Analysis of this mutant yielded stringent evidence that Pasha is essential for the biogenesis of canonical miRNAs but is dispensable for the processing and function of mirtron-derived regulatory RNAs. The pasha mutant also provided a unique tool to study the developmental requirements for Drosophila miRNAs. While pasha adult somatic clones are similar in many respects to those of dicer-1 clones, pasha mutant larvae revealed an unexpected requirement for the miRNA pathway in imaginal disc growth. These data suggest limitations to somatic clonal analysis of miRNA pathway components.
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171
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172
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Soifer HS, Sano M, Sakurai K, Chomchan P, Saetrom P, Sherman MA, Collingwood MA, Behlke MA, Rossi JJ. A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs. Nucleic Acids Res 2008; 36:6511-22. [PMID: 18927112 PMCID: PMC2582626 DOI: 10.1093/nar/gkn687] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
In humans a single species of the RNAseIII enzyme Dicer processes both microRNA precursors into miRNAs and long double-stranded RNAs into small interfering RNAs (siRNAs). An interesting but poorly understood domain of the mammalian Dicer protein is the N-terminal helicase-like domain that possesses a signature DExH motif. Cummins et al. created a human Dicer mutant cell line by inserting an AAV targeting cassette into the helicase domain of both Dicer alleles in HCT116 cells generating an in-frame 43-amino-acid insertion immediately adjacent to the DExH box. This insertion creates a Dicer mutant protein with defects in the processing of most, but not all, endogenous pre-miRNAs into mature miRNA. Using both biochemical and computational approaches, we provide evidence that the Dicer helicase mutant is sensitive to the thermodynamic properties of the stems in microRNAs and short-hairpin RNAs, with thermodynamically unstable stems resulting in poor processing and a reduction in the levels of functional mi/siRNAs. Paradoxically, this mutant exhibits enhanced processing efficiency and concomitant RNA interference when thermodynamically stable, long-hairpin RNAs are used. These results suggest an important function for the Dicer helicase domain in the processing of thermodynamically unstable hairpin structures.
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Affiliation(s)
- Harris S Soifer
- Department of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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173
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Ludwig LB. RNA silencing and HIV: a hypothesis for the etiology of the severe combined immunodeficiency induced by the virus. Retrovirology 2008; 5:79. [PMID: 18786256 PMCID: PMC2553099 DOI: 10.1186/1742-4690-5-79] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Accepted: 09/11/2008] [Indexed: 12/29/2022] Open
Abstract
A novel intrinsic HIV-1 antisense gene was previously described with RNA initiating from the region of an HIV-1 antisense initiator promoter element (HIVaINR). The antisense RNA is exactly complementary to HIV-1 sense RNA and capable of forming ~400 base-pair (bp) duplex RNA in the region of the long terminal repeat (LTR) spanning the beginning portion of TAR in the repeat (R) region and extending through the U3 region. Duplex or double-stranded RNA of several hundred nucleotides in length is a key initiating element of RNA interference (RNAi) in several species. This HIVaINR antisense RNA is also capable of forming multiple stem-loop or hairpin-like secondary structures by M-fold analysis, with at least one that perfectly fits the criteria for a microRNA (miRNA) precursor. MicroRNAs (miRNAs) interact in a sequence-specific manner with target messenger RNAs (mRNAs) to induce either cleavage of the message or impede translation. Human mRNA targets of the predicted HIVaINR antisense RNA (HAA) microRNAs include mRNA for the human interleukin-2 receptor gamma chain (IL-2RG), also called the common gamma (γc) receptor chain, because it is an integral part of 6 receptors mediating interleukin signalling (IL-2R, IL-4R, IL-7R, IL-9R, IL-15R and IL-21R). Other potential human mRNA targets include interleukin-15 (IL-15) mRNA, the fragile × mental retardation protein (FMRP) mRNA, and the IL-1 receptor-associated kinase 1 (IRAK1) mRNA, amongst others. Thus the proposed intrinsic HIVaINR antisense RNA microRNAs (HAAmiRNAs) of the human immunodeficiency virus form complementary targets with mRNAs of a key human gene in adaptive immunity, the IL-2Rγc, in which genetic defects are known to cause an X-linked severe combined immunodeficiency syndrome (X-SCID), as well as mRNAs of genes important in innate immunity. A new model of intrinsic RNA silencing induced by the HIVaINR antisense RNA in the absence of Tat is proposed, with elements suggestive of both small interfering RNA (siRNA) and miRNA.
