401
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402
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In vitro analyses of the production and activity of secondary small interfering RNAs in C. elegans. EMBO J 2007; 26:5007-19. [PMID: 18007599 DOI: 10.1038/sj.emboj.7601910] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 10/10/2007] [Indexed: 11/08/2022] Open
Abstract
In the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) play important roles as intermediates. Primary siRNAs are produced from trigger dsRNAs by an RNaseIII-related enzyme called Dicer; in some organisms, secondary siRNAs are also produced by processes involving RNA-dependent RNA polymerases (RdRPs), which act on target mRNAs. Using a cell-free assay system prepared from Caenorhabditis elegans, we analyzed the production and activity of secondary siRNAs. In this cell-free system, RdRP activity acts on mRNA-derived templates to produce small RNAs. The RRF-1 complex is predominantly responsible for the RdRP activity, and synthesizes secondary-type siRNA molecules in a Dicer-independent manner. Notably, secondary-type siRNAs induce a prominent Slicer activity to cleave target mRNAs far more effectively than primary-type siRNAs. An Argonaute protein, CSR-1, is responsible for the Slicer activity induced by secondary-type siRNAs. Secondary rather than primary siRNAs may play a major role in the destabilization of target transcripts during RNAi in C. elegans.
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403
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Abstract
The specificity of RNA silencing is conferred by small RNA guides that are processed from structured RNA or dsRNA. The core components for small RNA biogenesis and effector functions have proliferated and specialized in eukaryotic lineages, resulting in diversified pathways that control expression of endogenous and exogenous genes, invasive elements and viruses, and repeated sequences. Deployment of small RNA pathways for spatiotemporal regulation of the transcriptome has shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms.
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404
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Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, Fire AZ. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 2007; 35:e130. [PMID: 17932070 PMCID: PMC2095802 DOI: 10.1093/nar/gkm760] [Citation(s) in RCA: 285] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Multiplexed high-throughput pyrosequencing is currently limited in complexity (number of samples sequenced in parallel), and in capacity (number of sequences obtained per sample). Physical-space segregation of the sequencing platform into a fixed number of channels allows limited multiplexing, but obscures available sequencing space. To overcome these limitations, we have devised a novel barcoding approach to allow for pooling and sequencing of DNA from independent samples, and to facilitate subsequent segregation of sequencing capacity. Forty-eight forward–reverse barcode pairs are described: each forward and each reverse barcode unique with respect to at least 4 nt positions. With improved read lengths of pyrosequencers, combinations of forward and reverse barcodes may be used to sequence from as many as n2 independent libraries for each set of ‘n’ forward and ‘n’ reverse barcodes, for each defined set of cloning-linkers. In two pilot series of barcoded sequencing using the GS20 Sequencer (454/Roche), we found that over 99.8% of obtained sequences could be assigned to 25 independent, uniquely barcoded libraries based on the presence of either a perfect forward or a perfect reverse barcode. The false-discovery rate, as measured by the percentage of sequences with unexpected perfect pairings of unmatched forward and reverse barcodes, was estimated to be <0.005%.
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Affiliation(s)
- Poornima Parameswaran
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford Genome Technology Center, Stanford University, Stanford, CA-94305, USA
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405
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Martín R, Arenas C, Daròs JA, Covarrubias A, Reyes JL, Chua NH. Characterization of small RNAs derived from Citrus exocortis viroid (CEVd) in infected tomato plants. Virology 2007; 367:135-46. [PMID: 17559901 DOI: 10.1016/j.virol.2007.05.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 04/05/2007] [Accepted: 05/07/2007] [Indexed: 01/04/2023]
Abstract
In plants, RNA silencing provides an adaptive immune system that inactivates pathogenic nucleic acids, guided by 21-24-mer RNAs of pathogen origin. The characterization of pathogen-related small RNAs (sRNAs) is relevant to uncovering the strategies used by pathogens to evade host defense responses. Several groups have reported the detection of viroid-derived sRNAs during infections, although the origin of these sRNAs and their chemical characteristics were poorly understood. Here, we describe the in vivo cleavage of Citrus exocortis viroid (CEVd) RNA into sRNAs of 21-22 nt, that are phosphorylated at their 5'-end and methylated at 3'. Our studies suggested that the CEVd genomic RNA might be the predominant in vivo substrate for cleavage by Dicer-like enzyme(s), which preferentially targeted residues mainly located within the right-end domain of the viroid. Further analysis on the accumulation levels of specific miRNAs controlling major regulators of leaf development and the miRNA pathway and the levels of their target mRNAs provided evidence that the endogenous tomato miRNA pathway was not affected by CEVd infection.
