401
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Abstract
Non-coding small RNAs (19-24 nucleotide long) have recently been recognized as the important regulator of gene expression in both plants and animals. Several classes of endogenous short RNAs have partial or near perfect complementarity to mRNAs and a protein complex is guided by short RNAs to target mRNAs. The targeted mRNA is either cleaved or its translation is suppressed. Initially, short RNAs were believed to primarily regulate the normal development of plants and animals, but recent advances implicate short RNAs in environmental adaptation.
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Affiliation(s)
- Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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402
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Sulmon C, Gouesbet G, Couée I, Cabello-Hurtado F, Cavalier A, Penno C, Zaka R, Bechtold N, Thomas D, El Amrani A. The pleiotropic Arabidopsis frd mutation with altered coordination of chloroplast biogenesis, cell size and differentiation, organ size and number. Gene 2006; 382:88-99. [PMID: 16973304 DOI: 10.1016/j.gene.2006.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Revised: 06/26/2006] [Accepted: 06/27/2006] [Indexed: 10/24/2022]
Abstract
In higher plants, plastid development must be tightly coordinated with cell and organ development. In this paper, a novel T-DNA-mutagenized Arabidopsis line showing chlorotic leaves and minute stature was identified in a genetic screen for altered chloroplast development. The mutation corresponded to a single locus on chromosome IV and was associated with insertion of the T-DNA. This locus was named FARFADET and resulted in pleiotropic effects on chloroplast biogenesis, cell size and differentiation, organ size and number. Thus, in contrast with previously described chlorotic mutants, frd mutants were affected not only in chloroplast development and chlorophyll accumulation, but also in cell and organ development. Alteration of differentiation affected different cell types such as leaf epidermal cells, trichomes, mesophyll cells, and columella cells. A major effect on mesophyll cell differentiation was the lack of palisadic parenchyma and absence of grana stacks. Moreover, meristem size and lateral meristem initiation were affected. Genetic and molecular characterisation showed that the T-DNA insertion generated 41 bp deletion in a potential miRNA precursor. The predicted miRNA target genes were involved in plant development and stress. It is therefore hypothesized that the frd mutation had affected coordination of cell developmental span and the control of the division-differentiation balance.
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Affiliation(s)
- Cécile Sulmon
- Centre National de la Recherche Scientifique, Université de Rennes 1, UMR 6553 Fonctionnement des écosystèmes, Campus de Beaulieu, bâtiment 14A, F-35042 Rennes Cedex, France
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403
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Ronemus M, Vaughn MW, Martienssen RA. MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis. THE PLANT CELL 2006; 18:1559-74. [PMID: 16798886 PMCID: PMC1488920 DOI: 10.1105/tpc.106.042127] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
ARGONAUTE1 (AGO1) of Arabidopsis thaliana mediates the cleavage of microRNA (miRNA)-targeted mRNAs, and it has also been implicated in the posttranscriptional silencing of transgenes and the maintenance of chromatin structure. Mutations in AGO1 severely disrupt plant development, indicating that miRNA function and possibly other aspects of RNA interference are essential for maintaining normal patterns of gene expression. Using microarrays, we found that 1 to 6% of genes display significant expression changes in several alleles of ago1 at multiple developmental stages, with the majority showing higher levels. Several classes of known miRNA targets increased markedly in ago1, whereas others showed little or no change. Cleavage of mRNAs within miRNA-homologous sites was reduced but not abolished in an ago1 -null background, indicating that redundant slicer activity exists in Arabidopsis. Small interfering RNAs and larger 30- to 60-nucleotide RNA fragments corresponding to highly upregulated miRNA target genes accumulated in wild-type plants but not in ago1, the RNA-dependent RNA polymerase mutants rdr2 and rdr6, or the Dicer-like mutants dcl1 and dcl3. Both sense and antisense RNAs corresponding to these miRNA targets accumulated in the ago1 and dcl1 backgrounds. These results indicate that a subset of endogenous mRNA targets of RNA interference may be regulated through a mechanism of second-strand RNA synthesis and degradation initiated by or in addition to miRNA-mediated cleavage.
