201
|
Braun L, Cannella D, Ortet P, Barakat M, Sautel CF, Kieffer S, Garin J, Bastien O, Voinnet O, Hakimi MA. A complex small RNA repertoire is generated by a plant/fungal-like machinery and effected by a metazoan-like Argonaute in the single-cell human parasite Toxoplasma gondii. PLoS Pathog 2010; 6:e1000920. [PMID: 20523899 PMCID: PMC2877743 DOI: 10.1371/journal.ppat.1000920] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 04/23/2010] [Indexed: 12/21/2022] Open
Abstract
In RNA silencing, small RNAs produced by the RNase-III Dicer guide Argonaute-like proteins as part of RNA-induced silencing complexes (RISC) to regulate gene expression transcriptionally or post-transcriptionally. Here, we have characterized the RNA silencing machinery and exhaustive small RNAome of Toxoplasma gondii, member of the Apicomplexa, a phylum of animal- and human-infecting parasites that cause extensive health and economic damages to human populations worldwide. Remarkably, the small RNA-generating machinery of Toxoplasma is phylogenetically and functionally related to that of plants and fungi, and accounts for an exceptionally diverse array of small RNAs. This array includes conspicuous populations of repeat-associated small interfering RNA (siRNA), which, as in plants, likely generate and maintain heterochromatin at DNA repeats and satellites. Toxoplasma small RNAs also include many microRNAs with clear metazoan-like features whose accumulation is sometimes extremely high and dynamic, an unexpected finding given that Toxoplasma is a unicellular protist. Both plant-like heterochromatic small RNAs and metazoan-like microRNAs bind to a single Argonaute protein, Tg-AGO. Toxoplasma miRNAs co-sediment with polyribosomes, and thus, are likely to act as translational regulators, consistent with the lack of catalytic residues in Tg-AGO. Mass spectrometric analyses of the Tg-AGO protein complex revealed a common set of virtually all known RISC components so far characterized in human and Drosophila, as well as novel proteins involved in RNA metabolism. In agreement with its loading with heterochromatic small RNAs, Tg-AGO also associates substoichiometrically with components of known chromatin-repressing complexes. Thus, a puzzling patchwork of silencing processor and effector proteins from plant, fungal and metazoan origin accounts for the production and action of an unsuspected variety of small RNAs in the single-cell parasite Toxoplasma and possibly in other apicomplexans. This study establishes Toxoplasma as a unique model system for studying the evolution and molecular mechanisms of RNA silencing among eukaryotes. Toxoplasma gondii is an important human parasite that causes life-threatening diseases in developing fetuses and in immunocompromised individuals, especially AIDS and transplant patients. Curiously, the Toxoplasma genome is deprived of most of the basic transcription factors that regulate gene expression in other eukaryotic cells. Therefore, alternative strategies must exist to modulate the many phases of the Toxoplasma complex life cycle that includes invasion of several hosts. Here, we investigate one of these strategies, by studying the repertoire of Toxoplasma silencing small RNAs (sRNAs). In eukaryotes, most of these regulatory molecules, 20–30nt-long, are produced by members of the Dicer RNase-III family, and exert their various functions through ubiquitous proteins called Argonaute (Ago). The surprising diversity of the Toxoplasma sRNAome uncovered in our study is consistent with those molecules exerting key functions during the parasite's life cycle, including, possibly, during virulent infection. The study also unravels an unsuspected level of complexity in the origin and mechanisms of action of the factors that generate and affect Toxoplasma sRNA, prompting a re-evaluation of our current views on RNA silencing in eukaryotes.