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Affiliation(s)
- Raquel Martín
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Ave. New York, NY10021, USA
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406
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Asikainen S, Storvik M, Lakso M, Wong G. Whole genome microarray analysis of C. elegans rrf-3 and eri-1 mutants. FEBS Lett 2007; 581:5050-4. [PMID: 17919598 DOI: 10.1016/j.febslet.2007.09.043] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 09/19/2007] [Indexed: 10/22/2022]
Abstract
We performed genome wide gene expression analysis on L4 stage Caenorhabditis elegans rrf-3(pk1426) and eri-1(mg366) mutant strains to study the effects caused by loss of their encoded proteins, which are required for the accumulation of endogenous secondary siRNAs. Mutant rrf-3 and eri-1 strains exhibited 72 transcripts that were co-over-expressed and 4 transcripts co-under-expressed (>2-fold, P<0.05) compared to N2 wild type strain. Ontology analysis indicated these transcripts were over represented for protein phosphorylation and sperm function genes. These results provide additional support for the hypothesis that RRF-3 and ERI-1 act together in the endo-siRNA pathway, and furthermore suggests their involvement in additional biological processes.
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Affiliation(s)
- Suvi Asikainen
- Department of Neurobiology, A.I. Virtanen Institute, Kuopio University, Kuopio 70211, Finland
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407
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Steiner FA, Hoogstrate SW, Okihara KL, Thijssen KL, Ketting RF, Plasterk RHA, Sijen T. Structural features of small RNA precursors determine Argonaute loading in Caenorhabditis elegans. Nat Struct Mol Biol 2007; 14:927-33. [PMID: 17891148 DOI: 10.1038/nsmb1308] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 09/04/2007] [Indexed: 01/28/2023]
Abstract
In C. elegans, DCR-1 is required for the maturation of both short interfering RNAs (siRNAs) and microRNAs (miRNAs), which are subsequently loaded into different Argonaute proteins to mediate silencing via distinct mechanisms. We used in vivo analyses to show that precursors of small RNAs contain structural features that direct the small RNAs into the RNA interference (RNAi) pathway or the miRNA-processing pathway. Nucleotide changes in the pre-let-7 miRNA precursor that make its stem fully complementary cause the resulting small RNA to be recognized as siRNA and induce binding to RDE-1, which leads to RNAi. Mismatches of 1 to 3 nucleotides at various positions in the stem of the precursor restore direction into the miRNA pathway, as the largest portion of such small RNA variants is associated with ALG-1. The Argonaute proteins to which the small RNAs are bound determine the silencing mode, and no functional overlap between RDE-1 and ALG-1 was detected.
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Affiliation(s)
- Florian A Steiner
- Hubrecht Institute, Koninklijke Nederlandse Akademie van Wetenschappen, Utrecht, 3584 CT, The Netherlands.
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408
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Abstract
Plants and invertebrates can protect themselves from viral infection through RNA silencing. This antiviral immunity involves production of virus-derived small interfering RNAs (viRNAs) and results in specific silencing of viruses by viRNA-guided effector complexes. The proteins required for viRNA production as well as several key downstream components of the antiviral immunity pathway have been identified in plants, flies, and worms. Meanwhile, viral mechanisms to suppress this small RNA-directed immunity by viruses are being elucidated, thereby illuminating an ongoing molecular arms race that likely impacts the evolution of both viral and host genomes.
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Affiliation(s)
- Shou-Wei Ding
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Correspondence: (S.W.D.), (O.V.)
| | - Olivier Voinnet
- Institut de Biologie Moléculaire des plantes, CNRS, Université Louis Pasteur, 67084 Strasbourg Cedex, France
- Correspondence: (S.W.D.), (O.V.)
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409
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Affiliation(s)
- Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Room L235, Stanford, CA 94305-5324, USA.