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174
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Hagen C, Rojas MR, Kon T, Gilbertson RL. Recovery from Cucurbit leaf crumple virus (family Geminiviridae, genus Begomovirus) infection is an adaptive antiviral response associated with changes in viral small RNAs. PHYTOPATHOLOGY 2008; 98:1029-37. [PMID: 18943741 DOI: 10.1094/phyto-98-9-1029] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A strong recovery response occurs in cantaloupe (Cucumis melo) and watermelon (Citrullus lanatus) infected with the bipartite begomovirus Cucurbit leaf crumple virus (CuLCrV). This response is characterized by initially severe symptoms, which gradually become attenuated (almost symptomless). An inverse relationship was detected between viral DNA levels and recovery, indicating that recovered tissues had reduced viral titers. Recovered tissues also were resistant to reinfection with CuLCrV; i.e., recovered leaves reinoculated with the virus did not develop symptoms or have an increased level of viral DNA. In contrast, infection of CuLCrV-recovered leaves with the RNA virus, Cucumber mosaic virus (CMV), disrupted recovery, resulting in the development of severe disease symptoms (more severe than those induced by CMV or CuLCrV alone) and increased CuLCrV DNA levels. Small RNAs with homology to CuLCrV DNA were detected in recovered and nonrecovered tissues; as well as in phloem exudates from infected, but not uninfected plants. Levels of these small RNAs were positively correlated with viral titer; thus, recovered tissues had lower levels than symptomatic tissues. In addition, viral DNA from a host that undergoes strong recovery (watermelon) was more highly methylated compared with that from a host that undergoes limited recovery (zucchini). Furthermore, inoculation of CuLCrV-infected zucchini with a construct expressing an inverted repeat of the CuLCrV common region enhanced recovery and reduced viral symptoms and viral DNA levels in newly emerged leaves. Taken together, these results suggest that recovery from CuLCrV infection is an adaptive antiviral defense mechanism, most likely mediated by gene silencing.
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Affiliation(s)
- C Hagen
- Department of Plant Pathology, University of California-Davis, 95616, USA
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175
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Lee NS, Kim DH, Alluin J, Robbins M, Gu S, Li H, Kim J, Salvaterra PM, Rossi JJ. Functional and intracellular localization properties of U6 promoter-expressed siRNAs, shRNAs, and chimeric VA1 shRNAs in mammalian cells. RNA (NEW YORK, N.Y.) 2008; 14:1823-1833. [PMID: 18697923 PMCID: PMC2525953 DOI: 10.1261/rna.1014008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Accepted: 06/09/2008] [Indexed: 05/26/2023]
Abstract
RNA polymerase III (Pol III) expression systems for short hairpin RNAs (U6 shRNAs or chimeric VA1 shRNAs) or individually expressed sense/antisense small interfering RNA (siRNA) strands have been used to trigger RNA interference (RNAi) in mammalian cells. Here we show that individually expressed siRNA expression constructs produce 21-nucleotide siRNAs that strongly accumulate as duplex siRNAs in the nucleus of human cells, exerting sequence-specific silencing activity similar to cytoplasmic siRNAs derived from U6 or VA1-expressed hairpin precursors. In contrast, 29-mer siRNAs separately expressed as sense/antisense strands fail to elicit RNAi activity, despite accumulation of these RNAs in the nucleus. Our findings delineate different intracellular accumulation patterns for the three expression strategies and suggest the possibility of a nuclear RNAi pathway that requires 21-mer duplexes.
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Affiliation(s)
- Nan Sook Lee
- Division of Molecular Medicine, Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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176
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Lavoie M, Abou Elela S. Yeast ribonuclease III uses a network of multiple hydrogen bonds for RNA binding and cleavage. Biochemistry 2008; 47:8514-26. [PMID: 18646867 DOI: 10.1021/bi800238u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Members of the bacterial RNase III family recognize a variety of short structured RNAs with few common features. It is not clear how this group of enzymes supports high cleavage fidelity while maintaining a broad base of substrates. Here we show that the yeast orthologue of RNase III (Rnt1p) uses a network of 2'-OH-dependent interactions to recognize substrates with different structures. We designed a series of bipartite substrates permitting the distinction between binding and cleavage defects. Each substrate was engineered to carry a single or multiple 2'- O-methyl or 2'-fluoro ribonucleotide substitutions to prevent the formation of hydrogen bonds with a specific nucleotide or group of nucleotides. Interestingly, introduction of 2'- O-methyl ribonucleotides near the cleavage site increased the rate of catalysis, indicating that 2'-OH are not required for cleavage. Substitution of nucleotides in known Rnt1p binding site with 2'- O-methyl ribonucleotides inhibited cleavage while single 2'-fluoro ribonucleotide substitutions did not. This indicates that while no single 2'-OH is essential for Rnt1p cleavage, small changes in the substrate structure are not tolerated. Strikingly, several nucleotide substitutions greatly increased the substrate dissociation constant with little or no effect on the Michaelis-Menten constant or rate of catalysis. Together, the results indicate that Rnt1p uses a network of nucleotide interactions to identify its substrate and support two distinct modes of binding. One mode is primarily mediated by the dsRNA binding domain and leads to the formation of stable RNA/protein complex, while the other requires the presence of the nuclease and N-terminal domains and leads to RNA cleavage.