Collapse
Affiliation(s)
- Laurence Braun
- Laboratoire Adaptation et Pathogénie des Micro-organismes, CNRS UMR 5163-ATIP+ group, Université Joseph Fourier, Grenoble, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
202
|
Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis. PLoS One 2010; 5:e10698. [PMID: 20502668 PMCID: PMC2873431 DOI: 10.1371/journal.pone.0010698] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 04/26/2010] [Indexed: 11/29/2022] Open
Abstract
Background miRNAs are a class of non-coding, small RNAs that are approximately 22 nucleotides long and play important roles in the translational level regulation of gene expression by either directly binding or cleaving target mRNAs. The red alga, Porphyra yezoensis is one of the most important marine economic crops worldwide. To date, only a few miRNAs have been identified in green unicellar alga and there is no report about Porphyra miRNAs. Methodology/Principal Findings To identify miRNAs in Porphyra yezoensis, a small RNA library was constructed. Solexa technology was used to perform high throughput sequencing of the library and subsequent bioinformatics analysis to identify novel miRNAs. Specifically, 180,557,942 reads produced 13,324 unique miRNAs representing 224 conserved miRNA families that have been identified in other plants species. In addition, seven novel putative miRNAs were predicted from a limited number of ESTs. The potential targets of these putative miRNAs were also predicted based on sequence homology search. Conclusions/Significance This study provides a first large scale cloning and characterization of Porphyra miRNAs and their potential targets. These miRNAs belong to 224 conserved miRNA families and 7 miRNAs are novel in Porphyra. These miRNAs add to the growing database of new miRNA and lay the foundation for further understanding of miRNA function in the regulation of Porphyra yezoensis development.
Collapse
|
203
|
Abstract
microRNAs (miRNAs) in higher multicellular eukaryotes have been extensively studied in recent years. Great progresses have also been achieved for miRNAs in unicellular eukaryotes. All these studies not only enrich our knowledge about the complex expression regulation system in diverse organisms, but also have evolutionary significance for understanding the origin of this system. In this review, Authors summarize the recent advance in the studies of miRNA in unicellular eukaryotes, including that on the most primitive unicellular eukaryote--Giardia. The origin and evolution of miRNA system is also discussed.
Collapse
|
204
|
An inducible artificial microRNA system for Chlamydomonas reinhardtii confirms a key role for heat shock factor 1 in regulating thermotolerance. Curr Genet 2010; 56:383-9. [DOI: 10.1007/s00294-010-0304-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 04/19/2010] [Accepted: 04/19/2010] [Indexed: 12/29/2022]
|
205
|
Bermudez-Santana C, Attolini CSO, Kirsten T, Engelhardt J, Prohaska SJ, Steigele S, Stadler PF. Genomic organization of eukaryotic tRNAs. BMC Genomics 2010; 11:270. [PMID: 20426822 PMCID: PMC2888827 DOI: 10.1186/1471-2164-11-270] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 04/28/2010] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Surprisingly little is known about the organization and distribution of tRNA genes and tRNA-related sequences on a genome-wide scale. While tRNA gene complements are usually reported in passing as part of genome annotation efforts, and peculiar features such as the tandem arrangements of tRNA gene in Entamoeba histolytica have been described in some detail, systematic comparative studies are rare and mostly restricted to bacteria. We therefore set out to survey the genomic arrangement of tRNA genes and pseudogenes in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities. RESULTS In line with previous reports, we find that tRNA complements evolve rapidly and tRNA gene and pseudogene locations are subject to rapid turnover. At phylum level, the distributions of the number of tRNA genes and pseudogenes numbers are very broad, with standard deviations on the order of the mean. Even among closely related species we observe dramatic changes in local organization. For instance, 65% and 87% of the tRNA genes and pseudogenes are located in genomic clusters in zebrafish and stickleback, resp., while such arrangements are relatively rare in the other three sequenced teleost fish genomes. Among basal metazoa, Trichoplax adherens has hardly any duplicated tRNA gene, while the sea anemone Nematostella vectensis boasts more than 17000 tRNA genes and pseudogenes. Dramatic variations are observed even within the eutherian mammals. Higher primates, for instance, have 616 +/- 120 tRNA genes and pseudogenes of which 17% to 36% are arranged in clusters, while the genome of the bushbaby Otolemur garnetti has 45225 tRNA genes and pseudogenes of which only 5.6% appear in clusters. In contrast, the distribution is surprisingly uniform across plant genomes. Consistent with this variability, syntenic conservation of tRNA genes and pseudogenes is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. Despite this large variation in abundance in Eukarya we observe a significant correlation between the number of tRNA genes, tRNA pseudogenes, and genome size. CONCLUSIONS The genomic organization of tRNA genes and pseudogenes shows complex lineage-specific patterns characterized by an extensive variability that is in striking contrast to the extreme levels of sequence-conservation of the tRNAs themselves. The comprehensive analysis of the genomic organization of tRNA genes and pseudogenes in Eukarya provides a basis for further studies into the interplay of tRNA gene arrangements and genome organization in general.