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Affiliation(s)
- Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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404
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Bouché N, Lauressergues D, Gasciolli V, Vaucheret H. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J 2006; 25:3347-56. [PMID: 16810317 PMCID: PMC1523179 DOI: 10.1038/sj.emboj.7601217] [Citation(s) in RCA: 346] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Accepted: 06/03/2006] [Indexed: 11/08/2022] Open
Abstract
Plants contain more DICER-LIKE (DCL) enzymes and double-stranded RNA binding (DRB) proteins than other eukaryotes, resulting in increased small RNA network complexities. Analyses of single, double, triple and quadruple dcl mutants exposed DCL1 as a sophisticated enzyme capable of producing both microRNAs (miRNAs) and siRNAs, unlike the three other DCLs, which only produce siRNAs. Depletion of siRNA-specific DCLs results in unbalanced small RNA levels, indicating a redeployment of DCL/DRB complexes. In particular, DCL2 antagonizes the production of miRNAs and siRNAs by DCL1 in certain circumstances and affects development deleteriously in dcl1 dcl4 and dcl1 dcl3 dcl4 mutant plants, whereas dcl1 dcl2 dcl3 dcl4 quadruple mutant plants are viable. We also show that viral siRNAs are produced by DCL4, and that DCL2 can substitute for DCL4 when this latter activity is reduced or inhibited by viruses, pointing to the competitiveness of DCL2. Given the complexity of the small RNA repertoire in plants, the implication of each DCL, in particular DCL2, in the production of small RNAs that have no known function will constitute one of the next challenges.
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Affiliation(s)
- Nicolas Bouché
- Laboratoire de Biologie Cellulaire, Institut Jean-Pierre Bourgin, INRA, Versailles, France
| | | | - Virginie Gasciolli
- Laboratoire de Biologie Cellulaire, Institut Jean-Pierre Bourgin, INRA, Versailles, France
| | - Hervé Vaucheret
- Laboratoire de Biologie Cellulaire, Institut Jean-Pierre Bourgin, INRA, Versailles, France
- Laboratoire de Biologie Cellulaire, Institut Jean-Pierre Bourgin, INRA, Route de St-Cyr, 78026 Versailles Cedex, France. Tel.: +33 1308 33170; Fax: +33 1308 33099; E-mail:
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405
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Huettel B, Kanno T, Daxinger L, Aufsatz W, Matzke AJM, Matzke M. Endogenous targets of RNA-directed DNA methylation and Pol IV in Arabidopsis. EMBO J 2006; 25:2828-36. [PMID: 16724114 PMCID: PMC1500864 DOI: 10.1038/sj.emboj.7601150] [Citation(s) in RCA: 218] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2005] [Accepted: 04/27/2006] [Indexed: 11/09/2022] Open
Abstract
DRD1 is a SWI/SNF-like protein that cooperates with a plant-specific RNA polymerase, Pol IVb, to facilitate RNA-directed de novo methylation and silencing of homologous DNA. Screens to identify endogenous targets of this pathway in Arabidopsis revealed intergenic regions and plant genes located primarily in euchromatin. Many putative targets are near retrotransposon LTRs or other intergenic sequences that encode short RNAs, which might epigenetically regulate adjacent genes. Consistent with this, derepression of a solo LTR in drd1 and pol IVb mutants was accompanied by reduced cytosine methylation and transcriptional upregulation of neighboring sequences. The solo LTR and several other LTRs that flank reactivated targets are associated with euchromatic histone modifications but little or no H3K9 dimethylation, a hallmark of constitutive heterochromatin. By contrast, LTRs of retrotransposons that remain silent in the mutants despite reduced cytosine methylation lack euchromatic marks and have H3K9 dimethylation. We propose that DRD1 and Pol IVb establish a basal level of silencing that can potentially be reversed in euchromatin, and further reinforced in heterochromatin by other proteins that induce more stable modifications.
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Affiliation(s)
- Bruno Huettel
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Tatsuo Kanno
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Lucia Daxinger
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Werner Aufsatz
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Antonius J M Matzke
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
| | - Marjori Matzke
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria
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406
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Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ, Jacobsen SE. Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet 2006; 38:721-5. [PMID: 16699516 DOI: 10.1038/ng1804] [Citation(s) in RCA: 430] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Accepted: 04/19/2006] [Indexed: 01/05/2023]
Abstract
Small RNAs have several important biological functions. MicroRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) regulate mRNA stability and translation, and siRNAs cause post-transcriptional gene silencing of transposons, viruses and transgenes and are important in both the establishment and maintenance of cytosine DNA methylation. Here, we study the role of the four Arabidopsis thaliana DICER-LIKE genes (DCL1-DCL4) in these processes. Sequencing of small RNAs from a dcl2 dcl3 dcl4 triple mutant showed markedly reduced tasiRNA and siRNA production and indicated that DCL1, in addition to its role as the major enzyme for processing miRNAs, has a previously unknown role in the production of small RNAs from endogenous inverted repeats. DCL2, DCL3 and DCL4 showed functional redundancy in siRNA and tasiRNA production and in the establishment and maintenance of DNA methylation. Our studies also suggest that asymmetric DNA methylation can be maintained by pathways that do not require siRNAs.