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Affiliation(s)
- Mathieu Lavoie
- Groupe ARN/RNA Group, Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
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177
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Otsuka M, Zheng M, Hayashi M, Lee JD, Yoshino O, Lin S, Han J. Impaired microRNA processing causes corpus luteum insufficiency and infertility in mice. J Clin Invest 2008; 118:1944-54. [PMID: 18398510 DOI: 10.1172/jci33680] [Citation(s) in RCA: 255] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Accepted: 02/06/2008] [Indexed: 12/12/2022] Open
Abstract
The microRNA (miRNA) processing enzyme Dicer1 is required for zygotic and embryonic development, but the early embryonic lethality of Dicer1 null alleles in mice has limited our ability to address the role of Dicer1 in normal mouse growth and development. To address this question, we used a mouse mutant with a hypomorphic Dicer1 allele (Dicer(d/d)) and found that Dicer1 deficiency resulted in female infertility. This defect in female Dicer(d/d) mice was caused by corpus luteum (CL) insufficiency and resulted, at least in part, from the impaired growth of new capillary vessels in the ovary. We found that the impaired CL angiogenesis in Dicer(d/d) mice was associated with a lack of miR17-5p and let7b, 2 miRNAs that participate in angiogenesis by regulating the expression of the antiangiogenic factor tissue inhibitor of metalloproteinase 1. Furthermore, injection of miR17-5p and let7b into the ovaries of Dicer(d/d) mice partially normalized tissue inhibitor of metalloproteinase 1 expression and CL angiogenesis. Our data indicate that the development and function of the ovarian CL is a physiological process that appears to be regulated by miRNAs and requires Dicer1 function.
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Affiliation(s)
- Motoyuki Otsuka
- Department of Immunology, The Scripps Research Institute, La Jolla, California 92037, USA
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178
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Ye X, Liu Q. Expression, purification, and analysis of recombinant Drosophila Dicer-1 and Dicer-2 enzymes. Methods Mol Biol 2008; 442:11-27. [PMID: 18369775 DOI: 10.1007/978-1-59745-191-8_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
RNA interference (RNAi) is a form of posttranscriptional gene silencing mediated by microRNA (miRNA) and small interfering RNA (siRNA). In Drosophila melanogaster, the RNase III enzymes Dicer-1 and Dicer-2 generate miRNA and siRNA, respectively. We describe the methods for the expression, purification, and analysis of recombinant Dicer-1 and Dicer-2 enzymes. Our studies demonstrate that Dicer-1 and Dicer-2 display different substrate specificities and ATP requirements.
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Affiliation(s)
- Xuecheng Ye
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
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179
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DasGupta R, Nybakken K, Booker M, Mathey-Prevot B, Gonsalves F, Changkakoty B, Perrimon N. A case study of the reproducibility of transcriptional reporter cell-based RNAi screens in Drosophila. Genome Biol 2008; 8:R203. [PMID: 17903264 PMCID: PMC2375041 DOI: 10.1186/gb-2007-8-9-r203] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 09/05/2007] [Accepted: 09/28/2007] [Indexed: 11/12/2022] Open
Abstract
A second generation dsRNA library was used to re-assess factors that influence the outcome of transcriptional reporter-based whole-genome RNAi screens for the Wnt/Wingless (wg) and Hedgehog (hh)-signaling pathways. Off-target effects have been demonstrated to be a major source of false-positives in RNA interference (RNAi) high-throughput screens. In this study, we re-assess the previously published transcriptional reporter-based whole-genome RNAi screens for the Wingless and Hedgehog signaling pathways using second generation double-stranded RNA libraries. Furthermore, we investigate other factors that may influence the outcome of such screens, including cell-type specificity, robustness of reporters, and assay normalization, which determine the efficacy of RNAi-knockdown of target genes.
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Affiliation(s)
- Ramanuj DasGupta
- New York University School of Medicine/Cancer Institute, Department of Pharmacology, First Avenue, New York, NY 10016, USA
| | - Kent Nybakken
- Boston Biomedical Research Institute, 64 Grove Street, Watertown, MA, 02472, USA
| | - Matthew Booker
- Department of Genetics, Harvard Medical School, Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Bernard Mathey-Prevot
- Department of Genetics, Harvard Medical School, Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Foster Gonsalves
- New York University School of Medicine/Cancer Institute, Department of Pharmacology, First Avenue, New York, NY 10016, USA
| | - Binita Changkakoty
- New York University School of Medicine/Cancer Institute, Department of Pharmacology, First Avenue, New York, NY 10016, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Avenue Louis Pasteur, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Avenue Louis Pasteur, Boston, MA 02115, USA
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180
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Ma E, MacRae IJ, Kirsch JF, Doudna JA. Autoinhibition of human dicer by its internal helicase domain. J Mol Biol 2008; 380:237-43. [PMID: 18508075 DOI: 10.1016/j.jmb.2008.05.005] [Citation(s) in RCA: 178] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Revised: 05/02/2008] [Accepted: 05/02/2008] [Indexed: 10/22/2022]
Abstract
Dicer, a member of the ribonuclease III family of enzymes, processes double-stranded RNA substrates into approximately 21- to 27-nt products that trigger sequence-directed gene silencing by RNA interference. Although the mechanism of RNA recognition and length-specific cleavage by Dicer has been established, the way in which dicing activity is regulated is unclear. Here, we show that the N-terminal domain of human Dicer, which is homologous to DExD/H-box helicases, substantially attenuates the rate of substrate cleavage. Deletion or mutation of this domain activates human Dicer in both single- and multiple-turnover assays. The catalytic efficiency (k(cat)/K(m)) of the deletion construct is increased by 65-fold over that exhibited by the intact enzyme. Kinetic analysis shows that this activation is almost entirely due to an enhancement in k(cat). Modest stimulation of catalysis by the full-length Dicer enzyme was observed in the presence of the TAR-RNA binding protein, which physically interacts with the DExD/H-box domain. These results suggest that the DExD/H-box domain likely disrupts the functionality of the Dicer active site until a structural rearrangement occurs, perhaps upon assembly with its molecular partners.