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410
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411
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Two hypotheses to explain why RNA interference does not work in animal parasitic nematodes. Int J Parasitol 2007; 38:43-7. [PMID: 18028931 DOI: 10.1016/j.ijpara.2007.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 08/15/2007] [Accepted: 08/21/2007] [Indexed: 01/18/2023]
Abstract
RNA interference (RNAi) has been used extensively in model organisms such as Caenorhabditis elegans. Methods developed for RNAi in C. elegans have also been used in parasitic nematodes. However, RNAi in parasitic nematodes has been unsuccessful or has had limited success. Studies of genes essential for RNAi in C. elegans and of RNAi in Caenorhabditis spp. other than C. elegans suggest two complementary, and testable, hypotheses for the limited success of RNAi in animal parasitic nematodes. These are: (i) that the external supply of double stranded RNA (dsRNA) to parasitic nematodes is inappropriate to achieve RNAi and (ii) that parasitic nematodes are functionally defective in genes required to initiate RNAi from externally supplied dsRNA.
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412
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Hartig JV, Tomari Y, Förstemann K. piRNAs--the ancient hunters of genome invaders. Genes Dev 2007; 21:1707-13. [PMID: 17639076 DOI: 10.1101/gad.1567007] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In addition to miRNAs and siRNAs, a third small RNA silencing system has been uncovered that prevents the spreading of selfish genetic elements. Production of the Piwi-associated RNAs (piRNAs), which mediate the silencing activity in this pathway, is initiated at a few master control regions within the genome. The nature of the primary piRNA-generating transcript is still unknown, but RNA interference (RNAi)-like cleavage events are likely defining the 5'-ends of mature piRNAs. We summarize the recent literature on piRNA biogenesis and function with an emphasis on work in Drosophila, where genetics and biochemistry have met very successfully.
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413
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Gu SG, Pak J, Barberan-Soler S, Ali M, Fire A, Zahler AM. Distinct ribonucleoprotein reservoirs for microRNA and siRNA populations in C. elegans. RNA (NEW YORK, N.Y.) 2007; 13:1492-504. [PMID: 17652138 PMCID: PMC1950768 DOI: 10.1261/rna.581907] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
MicroRNAs (miRNAs) are regulatory molecules that share both biosynthetic derivation (cleavage from short hairpin precursor RNAs) and functional roles (downregulation of specific mRNAs through targeted degradation and/or translational inhibition). A distinct family of small RNAs, termed siRNAs, have some common characteristics but exhibit distinct modes of biosynthesis and function. In this study, we report procedures for purification of a predominant species of miRNA-containing ribonucleoprotein complexes from Caenorhabditis elegans and demonstrate that this population is distinct from the predominant pool of siRNA-containing ribonucleoprotein complexes. An observed miRNP-associated RNA population consisting predominantly (>95%) of miRNAs supported the unique identity of miRNPs as biological effectors within the cell, provided clean material for analysis of changes in miRNA spectra during development, and provided strong evidence of miRNA character for a number of novel small RNAs. Likewise, the RNA spectrum derived from partial siRNP purification was useful in defining functional characteristics of this more diverse population of small RNAs.
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Affiliation(s)
- Sam G Gu
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California Santa Cruz 95064, USA
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414
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Lilley CJ, Bakhetia M, Charlton WL, Urwin PE. Recent progress in the development of RNA interference for plant parasitic nematodes. MOLECULAR PLANT PATHOLOGY 2007; 8:701-11. [PMID: 20507531 DOI: 10.1111/j.1364-3703.2007.00422.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
SUMMARY RNA interference (RNAi), first described for Caenorhabditis elegans, has emerged as a powerful gene silencing tool for investigating gene function in a range of organisms. Recent studies have described its application to plant parasitic nematodes. Genes expressed in a range of cell types are silenced when preparasitic juvenile nematodes take up double-stranded (ds)RNA that elicits a systemic RNAi response. Important developments over the last year have shown that in planta expression of a dsRNA targeting a nematode gene can successfully induce silencing in parasitizing nematodes. When the targeted gene has an essential function, a resistance effect is observed paving the way for the potential use of RNAi technology to control plant parasitic nematodes.