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Affiliation(s)
- Ian R Henderson
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095, USA
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407
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Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D. Highly specific gene silencing by artificial microRNAs in Arabidopsis. THE PLANT CELL 2006; 18:1121-33. [PMID: 16531494 PMCID: PMC1456875 DOI: 10.1105/tpc.105.039834] [Citation(s) in RCA: 935] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Plant microRNAs (miRNAs) affect only a small number of targets with high sequence complementarity, while animal miRNAs usually have hundreds of targets with limited complementarity. We used artificial miRNAs (amiRNAs) to determine whether the narrow action spectrum of natural plant miRNAs reflects only intrinsic properties of the plant miRNA machinery or whether it is also due to past selection against natural miRNAs with broader specificity. amiRNAs were designed to target individual genes or groups of endogenous genes. Like natural miRNAs, they had varying numbers of target mismatches. Previously determined parameters of target selection for natural miRNAs could accurately predict direct targets of amiRNAs. The specificity of amiRNAs, as deduced from genome-wide expression profiling, was as high as that of natural plant miRNAs, supporting the notion that extensive base pairing with targets is required for plant miRNA function. amiRNAs make an effective tool for specific gene silencing in plants, especially when several related, but not identical, target genes need to be downregulated. We demonstrate that amiRNAs are also active when expressed under tissue-specific or inducible promoters, with limited nonautonomous effects. The design principles for amiRNAs have been generalized and integrated into a Web-based tool (http://wmd.weigelworld.org).
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Affiliation(s)
- Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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408
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Abstract
The term non-coding RNA (ncRNA) is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. Although it has been generally assumed that most genetic information is transacted by proteins, recent evidence suggests that the majority of the genomes of mammals and other complex organisms is in fact transcribed into ncRNAs, many of which are alternatively spliced and/or processed into smaller products. These ncRNAs include microRNAs and snoRNAs (many if not most of which remain to be identified), as well as likely other classes of yet-to-be-discovered small regulatory RNAs, and tens of thousands of longer transcripts (including complex patterns of interlacing and overlapping sense and antisense transcripts), most of whose functions are unknown. These RNAs (including those derived from introns) appear to comprise a hidden layer of internal signals that control various levels of gene expression in physiology and development, including chromatin architecture/epigenetic memory, transcription, RNA splicing, editing, translation and turnover. RNA regulatory networks may determine most of our complex characteristics, play a significant role in disease and constitute an unexplored world of genetic variation both within and between species.
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Affiliation(s)
- John S Mattick
- Australian Research Council Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia.
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409
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Ebhardt HA, Wiese KC, Unrau PJ. Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server. BMC Bioinformatics 2006; 7:185. [PMID: 16584563 PMCID: PMC1450305 DOI: 10.1186/1471-2105-7-185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Accepted: 04/03/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA sequencing is used ubiquitously: from deciphering genomes to determining the primary sequence of small RNAs (smRNAs). The cloning of smRNAs is currently the most conventional method to determine the actual sequence of these important regulators of gene expression. Typical smRNA cloning projects involve the sequencing of hundreds to thousands of smRNA clones that are delimited at their 5' and 3' ends by fixed sequence regions. These primers result from the biochemical protocol used to isolate and convert the smRNA into clonable PCR products. Recently we completed a smRNA cloning project involving tobacco plants, where analysis was required for approximately 700 smRNA sequences. Finding no easily accessible research tool to enter and analyze smRNA sequences we developed Ebbie to assist us with our study. RESULTS Ebbie is a semi-automated smRNA cloning data processing algorithm, which initially searches for any substring within a DNA sequencing text file, which is flanked by two constant strings. The substring, also termed smRNA or insert, is stored in a MySQL and BlastN database. These inserts are then compared using BlastN to locally installed databases allowing the rapid comparison of the insert to both the growing smRNA database and to other static sequence databases. Our laboratory used Ebbie to analyze scores of DNA sequencing data originating from an smRNA cloning project. Through its built-in instant analysis of all inserts using BlastN, we were able to quickly identify 33 groups of smRNAs from approximately 700 database entries. This clustering allowed the easy identification of novel and highly expressed clusters of smRNAs. Ebbie is available under GNU GPL and currently implemented on http://bioinformatics.org/ebbie/. CONCLUSION Ebbie was designed for medium sized smRNA cloning projects with about 1,000 database entries. Ebbie can be used for any type of sequence analysis where two constant primer regions flank a sequence of interest. The reliable storage of inserts, and their annotation in a MySQL database, BlastN comparison of new inserts to dynamic and static databases make it a powerful new tool in any laboratory using DNA sequencing. Ebbie also prevents manual mistakes during the excision process and speeds up annotation and data-entry. Once the server is installed locally, its access can be restricted to protect sensitive new DNA sequencing data. Ebbie was primarily designed for smRNA cloning projects, but can be applied to a variety of RNA and DNA cloning projects.