Collapse
Affiliation(s)
- Clara Bermudez-Santana
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
- Department of Biology, Universidad Nacional de Colombia. Carrera45 # 26-85 - Edificio Uriel Gutiérrez, Bogotá D.C., Colombia
| | - Camille Stephan-Otto Attolini
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
- Biostatistics and Bioinformatics unit, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
| | - Toralf Kirsten
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Jan Engelhardt
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | - Sonja J Prohaska
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
| | | | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraß 22 D-04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany
- Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria
| |
Collapse
|
206
|
Lee HC, Li L, Gu W, Xue Z, Crosthwaite SK, Pertsemlidis A, Lewis ZA, Freitag M, Selker EU, Mello CC, Liu Y. Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi. Mol Cell 2010; 38:803-14. [PMID: 20417140 DOI: 10.1016/j.molcel.2010.04.005] [Citation(s) in RCA: 252] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 03/10/2010] [Accepted: 04/02/2010] [Indexed: 12/30/2022]
Abstract
A variety of small RNAs, including the Dicer-dependent miRNAs and the Dicer-independent Piwi-interacting RNAs, associate with Argonaute family proteins to regulate gene expression in diverse cellular processes. These two species of small RNA have not been found in fungi. Here, by analyzing small RNAs associated with the Neurospora Argonaute protein QDE-2, we show that diverse pathways generate miRNA-like small RNAs (milRNAs) and Dicer-independent small interfering RNAs (disiRNAs) in this filamentous fungus. Surprisingly, milRNAs are produced by at least four different mechanisms that use a distinct combination of factors, including Dicers, QDE-2, the exonuclease QIP, and an RNase III domain-containing protein, MRPL3. In contrast, disiRNAs originate from loci producing overlapping sense and antisense transcripts, and do not require the known RNAi components for their production. Taken together, these results uncover several pathways for small RNA production in filamentous fungi, shedding light on the diversity and evolutionary origins of eukaryotic small RNAs.
Collapse
Affiliation(s)
- Heng-Chi Lee
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
207
|
Fahlgren N, Jogdeo S, Kasschau KD, Sullivan CM, Chapman EJ, Laubinger S, Smith LM, Dasenko M, Givan SA, Weigel D, Carrington JC. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. THE PLANT CELL 2010; 22:1074-89. [PMID: 20407027 PMCID: PMC2879733 DOI: 10.1105/tpc.110.073999] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 03/16/2010] [Accepted: 04/05/2010] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are short regulatory RNAs processed from partially self-complementary foldbacks within longer MIRNA primary transcripts. Several MIRNA families are conserved deeply through land plants, but many are present only in closely related species or are species specific. The finding of numerous evolutionarily young MIRNA, many with low expression and few if any targets, supports a rapid birth-death model for MIRNA evolution. A systematic analysis of MIRNA genes and families in the close relatives, Arabidopsis thaliana and Arabidopsis lyrata, was conducted using both whole-genome comparisons and high-throughput sequencing of small RNAs. Orthologs of 143 A. thaliana MIRNA genes were identified in A. lyrata, with nine having significant sequence or processing changes that likely alter function. In addition, at least 13% of MIRNA genes in each species are unique, despite their relatively recent speciation (approximately 10 million years ago). Alignment of MIRNA foldbacks to the Arabidopsis genomes revealed evidence for recent origins of 32 families by inverted or direct duplication of mostly protein-coding gene sequences, but less than half of these yield miRNA that are predicted to target transcripts from the originating gene family. miRNA nucleotide divergence between A. lyrata and A. thaliana orthologs was higher for young MIRNA genes, consistent with reduced purifying selection compared with deeply conserved MIRNA genes. Additionally, target sites of younger miRNA were lost more frequently than for deeply conserved families. In summary, our systematic analyses emphasize the dynamic nature of the MIRNA complement of plant genomes.