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415
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Moissiard G, Parizotto EA, Himber C, Voinnet O. Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins. RNA (NEW YORK, N.Y.) 2007; 13:1268-78. [PMID: 17592042 PMCID: PMC1924903 DOI: 10.1261/rna.541307] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In plants, worms, and fungi, RNA-dependent RNA polymerases (RDRs) amplify the production of short-interfering RNAs (siRNAs) that mediate RNA silencing. In Arabidopsis, RDR6 is thought to copy endogenous and exogenous RNA templates into double-stranded RNAs (dsRNAs), which are subsequently processed into siRNAs by one or several of the four Dicer-like enzymes (DCL1-->4). This reaction produces secondary siRNAs corresponding to sequences outside the primary targeted regions of a transcript, a phenomenon called transitivity. One recognized role of RDR6 is to strengthen the RNA silencing response mounted by plants against viruses. Accordingly, suppressor proteins deployed by viruses inhibit this defense. However, interactions between silencing suppressors and RDR6 have not yet been documented. Additionally, the mechanism underlying transitivity remains poorly understood. Here, we report how several viral silencing suppressors inhibit the RDR6-dependent amplification of virus-induced and transgene-induced gene silencing. Viral suppression of primary siRNA accumulation shows that transitivity can be initiated with minute amounts of DCL4-dependent 21-nucleotide (nt)-long siRNAs, whereas DCL3-dependent 24-nt siRNAs appear dispensable for this process. We further show that unidirectional (3-->5') transitivity requires the hierarchical and redundant functions of DCL4 and DCL2 acting downstream from RDR6 to produce 21- and 22-nt-long siRNAs, respectively. The 3-->5' transitive reaction is likely to be processive over >750 nt, with secondary siRNA production progressively decreasing as the reaction proceeds toward the 5'-proximal region of target transcripts. Finally, we show that target cleavage by a primary small RNA and 3-->5' transitivity can be genetically uncoupled, and we provide in vivo evidence supporting a key role for priming in this specific reaction.
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416
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Lee SR, Collins K. Physical and functional coupling of RNA-dependent RNA polymerase and Dicer in the biogenesis of endogenous siRNAs. Nat Struct Mol Biol 2007; 14:604-10. [PMID: 17603500 DOI: 10.1038/nsmb1262] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Accepted: 05/22/2007] [Indexed: 12/23/2022]
Abstract
Many classes of small RNA (sRNA) involved in RNA silencing are generated by double-stranded RNA (dsRNA) processing. Although principles of sRNA biogenesis have emerged, newly identified classes of sRNAs have features that suggest additional biogenesis mechanisms. Tetrahymena thermophila expresses one such class, comprising sRNAs of 23 and 24 nucleotides (nt) with an absolute strand bias in accumulation. Here we demonstrate sRNA production by the T. thermophila Dicer Dcr2 and the RNA-dependent RNA polymerase Rdr1, which purifies as a multisubunit RNA-dependent RNA polymerase complex (RDRC). Dcr2 and RDRC interact, stimulating Dcr2 activity. Moreover, Dcr2 specificity is influenced by RDRC beyond this physical interaction, as Dcr2 generates discrete 23- and 24-nt sRNAs only from dsRNA with a 5'-triphosphate. These findings suggest that sRNA strand bias arises from Dcr2 processing polarity, conferred by physical and functional coupling of RDRC and Dicer enzymes.
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Affiliation(s)
- Suzanne R Lee
- Department of Molecular and Cell Biology, University of California - Berkeley, 142 Life Sciences Addition 3200, Berkeley, California 94720-3200, USA
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417
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Welker NC, Habig JW, Bass BL. Genes misregulated in C. elegans deficient in Dicer, RDE-4, or RDE-1 are enriched for innate immunity genes. RNA (NEW YORK, N.Y.) 2007; 13:1090-102. [PMID: 17526642 PMCID: PMC1894926 DOI: 10.1261/rna.542107] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 04/23/2007] [Indexed: 05/15/2023]
Abstract
We describe the first microarray analysis of a whole animal containing a mutation in the Dicer gene. We used adult Caenorhabditis elegans and, to distinguish among different roles of Dicer, we also performed microarray analyses of animals with mutations in rde-4 and rde-1, which are involved in silencing by siRNA, but not miRNA. Surprisingly, we find that the X chromosome is greatly enriched for genes regulated by Dicer. Comparison of all three microarray data sets indicates the majority of Dicer-regulated genes are not dependent on RDE-4 or RDE-1, including the X-linked genes. However, all three data sets are enriched in genes important for innate immunity and, specifically, show increased expression of innate immunity genes.