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Affiliation(s)
- H Alexander Ebhardt
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, B.C., Canada
| | - Kay C Wiese
- School of Computing Science, Simon Fraser University Surrey, 13450 102nd Ave, V3T 5X3 Surrey, B.C., Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, B.C., Canada
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410
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Abstract
The Human Immunodeficiency Virus type 1 (HIV-1), a member of the lentivirus subfamily, infects both dividing and nondividing cells and, following reverse transcription of the viral RNA genome, integrates into the host chromatin where it enters into a latent state. Many of the factors governing viral latency remain unresolved and current antiviral treatment regimens are largely ineffective at eliminating cellular reservoirs of latent virus. The recent identification of microRNA (miRNA) encoding sequences embedded in the HIV-1 genome, and the discovery of functional virus-derived miRNAs, suggests a role for RNA Interference (RNAi) in the regulation of HIV-1 gene expression. Recently, the mammalian RNAi machinery was shown to regulate gene expression epigenetically by transcriptional modulation, providing a direct link between RNAi and a mechanism for inducing latency. Interestingly, both HIV-1 Tat, and the host TAR RNA-binding protein (TRBP), bind to the transactivating response (TAR) RNA of HIV-1 and affect the function of RNAi in human cells. Specifically, TRBP, a cofactor in Tat-TAR interactions, is a vital component of Dicer-mediated dsRNA processing. These novel observations support a central role for HIV-1 and associated host factors in regulating cellular RNAi and viral gene expression through RNA directed processes. Thus, HIV-1 may have evolved mechanisms to exploit the RNAi pathway at both the transcriptional and posttranscriptional level to affect and/or maintain a latent infection.
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Affiliation(s)
- Marc S Weinberg
- Department of Molecular Medicine and Haematology, University of the Witwatersrand Medical School, Parktown, South Africa
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411
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Mineno J, Okamoto S, Ando T, Sato M, Chono H, Izu H, Takayama M, Asada K, Mirochnitchenko O, Inouye M, Kato I. The expression profile of microRNAs in mouse embryos. Nucleic Acids Res 2006; 34:1765-71. [PMID: 16582102 PMCID: PMC1421506 DOI: 10.1093/nar/gkl096] [Citation(s) in RCA: 185] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs (miRNAs), which are non-coding RNAs 18–25 nt in length, regulate a variety of biological processes, including vertebrate development. To identify new species of miRNA and to simultaneously obtain a comprehensive quantitative profile of small RNA expression in mouse embryos, we used the massively parallel signature sequencing technology that potentially identifies virtually all of the small RNAs in a sample. This approach allowed us to detect a total of 390 miRNAs, including 195 known miRNAs covering ∼80% of previously registered mouse miRNAs as well as 195 new miRNAs, which are so far unknown in mouse. Some of these miRNAs showed temporal expression profiles during prenatal development (E9.5, E10.5 and E11.5). Several miRNAs were positioned in polycistron clusters, including one particular large transcription unit consisting of 16 known and 23 new miRNAs. Our results indicate existence of a significant number of new miRNAs expressed at specific stages of mammalian embryonic development and which were not detected by earlier methods.