Collapse
Affiliation(s)
- Noah Fahlgren
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Sanjuro Jogdeo
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Kristin D. Kasschau
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Christopher M. Sullivan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Elisabeth J. Chapman
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Sascha Laubinger
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Lisa M. Smith
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - Mark Dasenko
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Scott A. Givan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
| | - James C. Carrington
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Address correspondence to
| |
Collapse
|
208
|
Allen E, Howell MD. miRNAs in the biogenesis of trans-acting siRNAs in higher plants. Semin Cell Dev Biol 2010; 21:798-804. [PMID: 20359543 DOI: 10.1016/j.semcdb.2010.03.008] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 03/22/2010] [Indexed: 11/25/2022]
Abstract
Multicellular eukaryotes utilize many complex small RNA mechanisms to regulate gene expression from DNA modifications to RNA stability. RNA interference also regulates exogenous gene expression by degrading invading pathogen RNAs or preventing expression of foreign DNA incorporated into the host genome. Here we review the mechanisms for trans-acting (ta)-siRNA biogenesis and function, including pathways that utilize components of the miRNA and transitive RNAi defense. There are several distinguishing features of ta-siRNA pathways including the requirement for a miRNA-guided cleavage event that sets a processing register, RDR6 dependent dsRNA production, and DCL4 dependent processing to create unique, phased 21 nucleotide small RNAs. These phased small RNAs function to suppress target genes that only show similarity at the ta-siRNA recognition site, and act in trans to repress expression non-cell autonomously of specific target genes. Since the advent of high throughput sequencing technologies, phased siRNAs have been identified in a number of organisms [Heisel SE, Zhang Y, Allen E, Guo L, Reynolds TL, Yang X, et al. Characterization of unique small RNA populations from rice grain. PLoS One 2008;3:e2871. Zhao T, Li G, Mi S, Li S, Hannon GJ, Wang XJ, et al. A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii. Genes Dev 2007;21:1190-203. Johnson C, et al. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res 2009;19:1429-40. Zhu QH, Spriggs A, Matthew L, Fan L, Kennedy G, Gubler F, et al. A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains. Genome Res 2008;18:1456-65. Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, et al. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and ta-siRNA-directed targeting. Plant Cell 2007;19:926-42.]. These include transcripts generated either from non-protein-coding or protein-coding transcripts, long imperfect dsRNA or through an unknown mechanism; therefore some of these may not necessarily be classified as canonical ta-siRNAs.