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Affiliation(s)
- Enbo Ma
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3206, USA
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181
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A study on the fundamental factors determining the efficacy of siRNAs with high C/G contents. Cell Mol Biol Lett 2008; 13:283-302. [PMID: 18197393 PMCID: PMC6275720 DOI: 10.2478/s11658-008-0001-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2007] [Accepted: 09/05/2007] [Indexed: 12/23/2022] Open
Abstract
Although there are many reports about the efficacy of siRNAs, it is not clear whether those siRNAs with high C/G contents can be used to silence their target mRNAs efficiently. In this study, we investigated the structure and function of a group of siRNAs with high C/G contents. The results showed that single siRNAs against the Calpain, Otoferlin and Her2 mRNAs could induce different silencing effects on their targets, suggesting that the accessibility to target sequences influences the efficacy of siRNA. Unexpectedly, a single siRNA could target its cognate sequence in the 3'UTR of EEF1D or the 5'UTR of hTRF2 or CDC6. Their interaction induced different modes of gene silencing. Furthermore, the introduction of mutations into the 3' end of the passenger strand showed that the position and number of mutated nucleotides could exert some influence on the efficacy of siRNA. However, these mutations did not completely block the passenger strand from exerting its RNAi effect. Interestingly, our findings also indicated that the target mRNA might play essential roles in maintaining or discarding the guide strand in RISCs. Thus, the conclusion could be drawn that favorable siRNA sequences, accessible target structures and the fast cleavage mode are necessary and sufficient prerequisites for efficient RNAi.
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182
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Heterodimer-based analysis of subunit and domain contributions to double-stranded RNA processing by Escherichia coli RNase III in vitro. Biochem J 2008; 410:39-48. [PMID: 17953512 DOI: 10.1042/bj20071047] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Members of the RNase III family are the primary cellular agents of dsRNA (double-stranded RNA) processing. Bacterial RNases III function as homodimers and contain two dsRBDs (dsRNA-binding domains) and two catalytic sites. The potential for functional cross-talk between the catalytic sites and the requirement for both dsRBDs for processing activity are not known. It is shown that an Escherichia coli RNase III heterodimer that contains a single functional wt (wild-type) catalytic site and an inactive catalytic site (RNase III[E117A/wt]) cleaves a substrate with a single scissile bond with a k(cat) value that is one-half that of wt RNase III, but exhibits an unaltered K(m). Moreover, RNase III[E117A/wt] cleavage of a substrate containing two scissile bonds generates singly cleaved intermediates that are only slowly cleaved at the remaining phosphodiester linkage, and in a manner that is sensitive to excess unlabelled substrate. These results demonstrate the equal probability, during a single binding event, of placement of a scissile bond in a functional or nonfunctional catalytic site of the heterodimer and reveal a requirement for substrate dissociation and rebinding for cleavage of both phosphodiester linkages by the mutant heterodimer. The rate of phosphodiester hydrolysis by RNase III[E117A/wt] has the same dependence on Mg(2+) ion concentration as that of the wt enzyme, and exhibits a Hill coefficient (h) of 2.0+/-0.1, indicating that the metal ion dependence essentially reflects a single catalytic site that employs a two-Mg(2+)-ion mechanism. Whereas an E. coli RNase III mutant that lacks both dsRBDs is inactive, a heterodimer that contains a single dsRBD exhibits significant catalytic activity. These findings support a reaction pathway involving the largely independent action of the dsRBDs and the catalytic sites in substrate recognition and cleavage respectively.
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183
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Pontes O, Pikaard CS. siRNA and miRNA processing: new functions for Cajal bodies. Curr Opin Genet Dev 2008; 18:197-203. [PMID: 18337083 DOI: 10.1016/j.gde.2008.01.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 01/13/2008] [Accepted: 01/16/2008] [Indexed: 12/27/2022]
Abstract
In diverse eukaryotes, micro-RNAs (miRNAs) and small interfering RNAs (siRNAs) regulate important processes that include mRNA inactivation, viral defense, chromatin modification, and transposon silencing. Recently, nucleolus-associated Cajal bodies in plants have been implicated as sites of siRNA and miRNA biogenesis, whereas in animals siRNA and miRNA dicing occurs in the cytoplasm. The plant nucleolus also contains proteins of the nonsense-mediated mRNA decay pathway that in animals are found associated with cytoplasmic processing bodies (P-bodies). P-bodies also function in the degradation of mRNAs subjected to miRNA and siRNA targeting. Collectively, these observations suggest interesting variations in the way siRNAs and miRNAs can accomplish their similar functions in plants and animals.