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Affiliation(s)
- Junichi Mineno
- Center for Cell and Gene Therapy, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
| | - Sachiko Okamoto
- Center for Cell and Gene Therapy, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
| | - Tatsuya Ando
- DNA Function Analysis Center, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
| | - Masahiro Sato
- DNA Function Analysis Center, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
| | - Hideto Chono
- Center for Cell and Gene Therapy, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
| | - Hiroyuki Izu
- DNA Function Analysis Center, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
| | - Masanori Takayama
- DNA Function Analysis Center, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
| | - Kiyozo Asada
- DNA Function Analysis Center, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
| | - Oleg Mirochnitchenko
- Department of Biochemistry, Robert Wood Johnson Medical School675 Hoes Lane, Piscataway, NJ 08854, USA
| | - Masayori Inouye
- Department of Biochemistry, Robert Wood Johnson Medical School675 Hoes Lane, Piscataway, NJ 08854, USA
- To whom correspondence should be addressed. Tel: +1 732 235 4115; Fax: +1 732 235 4559;
| | - Ikunoshin Kato
- Center for Cell and Gene Therapy, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
- DNA Function Analysis Center, Takara Bio Inc.Seta 3-4-1, Otsu, Shiga 520-2193, Japan
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412
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Hoen DR, Park KC, Elrouby N, Yu Z, Mohabir N, Cowan RK, Bureau TE. Transposon-mediated expansion and diversification of a family of ULP-like genes. Mol Biol Evol 2006; 23:1254-68. [PMID: 16581939 DOI: 10.1093/molbev/msk015] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transposons comprise a major component of eukaryotic genomes, yet it remains controversial whether they are merely genetic parasites or instead significant contributors to organismal function and evolution. In plants, thousands of DNA transposons were recently shown to contain duplicated cellular gene fragments, a process termed transduplication. Although transduplication is a potentially rich source of novel coding sequences, virtually all appear to be pseudogenes in rice. Here we report the results of a genome-wide survey of transduplication in Mutator-like elements (MULEs) in Arabidopsis thaliana, which shows that the phenomenon is generally similar to rice transduplication, with one important exception: KAONASHI (KI). A family of more than 97 potentially functional genes and apparent pseudogenes, evidently derived at least 15 MYA from a cellular small ubiquitin-like modifier-specific protease gene, KI is predominantly located in potentially autonomous non-terminal inverted repeat MULEs and has evolved under purifying selection to maintain a conserved peptidase domain. Similar to the associated transposase gene but unlike cellular genes, KI is targeted by small RNAs and silenced in most tissues but has elevated expression in pollen. In an Arabidopsis double mutant deficient in histone and DNA methylation with elevated KI expression compared to wild type, at least one KI-MULE is mobile. The existence of KI demonstrates that transduplicated genes can retain protein-coding capacity and evolve novel functions. However, in this case, our evidence suggests that the function of KI may be selfish rather than cellular.
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Affiliation(s)
- Douglas R Hoen
- Department of Biology, McGill University, Montreal, Québec, Canada
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413
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Wheeler G, Ntounia-Fousara S, Granda B, Rathjen T, Dalmay T. Identification of new central nervous system specific mouse microRNAs. FEBS Lett 2006; 580:2195-200. [PMID: 16566924 DOI: 10.1016/j.febslet.2006.03.019] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Accepted: 03/07/2006] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are small regulatory molecules suppressing mRNA activity in metazoans. Here we describe two new miRNAs cloned from brain tissue of mouse embryos. These miRNAs are expressed mainly during embryogenesis and specifically in the central nervous system. We also established the expression patterns of three recently identified miRNAs that were found in our short RNA library. All of them were expressed in the brain and spinal chord but while miR-410 and miR-431 were central nervous system specific, miR-500 was also expressed in limb buds. In addition, the expression of miR-500 in limb buds showed very strong asymmetry in favour of the left hand side.
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Affiliation(s)
- Guy Wheeler
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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414
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Abstract
Small RNAs are riboregulators that have critical roles in most eukaryotes. They repress gene expression by acting either on DNA to guide sequence elimination and chromatin remodeling, or on RNA to guide cleavage and translation repression. This review focuses on the various types of post-transcriptional small RNA-directed pathways in plants, describing their roles and their regulations.
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MESH Headings
- DNA Methylation
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Gene Expression Regulation, Plant
- Genes, Plant
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Models, Biological
- Plant Viruses/pathogenicity
- Plants/genetics
- Plants/metabolism
- RNA Interference
- RNA Processing, Post-Transcriptional
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
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Affiliation(s)
- Hervé Vaucheret
- Laboratoire de Biologie Cellulaire, Institut Jean-Pierre Bourgin, l'Institut National de la Recherche Agronomique, 78026 Versailles Cedex, France.
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415
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Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 2006; 123:1279-91. [PMID: 16377568 PMCID: PMC3137516 DOI: 10.1016/j.cell.2005.11.035] [Citation(s) in RCA: 731] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Revised: 09/30/2005] [Accepted: 11/08/2005] [Indexed: 02/06/2023]
Abstract
In higher eukaryotes, miRNAs and siRNAs guide translational inhibition, mRNA cleavage, or chromatin regulation. We found that the antisense overlapping gene pair of Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH), a stress-related gene, and SRO5, a gene of unknown function, generates two types of siRNAs. When both transcripts are present, a 24-nt siRNA is formed by a biogenesis pathway dependent on DCL2, RDR6, SGS3, and NRPD1A. Initial cleavage of the P5CDH transcript guided by the 24-nt siRNA establishes a phase for the subsequent generation of 21-nt siRNAs by DCL1 and further cleavage of P5CDH transcripts. The expression of SRO5 is induced by salt, and this induction is required to initiate siRNA formation. Our data suggest that the P5CDH and SRO5 proteins are also functionally related, and that the P5CDH-SRO5 gene pair defines a mode of siRNA function and biogenesis that may be applied to other natural cis-antisense gene pairs in eukaryotic genomes.