Collapse
|
209
|
Olive V, Jiang I, He L. mir-17-92, a cluster of miRNAs in the midst of the cancer network. Int J Biochem Cell Biol 2010; 42:1348-54. [PMID: 20227518 DOI: 10.1016/j.biocel.2010.03.004] [Citation(s) in RCA: 349] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Revised: 11/19/2009] [Accepted: 03/08/2010] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs (ncRNAs) that function to regulate gene expression at the post-transcriptional level. Although their functions were originally described during normal development, miRNAs have emerged as integral components of the oncogenic and tumor suppressor network, regulating nearly all cellular processes altered during tumor formation. In particular, mir-17-92, a miRNA polycistron also known as oncomir-1, is among the most potent oncogenic miRNAs. Genomic amplification and elevated expression of mir-17-92 were both found in several human B-cell lymphomas, and its enforced expression exhibits strong tumorigenic activity in multiple mouse tumor models. mir-17-92 carries out pleiotropic functions during both normal development and malignant transformation, as it acts to promote proliferation, inhibit differentiation, increase angiogenesis, and sustain cell survival. Unlike most protein coding genes, mir-17-92 is a polycistronic miRNA cluster that contains multiple miRNA components, each of which has a potential to regulate hundreds of target mRNAs. This unique gene structure of mir-17-92 may underlie the molecular basis for its pleiotropic functions in a cell type- and context-dependent manner. Here we review the recent literature on the functional studies of mir-17-92 and highlight its potential impacts on the oncogene network. These findings on mir-17-92 indicate that miRNAs are integrated components of the molecular pathways that regulate tumor development and tumor maintenance.
Collapse
Affiliation(s)
- Virginie Olive
- 535 LSA, Division of Cell and Developmental Biology, MCB Department, University of California at Berkeley, Berkeley, CA 94720-3200, USA
| | | | | |
Collapse
|
210
|
Yao Y, Ni Z, Peng H, Sun F, Xin M, Sunkar R, Zhu JK, Sun Q. Non-coding small RNAs responsive to abiotic stress in wheat (Triticum aestivum L.). Funct Integr Genomics 2010; 10:187-90. [PMID: 20217168 DOI: 10.1007/s10142-010-0163-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/23/2010] [Accepted: 01/31/2010] [Indexed: 11/30/2022]
Abstract
Plant small RNAs are emerging as significant components of epigenetic processes and of gene networks involved in development and homeostasis. In this paper, to identify small RNAs in wheat, 2,076 small RNAs were identified in a small RNA library from leaf, root, and spike. These small RNAs mapped to non-coding regions the CDS region of protein-coding genes and 5' UTR and 3' UTR regions. The expression of small RNAs in seedling leaves, roots, and spikes were analyzed by northern blot, which indicates that some small RNAs were responsive to abiotic stress treatments including heat, cold, salt and dehydration.
Collapse
Affiliation(s)
- Yingyin Yao
- Key Laboratory of Crop Heterosis and Utilization (MOE) and State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100094, China
| | | | | | | | | | | | | | | |
Collapse
|
211
|
Liu S, Li D, Li Q, Zhao P, Xiang Z, Xia Q. MicroRNAs of Bombyx mori identified by Solexa sequencing. BMC Genomics 2010; 11:148. [PMID: 20199675 PMCID: PMC2838851 DOI: 10.1186/1471-2164-11-148] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Accepted: 03/03/2010] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three small RNA libraries prepared from the whole body, and the anterior-middle and posterior silk glands of Bombyx mori, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland. RESULTS With the aid of large-scale Solexa sequencing technology, we validated 257 unique miRNA genes, including 202 novel and 55 previously reported genes, corresponding to 324 loci in the silkworm genome. Over 30 known silkworm miRNAs were further corrected in their sequence constitutes and length. A number of reads originated from the loop regions of the precursors of two previously reported miRNAs (bmo-miR-1920 and miR-1921). Interestingly, the majority of the newly identified miRNAs were silkworm-specific, 23 unique miRNAs were widely conserved from invertebrates to vertebrates, 13 unique miRNAs were limited to invertebrates, and 32 were confined to insects. We identified 24 closely positioned clusters and 45 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters were not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs were located in transposable elements, and displayed significant differences in abundance between the anterior-middle and posterior silk gland. CONCLUSIONS Conservative analysis revealed that miRNAs can serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enrich the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior-middle and posterior silk glands supports their involvement as new levels in the regulation of the silkworm silk gland.