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Affiliation(s)
- Olga Pontes
- Biology Department, Washington University, 1 Brookings Drive, St. Louis, MO 63130, USA
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184
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Hayashi K, Chuva de Sousa Lopes SM, Kaneda M, Tang F, Hajkova P, Lao K, O'Carroll D, Das PP, Tarakhovsky A, Miska EA, Surani MA. MicroRNA biogenesis is required for mouse primordial germ cell development and spermatogenesis. PLoS One 2008; 3:e1738. [PMID: 18320056 PMCID: PMC2254191 DOI: 10.1371/journal.pone.0001738] [Citation(s) in RCA: 355] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2007] [Accepted: 01/24/2008] [Indexed: 01/07/2023] Open
Abstract
Background MicroRNAs (miRNAs) are critical regulators of transcriptional and post-transcriptional gene silencing, which are involved in multiple developmental processes in many organisms. Apart from miRNAs, mouse germ cells express another type of small RNA, piwi-interacting RNAs (piRNAs). Although it has been clear that piRNAs play a role in repression of retrotransposons during spermatogenesis, the function of miRNA in mouse germ cells has been unclear. Methodology/Principal Findings In this study, we first revealed the expression pattern of miRNAs by using a real-time PCR-based 220-plex miRNA expression profiling method. During development of germ cells, miR-17-92 cluster, which is thought to promote cell cycling, and the ES cell-specific cluster encoding miR-290 to -295 (miR-290-295 cluster) were highly expressed in primordial germ cells (PGCs) and spermatogonia. A set of miRNAs was developmentally regulated. We next analysed function of miRNA biogenesis in germ cell development by using conditional Dicer-knockout mice in which Dicer gene was deleted specifically in the germ cells. Dicer-deleted PGCs and spermatogonia exhibited poor proliferation. Retrotransposon activity was unexpectedly suppressed in Dicer-deleted PGCs, but not affected in the spermatogonia. In Dicer-deleted testis, spermatogenesis was retarded at an early stage when proliferation and/or early differentiation. Additionally, we analysed spermatogenesis in conditional Argonaute2-deficient mice. In contrast to Dicer-deficient testis, spermatogenesis in Argonaute2-deficient testis was indistinguishable from that in wild type. Conclusion/Significance These results illustrate that miRNAs are important for the proliferation of PGCs and spermatogonia, but dispensable for the repression of retrotransposons in developing germ cells. Consistently, miRNAs promoting cell cycling are highly expressed in PGCs and spermatogonia. Furthermore, based on normal spermatogenesis in Argonaute2-deficient testis, the critical function of Dicer in spermatogenesis is independent of Argonaute2.
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Affiliation(s)
- Katsuhiko Hayashi
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Masahiro Kaneda
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Fuchou Tang
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Petra Hajkova
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Kaiqin Lao
- Advanced Research Technology, Applied Biosystems, Foster City, California, United States of America
| | - Donal O'Carroll
- Laboratory of Lymphocyte Signaling, The Rockefeller University, New York, New York, United States of America
| | - Partha P. Das
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Alexander Tarakhovsky
- Laboratory of Lymphocyte Signaling, The Rockefeller University, New York, New York, United States of America
| | - Eric A. Miska
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - M. Azim Surani
- Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- * To whom correspondence should be addressed. E-mail:
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185
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Gewirtz AM. On future's doorstep: RNA interference and the pharmacopeia of tomorrow. J Clin Invest 2008; 117:3612-4. [PMID: 18060018 DOI: 10.1172/jci34274] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Small molecules and antibodies have revolutionized the treatment of malignant diseases and appear promising for the treatment of many others. Nonetheless, there are many candidate therapeutic targets that are not amenable to attack by the current generation of targeted therapies, and in a small but growing number of patients, resistance to initially successful treatments evolves. This Review Series on the medicinal promise of posttranscriptional gene silencing with small interfering RNA and other molecules capable of inducing RNA interference (RNAi) is motivated by the hypothesis that effectors of RNAi can be developed into effective drugs for treating malignancies as well as many other types of disease. As this Review Series points out, there is still much to do, but many in the field now hope that the time has finally arrived when "antisense" therapies will finally come of age and fulfill their promise as the magic bullets of the 21st century.
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Affiliation(s)
- Alan M Gewirtz
- Division of Hematology/Oncology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-6061, USA.