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Affiliation(s)
- Noah C Welker
- Department of Biochemistry and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, 84112, USA
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418
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Abstract
Recent studies suggest that knowledge of differential expression of microRNAs (miRNA) in cancer may have substantial diagnostic and prognostic value. Here, we use a direct sequencing method to characterize the profiles of miRNAs and other small RNA segments for six human cervical carcinoma cell lines and five normal cervical samples. Of 166 miRNAs expressed in normal cervix and cancer cell lines, we observed significant expression variation of six miRNAs between the two groups. To further show the biological relevance of our findings, we examined the expression level of two significantly varying miRNAs in a panel of 29 matched pairs of human cervical cancer and normal cervical samples. Reduced expression of miR-143 and increased expression of miR-21 were reproducibly displayed in cancer samples, suggesting the potential value of these miRNAs as tumor markers. In addition to the known miRNAs, we found a number of novel miRNAs and an additional set of small RNAs that do not meet miRNA criteria.
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Affiliation(s)
- Weng-Onn Lui
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305-5324, USA
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419
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Dorner S, Eulalio A, Huntzinger E, Izaurralde E. Delving into the diversity of silencing pathways. Symposium on MicroRNAs and siRNAs: biological functions and mechanisms. EMBO Rep 2007; 8:723-9. [PMID: 17599087 PMCID: PMC1978081 DOI: 10.1038/sj.embor.7401015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Accepted: 05/22/2007] [Indexed: 01/09/2023] Open
Affiliation(s)
- Silke Dorner
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany
| | - Ana Eulalio
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany
| | - Eric Huntzinger
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany
| | - Elisa Izaurralde
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany
- Tel: +49 70 71 601 1350; Fax: +49 70 71 601 1353;
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420
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Axtell MJ, Snyder JA, Bartel DP. Common functions for diverse small RNAs of land plants. THE PLANT CELL 2007; 19:1750-69. [PMID: 17601824 PMCID: PMC1955733 DOI: 10.1105/tpc.107.051706] [Citation(s) in RCA: 297] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Revised: 06/06/2007] [Accepted: 06/08/2007] [Indexed: 05/16/2023]
Abstract
Endogenous small RNAs, including microRNAs (miRNAs) and short interfering RNAs (siRNAs), are critical components of plant gene regulation. Some abundant miRNAs involved in developmental control are conserved between anciently diverged plants, while many other less-abundant miRNAs appear to have recently emerged in the Arabidopsis thaliana lineage. Using large-scale sequencing of small RNAs, we extended the known diversity of miRNAs in basal plants to include 88 confidently annotated miRNA families in the moss Physcomitrella patens and 44 in the lycopod Selaginella moellendorffii. Cleavage of 29 targets directed by 14 distinct P. patens miRNA families and a trans-acting siRNA (ta-siRNA) was experimentally confirmed. Despite a core set of 12 miRNA families also expressed in angiosperms, weakly expressed and apparently lineage-specific miRNAs accounted for the majority of miRNA diversity in both species. Nevertheless, the molecular functions of several of these lineage-specific small RNAs matched those of angiosperms, despite dissimilarities in the small RNA sequences themselves, including small RNAs that mediated negative feedback regulation of the miRNA pathway and miR390-dependent ta-siRNAs that guided the cleavage of AUXIN RESPONSE FACTOR mRNAs. Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants.
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Affiliation(s)
- Michael J Axtell
- Department of Biology and Huck Institutes of the Life Sciences, Pensylvania State University, University Park, PA 16802, USA.
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421
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Reamon-Buettner SM, Borlak J. A new paradigm in toxicology and teratology: altering gene activity in the absence of DNA sequence variation. Reprod Toxicol 2007; 24:20-30. [PMID: 17596910 DOI: 10.1016/j.reprotox.2007.05.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Revised: 04/30/2007] [Accepted: 05/08/2007] [Indexed: 10/23/2022]
Abstract
'Epigenetics' is a heritable phenomenon without change in primary DNA sequence. In recent years, this field has attracted much attention as more epigenetic controls of gene activities are being discovered. Such epigenetic controls ensue from an interplay of DNA methylation, histone modifications, and RNA-mediated pathways from non-coding RNAs, notably silencing RNA (siRNA) and microRNA (miRNA). Although epigenetic regulation is inherent to normal development and differentiation, this can be misdirected leading to a number of diseases including cancer. All the same, many of the processes can be reversed offering a hope for epigenetic therapies such as inhibitors of enzymes controlling epigenetic modifications, specifically DNA methyltransferases, histone deacetylases, and RNAi therapeutics. 'In utero' or early life exposures to dietary and environmental exposures can have a profound effect on our epigenetic code, the so-called 'epigenome', resulting in birth defects and diseases developed later in life. Indeed, examples are accumulating in which environmental exposures can be attributed to epigenetic causes, an encouraging edge towards greater understanding of the contribution of epigenetic influences of environmental exposures. Routine analysis of epigenetic modifications as part of the mechanisms of action of environmental contaminants is in order. There is, however, an explosion of research in the field of epigenetics and to keep abreast of these developments could be a challenge. In this paper, we provide an overview of epigenetic mechanisms focusing on recent reviews and studies to serve as an entry point into the realm of 'environmental epigenetics'.