Collapse
Affiliation(s)
- Shiping Liu
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China
| | - Dong Li
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China
| | - Qibin Li
- Beijing Genomics Institute, Beishan Road, Yantian District, Shenzhen 518083, PR China
| | - Ping Zhao
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China
| | - Zhonghuai Xiang
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China
| | - Qingyou Xia
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China
- Institute of Agricultural and Life Sciences, Chongqing University, Shazhengjie, Shapingba, Chongqing 400030, PR China
| |
Collapse
|
212
|
Abstract
Small RNAs associated with post-transcriptional gene silencing were first discovered in plants in 1999. Although this study marked the beginning of small RNA biology in plants, the sequence of the Arabidopsis genome and related genomic resources that were soon to become available to the Arabidopsis community launched the research on small RNAs at a remarkable pace. In 2000, when the genetic blueprint of the first plant species was revealed, the tens of thousands of endogenous small RNA species as we know today remained hidden features of the genome. However, the subsequent 10 years have witnessed an explosion of our knowledge of endogenous small RNAs: their widespread existence, diversity, biogenesis, mode of action and biological functions. As key sequence-specific regulators of gene expression in the nucleus and the cytoplasm, small RNAs influence almost all aspects of plant biology. Because of the extensive conservation of mechanisms concerning the biogenesis and molecular actions of small RNAs, research in the model plant Arabidopsis has contributed vital knowledge to the small RNA field in general. Our knowledge of small RNAs gained primarily from Arabidopsis has also led to the invention of effective gene knock-down technologies that are applicable to diverse plant species, including crop plants. Here, I attempt to recount the developments of the small RNA field in the pre- and post-genomic era, in celebration of the 10th anniversary of the completion of the first plant genome.
Collapse
Affiliation(s)
- Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
| |
Collapse
|
213
|
Muljo SA, Kanellopoulou C, Aravind L. MicroRNA targeting in mammalian genomes: genes and mechanisms. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2010; 2:148-161. [PMID: 20836019 PMCID: PMC3427708 DOI: 10.1002/wsbm.53] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We briefly review the history of microRNA (miRNA) research and some of the lessons learnt. To provide some insights as to how and why miRNAs came into existence, we consider the evolution of the RNA interference machinery, miRNA genes, and their targets. We highlight the importance of systems biology approaches to integrate miRNAs as an essential subnetwork for modulating gene expression programs. Building accurate computational models that can simulate highly complex cell-specific gene expression patterns in mammals will lead to a better understanding of miRNAs and their targets in physiological and pathological situations. The impact of miRNAs on medicine, either as potential disease predisposing factors, biomarkers, or therapeutics, is highly anticipated and has started to reveal itself.
Collapse
Affiliation(s)
- S A Muljo
- Integrative Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - C Kanellopoulou
- Dana-Farber Cancer Institute, Department of Cancer Biology, Harvard Medical School, Boston, MA, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
214
|
Ibrahim F, Rymarquis LA, Kim EJ, Becker J, Balassa E, Green PJ, Cerutti H. Uridylation of mature miRNAs and siRNAs by the MUT68 nucleotidyltransferase promotes their degradation in Chlamydomonas. Proc Natl Acad Sci U S A 2010; 107:3906-11. [PMID: 20142471 PMCID: PMC2840426 DOI: 10.1073/pnas.0912632107] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Regulation of gene expression by small RNAs ( approximately 20-30 nucleotides in length) plays an essential role in developmental pathways and defense responses against genomic parasites in eukaryotes. MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) commonly direct the inactivation of cognate sequences through a variety of mechanisms, including RNA degradation, translation inhibition, and transcriptional repression. Recent studies have provided considerable insight into the biogenesis and the mode of action of miRNAs and siRNAs. However, relatively little is known about mechanisms of quality control and small RNA decay in RNA interference (RNAi) pathways. Here we show that deletion of MUT68, encoding a terminal nucleotidyltransferase in the alga Chlamydomonas reinhardtii, results in elevated miRNA and siRNA levels. We found that MUT68 plays a role in the untemplated uridylation of the 3' ends of small RNAs in vivo and stimulates their degradation by the RRP6 exosome subunit in vitro. Moreover, RRP6 depletion also leads to accumulation of small RNAs in vivo. We propose that MUT68 and RRP6 cooperate in the degradation of mature miRNAs and siRNAs, as a quality control mechanism to eliminate dysfunctional or damaged small RNA molecules.