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186
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Structural and biochemical insights into the dicing mechanism of mouse Dicer: a conserved lysine is critical for dsRNA cleavage. Proc Natl Acad Sci U S A 2008; 105:2391-6. [PMID: 18268334 DOI: 10.1073/pnas.0711506105] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dicer, an RNase III enzyme, initiates RNA interference by processing precursor dsRNAs into mature microRNAs and small-interfering RNAs. It is also involved in loading and activation of the RNA-induced silencing complex. Here, we report the crystal structures of a catalytically active fragment of mouse Dicer, containing the RNase IIIb and dsRNA binding domains, in its apo and Cd(2+)-bound forms, at 1.68- and 2.8-A resolution, respectively. Models of this structure with dsRNA reveal that a lysine residue, highly conserved in Dicer RNase IIIa and IIIb domains and in Drosha RNase IIIb domains, has the potential to participate in the phosphodiester bond cleavage reaction by stabilizing the transition state and leaving group of the scissile bond. Mutational and enzymatic assays confirm the importance of this lysine in dsRNA cleavage, suggesting that this lysine represents a conserved catalytic residue of Dicers. The structures also reveals a approximately 45-aa region within the RNase IIIb domain that harbors an alpha-helix at the N-terminal half and a flexible loop at the C-terminal half, features not present in previously reported structures of homologous RNase III domains from either bacterial RNase III enzymes or Giardia Dicer. N-terminal residues of this alpha-helix have the potential to engage in minor groove interaction with dsRNA substrates.
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187
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Agüero-Chapín G, González-Díaz H, de la Riva G, Rodríguez E, Sánchez-Rodríguez A, Podda G, Vazquez-Padrón RI. MMM-QSAR Recognition of Ribonucleases without Alignment: Comparison with an HMM Model and Isolation from Schizosaccharomyces pombe, Prediction, and Experimental Assay of a New Sequence. J Chem Inf Model 2008; 48:434-48. [DOI: 10.1021/ci7003225] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guillermín Agüero-Chapín
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Humberto González-Díaz
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Gustavo de la Riva
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Edrey Rodríguez
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Aminael Sánchez-Rodríguez
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Gianni Podda
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Roberto I. Vazquez-Padrón
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
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188
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Kalidas S, Sanders C, Ye X, Strauss T, Kuhn M, Liu Q, Smith DP. Drosophila R2D2 mediates follicle formation in somatic tissues through interactions with Dicer-1. Mech Dev 2008; 125:475-85. [PMID: 18299191 DOI: 10.1016/j.mod.2008.01.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 01/10/2008] [Accepted: 01/14/2008] [Indexed: 11/27/2022]
Abstract
The miRNA pathway has been shown to regulate developmentally important genes. Dicer-1 is required to cleave endogenously encoded microRNA (miRNA) precursors into mature miRNAs that regulate endogenous gene expression. RNA interference (RNAi) is a gene silencing mechanism triggered by double-stranded RNA (dsRNA) that protects organisms from parasitic nucleic acids. In Drosophila, Dicer-2 cleaves dsRNA into 21 base-pair small interfering RNA (siRNA) that are loaded into RISC (RNA induced silencing complex) that in turn cleaves mRNAs homologous to the siRNAs. Dicer-2 co-purifies with R2D2, a low-molecular weight protein that loads siRNA onto Ago-2 in RISC. Loss of R2D2 results in defective RNAi. However, unlike mutants in other RNAi components like Dicer-2 or Ago-2, we report here that r2d2(1) mutants have striking developmental defects. r2d2(1) mutants have reduced female fertility, producing less than 1/10 the normal number of progeny. These escapers have normal morphology. We show R2D2 functions in the ovary, specifically in the somatic tissues giving rise to the stalk and other follicle cells critical for establishing the cellular architecture of the oocyte. Most interestingly, the female fertility defects are dramatically enhanced when one copy of the dcr-1 gene is missing and Dicer-1 protein co-immunoprecipitates with R2D2 antisera. These data show that r2d2(1) mutants have reduced viability and defective female fertility that stems from abnormal follicle cell function, and Dicer-1 impacts this process. We conclude that R2D2 functions beyond its role in RNA interference to include ovarian development in Drosophila.
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Affiliation(s)
- Savitha Kalidas
- Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard Dallas, TX 75390-9111, USA
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189
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Tomoyasu Y, Miller SC, Tomita S, Schoppmeier M, Grossmann D, Bucher G. Exploring systemic RNA interference in insects: a genome-wide survey for RNAi genes in Tribolium. Genome Biol 2008; 9:R10. [PMID: 18201385 PMCID: PMC2395250 DOI: 10.1186/gb-2008-9-1-r10] [Citation(s) in RCA: 359] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 11/13/2007] [Accepted: 01/17/2008] [Indexed: 12/13/2022] Open
Abstract
Tribolium resembles C. elegans in showing a robust systemic RNAi response, but does not have C. elegans-type RNAi mechanisms; insect systemic RNAi probably uses a different mechanism. Background RNA interference (RNAi) is a highly conserved cellular mechanism. In some organisms, such as Caenorhabditis elegans, the RNAi response can be transmitted systemically. Some insects also exhibit a systemic RNAi response. However, Drosophila, the leading insect model organism, does not show a robust systemic RNAi response, necessitating another model system to study the molecular mechanism of systemic RNAi in insects. Results We used Tribolium, which exhibits robust systemic RNAi, as an alternative model system. We have identified the core RNAi genes, as well as genes potentially involved in systemic RNAi, from the Tribolium genome. Both phylogenetic and functional analyses suggest that Tribolium has a somewhat larger inventory of core component genes than Drosophila, perhaps allowing a more sensitive response to double-stranded RNA (dsRNA). We also identified three Tribolium homologs of C. elegans sid-1, which encodes a possible dsRNA channel. However, detailed sequence analysis has revealed that these Tribolium homologs share more identity with another C. elegans gene, tag-130. We analyzed tag-130 mutants, and found that this gene does not have a function in systemic RNAi in C. elegans. Likewise, the Tribolium sid-like genes do not seem to be required for systemic RNAi. These results suggest that insect sid-1-like genes have a different function than dsRNA uptake. Moreover, Tribolium lacks homologs of several genes important for RNAi in C. elegans. Conclusion Although both Tribolium and C. elegans show a robust systemic RNAi response, our genome-wide survey reveals significant differences between the RNAi mechanisms of these organisms. Thus, insects may use an alternative mechanism for the systemic RNAi response. Understanding this process would assist with rendering other insects amenable to systemic RNAi, and may influence pest control approaches.