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Affiliation(s)
- Stella Marie Reamon-Buettner
- Molecular Medicine and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine, Nikolai Fuchs Strasse 1, 30625 Hannover, Germany
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422
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423
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Smith LM, Pontes O, Searle I, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS, Baulcombe DC. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. THE PLANT CELL 2007; 19:1507-21. [PMID: 17526749 PMCID: PMC1913737 DOI: 10.1105/tpc.107.051540] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The silencing phenotype in Arabidopsis thaliana lines with an inverted repeat transgene under the control of a phloem-specific promoter was manifested in regions around veins due to a mobile signal of silencing. Genetic analysis implicates RNA-DEPENDENT RNA POLYMERASE2 (RDR2) and an RNA polymerase IVa subunit gene (NRPD1a) in the signaling mechanism. We also identified an SNF2 domain-containing protein (CLASSY1) that acts together with RDR2 and NRPD1a in the spread of transgene silencing and in the production of endogenous 24-nucleotide short interfering RNAs (siRNAs). Cytochemical analysis indicates that CLASSY1 may act in the nucleus with NRPD1a and RDR2 in the upstream part of RNA silencing pathways that generate a double-stranded RNA substrate for Dicer-like (DCL) nucleases. DCL3 and ARGONAUTE4 act in a downstream part of the pathway, leading to endogenous 24-nucleotide siRNA production, but are not required for intercellular signaling. From genetic analysis, we conclude that another downstream part of the pathway associated with intercellular signaling requires DCL4 and at least one other protein required for 21-nucleotide trans-acting siRNAs. We interpret the effect of polymerase IVa and trans-acting siRNA pathway mutations in terms of a modular property of RNA silencing pathways.
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Affiliation(s)
- Lisa M Smith
- Sainsbury Laboratory, John Ines Centre, Norwich NR4 7UH, United Kingdom
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424
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Abstract
A recent Keystone Symposium on 'MicroRNAs and siRNAs: Biological Functions and Mechanisms' was organized by David Bartel and Shiv Grewal (and was held in conjunction with 'RNAi for Target Validation and as a Therapeutic', organized by Stephen Friend and John Maraganore). The 'MicroRNAs and siRNAs' meeting brought together scientists working on diverse biological aspects of small regulatory RNAs, including microRNAs, small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs and rasiRNAs). Among the themes discussed were the diversity of small regulatory RNAs and their developmental functions, their biogenesis, the identification of their regulatory targets, their mechanisms of action, and their roles in the elaboration of multicellular complexity.
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425
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426
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MESH Headings
- Animals
- Base Pairing
- Caenorhabditis elegans/genetics
- Caenorhabditis elegans/metabolism
- Caenorhabditis elegans Proteins/metabolism
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Models, Genetic
- Phosphorylation
- Plant Proteins/metabolism
- Plants/genetics
- RNA Interference
- RNA, Antisense/metabolism
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/metabolism
- RNA, Helminth/biosynthesis
- RNA, Helminth/metabolism
- RNA, Messenger/metabolism
- RNA, Plant/biosynthesis
- RNA, Plant/metabolism
- RNA, Small Interfering/biosynthesis
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA-Dependent RNA Polymerase/metabolism
- Ribonuclease III/metabolism
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Searle IR, Mosher RA, Melnyk CW, Baulcombe DC. Small RNAs hit the big time. THE NEW PHYTOLOGIST 2007; 174:479-482. [PMID: 17447904 DOI: 10.1111/j.1469-8137.2007.02070.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
| | - Rebecca A Mosher
- The Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, UK
| | - Charles W Melnyk
- The Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, UK
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