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Affiliation(s)
- Omar Borsani
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - Jianhua Zhu
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - Paul E. Verslues
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - Ramanjulu Sunkar
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - Jian-Kang Zhu
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
- Contact:
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416
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Nakano M, Nobuta K, Vemaraju K, Tej SS, Skogen JW, Meyers BC. Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res 2006; 34:D731-5. [PMID: 16381968 PMCID: PMC1347440 DOI: 10.1093/nar/gkj077] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MPSS (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. We have created a series of databases for four species (Arabidopsis, rice, grape and Magnaporthe grisea, the rice blast fungus). Our MPSS databases measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alternative splice isoforms and regulatory intergenic transcripts). A modified version of MPSS has been used to perform deep profiling of small RNAs from Arabidopsis, and we have recently adapted our database to display these data. Interpretation of the small RNA MPSS data is facilitated by the inclusion of extensive repeat data in our genome viewer. All the data and the tools introduced in this article are available at .
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MESH Headings
- Arabidopsis/genetics
- Chromosomes, Plant
- Databases, Nucleic Acid
- Exons
- Genome, Plant
- Genomics
- Internet
- Magnaporthe/genetics
- MicroRNAs/chemistry
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Oryza/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Sequence Analysis, RNA
- Transcription, Genetic
- User-Computer Interface
- Vitis/genetics
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Affiliation(s)
- Mayumi Nakano
- Department of Plant and Soil Sciences, University of DelawareNewark, DE 19714, USA
| | - Kan Nobuta
- Department of Plant and Soil Sciences, University of DelawareNewark, DE 19714, USA
| | - Kalyan Vemaraju
- Delaware Biotechnology Institute, University of DelawareNewark, DE 19714, USA
| | | | - Jeremy W. Skogen
- Delaware Biotechnology Institute, University of DelawareNewark, DE 19714, USA
| | - Blake C. Meyers
- Department of Plant and Soil Sciences, University of DelawareNewark, DE 19714, USA
- Delaware Biotechnology Institute, University of DelawareNewark, DE 19714, USA
- To whom correspondence should be addressed. Tel: +1 302 831 3418; Fax: +1 302 831 4841;
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417
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Meyers BC, Souret FF, Lu C, Green PJ. Sweating the small stuff: microRNA discovery in plants. Curr Opin Biotechnol 2006; 17:139-46. [PMID: 16460926 DOI: 10.1016/j.copbio.2006.01.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 12/16/2005] [Accepted: 01/25/2006] [Indexed: 12/27/2022]
Abstract
The class of small RNAs known as microRNAs (miRNAs) has a demonstrated role in the negative regulation of gene expression in both plants and animals. These small molecules have been shown to play a critical role in a wide range of developmental and physiological pathways. Although hundreds of different miRNAs have now been identified using cloning and computational approaches, characterization of their targets and biological roles has been more limited. New sequencing technologies promise to accelerate the sequencing of small RNAs and additional genetic and genomic strategies are being applied to assess their regulatory function on RNA targets. These technologies will enable the identification of large numbers of small RNAs from diverse species, and comparative genomics approaches based on these data are likely to identify additional miRNAs. Combined with bioinformatics and experimental approaches to separate miRNAs from short-interfering RNAs (siRNAs), the pace of miRNA discovery is likely to accelerate, leading to an improved understanding of miRNA function and biological significance.
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Affiliation(s)
- Blake C Meyers
- Delaware Biotechnology Institute & Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19714, USA.
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418
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Affiliation(s)
- Paul D Berk
- The Division of Digestive Liver Diseases, Department of Medicine, Columbia University Medical Center, New York, NY
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419
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Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su CL. Regulation of phosphate homeostasis by MicroRNA in Arabidopsis. THE PLANT CELL 2006; 18:412-21. [PMID: 16387831 PMCID: PMC1356548 DOI: 10.1105/tpc.105.038943] [Citation(s) in RCA: 564] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In this study, we reveal a mechanism by which plants regulate inorganic phosphate (Pi) homeostasis to adapt to environmental changes in Pi availability. This mechanism involves the suppression of a ubiquitin-conjugating E2 enzyme by a specific microRNA, miR399. Upon Pi starvation, the miR399 is upregulated and its target gene, a ubiquitin-conjugating E2 enzyme, is downregulated in Arabidopsis thaliana. Accumulation of the E2 transcript is suppressed in transgenic Arabidopsis overexpressing miR399. Transgenic plants accumulated five to six times the normal Pi level in shoots and displayed Pi toxicity symptoms that were phenocopied by a loss-of-function E2 mutant. Pi toxicity was caused by increased Pi uptake and by translocation of Pi from roots to shoots and retention of Pi in the shoots. Moreover, unlike wild-type plants, in which Pi in old leaves was readily retranslocated to other developing young tissues, remobilization of Pi in miR399-overexpressing plants was impaired. These results provide evidence that miRNA controls Pi homeostasis by regulating the expression of a component of the proteolysis machinery in plants.