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Affiliation(s)
- Yoshinori Tomoyasu
- Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA.
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190
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Abstract
Genetic and biochemical analyses in model systems such as the fruitfly, Drosophila melanogaster, have successfully identified several genes that play key regulatory roles in fundamental cellular and developmental processes. However, the analyses of the complete genome sequences of Drosophila, as well as of humans, now reveal that traditional methods have ascribed functions to only a fraction of the total predicted genes. Thus, the roles for many, as yet unidentified genes, in normal development and cancer remain to be discovered. The challenge presented by the various large-scale genome projects is how to derive biologically relevant information from the raw sequences. The past few years have witnessed a rapid growth in the development and implementation high-throughput screening (HTS) technologies that researchers are now using to discover "gene-function" in an unbiased, systematic, and time-efficient manner. In fact one of the most promising functional genomic approach that has emerged in the past few years is based on RNA-interference (RNAi), in which the introduction of double-stranded RNA (dsRNA) into cells or whole organisms has been shown to be an effective tool to suppress endogenous gene expression. The RNAi technology has made it feasible to query the function of every gene in the genome for their potential function in a given cell-biological process using cell-based assays. This chapter discusses the application, advantages, and limitations of this powerful technology in the identification of novel modulators of cell-signaling pathways as well as its future scope and utility in designing more efficient genome-scale screens.
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Affiliation(s)
- Ramanuj DasGupta
- Department of Pharmacology, New York University School of Medicine/Cancer Institute, New York, NY, USA
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191
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Abstract
MicroRNAs (miRNAs) are approximately 22 nucleotide RNAs that mediate the posttranscriptional regulation of gene expression. miRNAs regulate diverse cellular processes such as development, differentiation, cell cycling, apoptosis, and immune responses. More than 400 miRNAs have been identified in humans and it is predicted that over 30% of human gene transcripts are regulated via miRNAs. Since 2004, many viral miRNAs have been described in several families of viruses. More than half of currently known viral miRNAs are encoded by viruses of the human Herepsviridae and 14 miRNAs have been found to be encoded by Human cytomegalovirus (HCMV). Thus far, HCMV is the only betaherpesvirus in which miRNAs have been described and these miRNAs possess many characteristics, including their genomic arrangement and temporal/spatial expression, which distinguish them from the other known herpesvirus miRNAs described. As a herpesvirus, HCMV establishes infection for the life of the host characterized by latent infection with periodic reactivation for production and spread of infectious progeny. This multifaceted life cycle of the herpesvirus requires an abundance of gene products and regulatory elements that makes cytomegalovirus genomes one of the most complex among human viruses. The defining characteristics of the cytomegalovirus and the minimal impact on genome size afforded by miRNAs inform the logic of virus-encoded miRNAs.
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192
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A multifunctional and reversibly polymerizable carrier for efficient siRNA delivery. Biomaterials 2008; 29:15-22. [DOI: 10.1016/j.biomaterials.2007.08.048] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Accepted: 08/30/2007] [Indexed: 11/17/2022]
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195
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Gonzalez-Alegre P, Paulson HL. Technology insight: therapeutic RNA interference--how far from the neurology clinic? ACTA ACUST UNITED AC 2007; 3:394-404. [PMID: 17611488 DOI: 10.1038/ncpneuro0551] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 05/10/2007] [Indexed: 12/15/2022]
Abstract
As an evolutionarily conserved cellular pathway to regulate endogenous gene expression, RNA interference (RNAi) has been implicated in diverse biological processes. Biologists now routinely exploit this cellular pathway to suppress virtually any target gene in a sequence-specific manner, including dominantly acting genes that cause incurable neurodegenerative disorders. The development of RNAi as potential therapy for such diseases has generated considerable interest, partly because of the success of early studies of therapeutic RNAi in rodent models for a range of neurodegenerative diseases. In this article, we review the progress of RNAi therapy to date, and assess the challenges ahead for the application of such therapy to neurodegenerative diseases. We discuss the various strategies that might be used to achieve this goal, outline the preclinical studies that have already been completed, and highlight the experimental questions that need to be answered before human clinical trials can begin.