Collapse
Affiliation(s)
- Fadia Ibrahim
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588; and
| | - Linda A. Rymarquis
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711
| | - Eun-Jeong Kim
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588; and
| | - James Becker
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588; and
| | - Eniko Balassa
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588; and
| | - Pamela J. Green
- Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588; and
| |
Collapse
|
215
|
Abstract
The discovery of RNA interference (RNAi) heralded a revolution in RNA biology. Researchers uncovered 'hidden' layers of regulation of gene expression, in which many previously unidentified families of small RNAs (consisting of approximately 20-30 nucleotides) mediate gene silencing in transcriptional and post-transcriptional levels. In eukaryotes, these small RNAs, including siRNAs, miRNAs, piRNAs, scnRNAs, 21U-RNAs, and some others, regulate gene expression, helping to control cellular metabolism, growth, and differentiation, to maintain genome integrity, to regulate stem cell renewal, and to combat viruses and mobile genetic elements. This review summarizes the current advancement in the identification and biosynthesis of small RNAs and their roles in gene regulation.
Collapse
|
216
|
Turnover of Mature miRNAs and siRNAs in Plants and Algae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 700:124-39. [PMID: 21755478 DOI: 10.1007/978-1-4419-7823-3_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
microRNAs (miRNAs) and small interfering RNAs (siRNAs) play important roles in gene regulation and defense responses against transposons and viruses in eukaryotes. These small RNAs generally trigger the silencing of cognate sequences through a variety of mechanisms, including RNA degradation, translational inhibition and transcriptional repression. In the past few years, the synthesis and the mode of action of miRNAs and siRNAs have attracted great attention. However, relatively little is known about mechanisms of quality control during small RNA biogenesis as well as those that regulate mature small RNA stability. Recent studies in Arabidopsis thaliana and Caenorhabditis elegans have implicated 3'-to-5' (SDNs) and 5'-to-3' (XRN-2) exoribonucleases in mature miRNA turnover and the modulation of small RNA levels and activity. In the green alga Chlamydomonas reinhardtii, a nucleotidyltransferase (MUT68) and an exosome subunit (RRP6) are involved in the 3' untemplated uridylation and the degradation of miRNAs and siRNAs. The latter enzymes appear to function as a quality control mechanism to eliminate putative dysfunctional or damaged small RNA molecules. Several post-transcriptional modifications of miRNAs and siRNAs such as 3' terminal methylation and untemplated nucleotide additions have also been reported to affect small RNA stability. These collective findings are beginning to uncover a new layer of regulatory control in the pathways involving small RNAs. We anticipate that understanding the mechanisms of mature miRNA and siRNA turnover will have direct implications for fundamental biology as well as for applications of RNA interference technology.