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Affiliation(s)
- Tzyy-Jen Chiou
- Institute of BioAgricultural Sciences, Academia Sinica, Taipei 115, Taiwan, Republic of China.
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420
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Hüttenhofer A, Vogel J. Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 2006; 34:635-46. [PMID: 16436800 PMCID: PMC1351373 DOI: 10.1093/nar/gkj469] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 01/10/2006] [Accepted: 01/10/2006] [Indexed: 12/12/2022] Open
Abstract
Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until recent genome-wide searches discovered thousands of these molecules and their genes in a variety of model organisms. Some of these screens were based on biocomputational prediction of ncRNA candidates within entire genomes of model organisms. Alternatively, direct biochemical isolation of expressed ncRNAs from cells, tissues or entire organisms has been shown to be a powerful approach to identify ncRNAs both at the level of individual molecules and at a global scale. In this review, we will survey several such wet-lab strategies, i.e. direct sequencing of ncRNAs, shotgun cloning of small-sized ncRNAs (cDNA libraries), microarray analysis and genomic SELEX to identify novel ncRNAs, and discuss the advantages and limits of these approaches.
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Affiliation(s)
- Alexander Hüttenhofer
- Innsbruck Biocenter, Division of Genomics and RNomics, Innsbruck Medical University, Fritz-Pregl-Str. 3, 6020 Innsbruck, Austria.
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421
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Edwards RG. Changing genetic world of IVF, stem cells and PGD. B. Polarities and gene expression in differentiating embryo cells and stem cells. Reprod Biomed Online 2006; 11:761-76. [PMID: 16417744 DOI: 10.1016/s1472-6483(10)61696-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Novel genetic techniques in the later twentieth century led to new analytical methods for assessing the growth of embryos and stem cells and improve preimplantation diagnosis. Increasing attention to the nature of polarities in mouse and human embryos revealed the existence of an animal-vegetal axis in human oocytes and embryos. Combinations of meridional and transverse cleavage divisions, the latter due to spindle rotation, determined the unequal division of ooplasm to embryonic blastomeres. Blastomeres with differing functions were accordingly formed in 4-cell embryos, including founders of inner cell mass and trophectoderm. New forms of gene analysis led to the polymerase chain reaction, while fluorescence in-situ hybridization revealed astonishingly high degrees of heteroploidy in human embryos. Developmental genetics gained immense analytical power as cDNA libraries, microarrays, transcriptomes RNAi and other methods clarified the roles of hundreds of genes in pre- and early post-implantation embryos and stem cells.
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422
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Kavi HH, Xie W, Fernandez HR, Birchler JA. Global analysis of siRNA-mediated transcriptional gene silencing. Bioessays 2006; 27:1209-12. [PMID: 16299769 DOI: 10.1002/bies.20328] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The RNAi machinery is not only involved with post-transcriptional degradation of messenger RNAs, but also used for targeting of chromatin changes associated with transcriptional silencing. Two recent papers determine the global patterns of gene expression and chromatin modifications produced by the RNAi machinery in fission yeast.(9, 10) The major sites include the outer centromere repeats, the mating-type locus and subtelomeric regions. By comparison, studies of Arabidopsis heterochromatin also implicate transposons as a major target for silencing. Analyses of siRNA libraries from Drosophila, nematodes and Arabidopsis indicate that major repeats at centromeres, telomeres and transposable elements are likely targets of RNAi. Also, intergenic regions are implicated as targets in Arabidopsis.
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Affiliation(s)
- Harsh H Kavi
- Division of Biological Sciences, University of Missouri-Columbia, Columbia, MO 65211, USA
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423
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Abstract
microRNAs (miRNAs) are an abundant class of newly identified endogenous non-protein-coding small RNAs. They exist in animals, plants, and viruses, and play an important role in gene silencing. Translational repression, mRNA cleavage, and mRNA decay initiated by miRNA-directed deadenylation of targeted mRNAs are three mechanisms of miRNA-guided gene regulation at the post-transcriptional levels. Many miRNAs are highly conserved in animals and plants, suggesting that they play an essential function in plants and animals. Lots of investigations indicate that miRNAs are involved in multiple biological processes, including stem cell differentiation, organ development, phase change, signaling, disease, cancer, and response to biotic and abiotic environmental stresses. This review provides a general background and current advance on the discovery, history, biogenesis, genomics, mechanisms, and functions of miRNAs.