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196
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Viegas SC, Pfeiffer V, Sittka A, Silva IJ, Vogel J, Arraiano CM. Characterization of the role of ribonucleases in Salmonella small RNA decay. Nucleic Acids Res 2007; 35:7651-64. [PMID: 17982174 PMCID: PMC2190706 DOI: 10.1093/nar/gkm916] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In pathogenic bacteria, a large number of sRNAs coordinate adaptation to stress and expression of virulence genes. To better understand the turnover of regulatory sRNAs in the model pathogen, Salmonella typhimurium, we have constructed mutants for several ribonucleases (RNase E, RNase G, RNase III, PNPase) and Poly(A) Polymerase I. The expression profiles of four sRNAs conserved among many enterobacteria, CsrB, CsrC, MicA and SraL, were analysed and the processing and stability of these sRNAs was studied in the constructed strains. The degradosome was a common feature involved in the turnover of these four sRNAs. PAPI-mediated polyadenylation was the major factor governing SraL degradation. RNase III was revealed to strongly affect MicA decay. PNPase was shown to be important in the decay of these four sRNAs. The stability of CsrB and CsrC seemed to be independent of the RNA chaperone, Hfq, whereas the decay of SraL and MicA was Hfq-dependent. Taken together, the results of this study provide initial insight into the mechanisms of sRNA decay in Salmonella, and indicate specific contributions of the RNA decay machinery components to the turnover of individual sRNAs.
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Affiliation(s)
- Sandra C Viegas
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Apartado 127, 2781-901 Oeiras, Portugal
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198
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Tougou M, Yamagishi N, Furutani N, Shizukawa Y, Takahata Y, Hidaka S. Soybean dwarf virus-resistant transgenic soybeans with the sense coat protein gene. PLANT CELL REPORTS 2007; 26:1967-75. [PMID: 17632723 DOI: 10.1007/s00299-007-0404-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Revised: 06/18/2007] [Accepted: 06/23/2007] [Indexed: 05/16/2023]
Abstract
We transformed a construct containing the sense coat protein (CP) gene of Soybean dwarf virus (SbDV) into soybean somatic embryos via microprojectile bombardment to acquire SbDV-resistant soybean plants. Six independent T(0) plants were obtained. One of these transgenic lines was subjected to further extensive analysis. Three different insertion patterns of Southern blot hybridization analysis in T(1) plants suggested that these insertions introduced in T(0) plants were segregated from each other or co-inherited in T(1) progenies. These insertions were classified into two types, which overexpressed SbDV-CP mRNA and accumulated SbDV-CP-specific short interfering RNA (siRNA), or repressed accumulation of SbDV-CP mRNA and siRNA by RNA analysis prior to SbDV inoculation. After inoculation of SbDV by the aphids, most T(2) plants of this transgenic line remained symptomless, contained little SbDV-specific RNA by RNA dot-blot hybridization analysis and exhibited SbDV-CP-specific siRNA. We discuss here the possible mechanisms of the achieved resistance, including the RNA silencing.
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Affiliation(s)
- Makoto Tougou
- National Agricultural Research Center for Tohoku Region, Morioka, Iwate 020-0198, Japan.
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199
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Abstract
RNA interference is involved in many aspects of cell biology, and the recent identification of germ-cell specific small RNAs has led to speculation that RNAi might also be involved in gametogenesis. Work in yeast indicates that RNAi is involved in establishing and maintaining heterochromatin at centromeres, an important component of yeast and mammalian meiosis. Here we review developments in the field of RNAi and relate these to possible roles in mammalian gametogenesis.
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Affiliation(s)
- Rebecca J Holmes
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14853, USA.
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Nelson PT, De Planell-Saguer M, Lamprinaki S, Kiriakidou M, Zhang P, O'Doherty U, Mourelatos Z. A novel monoclonal antibody against human Argonaute proteins reveals unexpected characteristics of miRNAs in human blood cells. RNA (NEW YORK, N.Y.) 2007; 13:1787-92. [PMID: 17720879 PMCID: PMC1986805 DOI: 10.1261/rna.646007] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Argonaute (Ago) proteins bind to microRNA (miRNAs) and short interfering RNAs (siRNAs) and form the core components of effector complexes that mediate miRNA and siRNA function. Currently, there is a paucity of reliable antibodies against mammalian Ago proteins, thus precluding studies of endogenous Ago proteins from tissues. Here we report the development of 2A8, a novel anti-Ago monoclonal antibody that recognizes human and mouse Ago proteins and efficiently immunoprecipitates miRNAs. We report the characterization of 2A8 and its use to clone miRNAs from human brain and from preparations of human polymorphonuclear leukocytes (neutrophils), which revealed a prevalent miRNA with unusual features.
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Affiliation(s)
- Peter T Nelson
- Department of Pathology, University of Kentucky, Lexington, KY 40536, USA.
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