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Affiliation(s)
- Baohong Zhang
- The Institute of Environmental and Human Health, and Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas 79409, USA.
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424
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Abstract
RNA has many functions in addition to being a simple messenger between the genome and the proteome. Over two decades, several classes of small noncoding RNAs c. 21 nucleotides (nt) long have been uncovered in eukaryotic genomes, which appear to play a central role in diverse and fundamental processes. In plants, small RNA-based mechanisms are involved in genome stability, gene expression and defense. Many of the discoveries in this new "small RNA world" were made by plant biologists. Here, we discuss the three major classes of small RNAs that are found in the plant kingdom, namely small interfering RNAs, microRNAs, and the recently discovered trans-acting small interfering RNAs. Recent results shed light on the identification, integration and specialization of the different components (Dicer-like, Argonaute, and others) involved in the biogenesis of the different classes of small RNAs in plants. Owing to the development of better experimental and computational methods, an ever increasing number of small noncoding RNAs are uncovered in different plant genomes. In particular the well-studied microRNAs seem to act as key regulators in several different developmental pathways, with a marked preference for transcription factors as targets. In addition, an increasing amount of data suggest that they also play an important role in other mechanisms, such as response to stress or environmental changes.
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Affiliation(s)
- Eric Bonnet
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Technologiepark 927, B-9052 Gent, Belgium
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425
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Zhang B, Pan X, Cobb GP, Anderson TA. Plant microRNA: a small regulatory molecule with big impact. Dev Biol 2005; 289:3-16. [PMID: 16325172 DOI: 10.1016/j.ydbio.2005.10.036] [Citation(s) in RCA: 441] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2005] [Revised: 10/10/2005] [Accepted: 10/17/2005] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) are an abundant new class of non-coding approximately 20-24 nt small RNAs. To date, 872 miRNAs, belonging to 42 families, have been identified in 71 plant species by genetic screening, direct cloning after isolation of small RNAs, computational strategy, and expressed sequence tag (EST) analysis. Many plant miRNAs are evolutionarily conserved from species to species, some from angiosperms to mosses. miRNAs may originate from inverted duplications of target gene sequences in plants. Although miRNA precursors display high variability, their mature sequences display extensive sequence complementarity to their target mRNA sequences. miRNAs play important roles in plant post-transcriptional gene regulation by targeting mRNAs for cleavage or repressing translation. miRNAs are involved in plant development, signal transduction, protein degradation, response to environmental stress and pathogen invasion, and regulate their own biogenesis. miRNAs regulate the expression of many important genes; a majority of these genes are transcriptional factors.
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Affiliation(s)
- Baohong Zhang
- The Institute of Environmental and Human Health (TIEHH), and Department of Environmental Toxicology, Texas Tech. University, Lubbock, 79409-1163, USA.
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426
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Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biol 2005; 6:R90. [PMID: 16277745 PMCID: PMC1297646 DOI: 10.1186/gb-2005-6-11-r90] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 08/26/2005] [Accepted: 09/21/2005] [Indexed: 11/16/2022] Open
Abstract
Microarray-based profiling of the involvement of two DNA methyltransferases (CMT3 and DRM), a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci in Arabidopsis reveals that transposable elements are the targets of both DNA methylation and histone H3K9 methylation pathways, irrespective of element type and position. Background DNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known. Results We used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants. Conclusion We conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements.
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Affiliation(s)
- Robert K Tran
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Daniel Zilberman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Cecilia de Bustos
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, 751 85 Sweden
| | - Renata F Ditt
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Jorja G Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Anders M Lindroth
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jeffrey Delrow
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Tom Boyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Samson Kwong
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Terri D Bryson
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
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427
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Abstract
Small RNAs (sRNAs) can regulate transcript and protein abundance. Previously, they have been identified using traditional cloning approaches, which has limited how many could be characterized. Now, the Meyers and Green laboratories have used massively parallel signature sequencing technology to find over 1.5 million sRNAs in Arabidopsis thaliana. These new sRNAs reveal a greater-than-expected potential role for sRNAs in gene regulation, preferential expression or usage of sRNAs in flowers, and the prospect of targeted sRNA-mediated regulation of pseudogenes. In addition, new plant microRNAs have been identified, some of which may be unique to Arabidopsis.
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Affiliation(s)
- Matthew W Vaughn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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