Collapse
|
217
|
Yu B, Wang H. Translational Inhibition by MicroRNAs in Plants. MIRNA REGULATION OF THE TRANSLATIONAL MACHINERY 2010; 50:41-57. [DOI: 10.1007/978-3-642-03103-8_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
218
|
Abstract
Small RNA-guided gene silencing is an evolutionarily conserved process that operates by a variety of molecular mechanisms and plays an essential role in developmental pathways and defense responses against genomic parasites in eukaryotes. Double-stranded RNA (dsRNA) triggered posttranscriptional gene silencing, termed RNA interference (RNAi), is also becoming a powerful tool for reverse genetics studies. Stable RNAi, induced by the expression of long dsRNAs or duplex small RNAs from genome-integrated transgenes, has been achieved in multiple organisms, including the green alga Chlamydomonas reinhardtii. However, the level of gene repression is often quite variable, depending on the type of construct, transgene copy number, site of integration, and target gene. Moreover, unintended transcripts partly complementary to a trigger dsRNA can also be silenced, making difficult the interpretation of observed phenotypes. To obviate some of these problems we have developed a tandem inverted repeat system that consistently induces cosilencing of a gene with a selectable RNAi-induced phenotype (encoding tryptophan synthase beta-subunit) and any other (nonessential) gene of interest. In addition, to circumvent off-target effects, for each tested gene, RNAi lines are generated with at least two transgenes, homologous to distinct and nonoverlapping sequences of the target transcript. A common phenotype among these independent RNAi strains is expected to result from suppression of expression of the gene of interest. We demonstrate this approach for the characterization of a gene of unknown function in Chlamydomonas, encoding a predicted exoribonuclease with weak similarity to 3'hExo/ERI-1.
Collapse
|
219
|
Chen R, Hu Z, Zhang H. Identification of microRNAs in wild soybean (Glycine soja). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2009; 51:1071-9. [PMID: 20021554 DOI: 10.1111/j.1744-7909.2009.00887.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) play important roles in post-transcriptional gene silencing by directing target mRNA cleavage or translational inhibition. Currently, hundreds of miRNAs have been identified in plants, but no report has been published of wild soybean (Glycine soja Sieb). We constructed a small-RNA library consisting of 2 880 sequences with high quality, in which 1 347 were 19-24 nt in length. By utilizing the miRNA, Rfam and domesticated soybean expressed sequence tag database, we have analyzed and predicted the secondary structure of these small RNAs. As a result, 15 conserved miRNA candidates belonging to eight different families and nine novel miRNA candidates comprising eight families were identified in wild soybean seedlings. All these miRNA candidates were validated by northern blot and the novel candidates expressed in a tissue-specific manner. Furthermore, putative target genes were predicted for novel miRNA candidates and two of them were verified by 5'-rapid amplification of cDNA ends experiments. These results provided useful information for miRNA research in wild soybean and plants.
Collapse
Affiliation(s)
- Rui Chen
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | | |
Collapse
|
220
|
Wu L, Zhang Q, Zhou H, Ni F, Wu X, Qi Y. Rice MicroRNA effector complexes and targets. THE PLANT CELL 2009; 21:3421-35. [PMID: 19903869 PMCID: PMC2798332 DOI: 10.1105/tpc.109.070938] [Citation(s) in RCA: 247] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Revised: 10/06/2009] [Accepted: 10/20/2009] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are small silencing RNAs with regulatory roles in gene expression. miRNAs interact with Argonaute (AGO) proteins to form effector complexes that cleave target mRNAs or repress translation. Rice (Oryza sativa) encodes four AGO1 homologs (AGO1a, AGO1b, AGO1c, and AGO1d). We used RNA interference (RNAi) to knock down the four AGO1s. The RNAi lines displayed pleiotropic developmental phenotypes and had increased accumulation of miRNA targets. AGO1a, AGO1b, and AGO1c complexes were purified and further characterized. The three AGO1s all have a strong preference for binding small RNAs (sRNAs) with 5' U and have Slicer activity. We cataloged the sRNAs in each AGO1 complex by deep sequencing and found that all three AGO1s predominantly bound known miRNAs. Most of the miRNAs were evenly distributed in the three AGO1 complexes, suggesting a redundant role for the AGO1s. Intriguingly, a subset of miRNAs were specifically incorporated into or excluded from one of the AGO1s, suggesting functional specialization among the AGO1s. Furthermore, we identified rice miRNA targets at a global level. The validated targets include transcription factors that control major stages of development and also genes involved in a variety of physiological processes, indicating a broad regulatory role for miRNAs in rice.
Collapse
Affiliation(s)
- Liang Wu
- National Institute of Biological Sciences, Beijing 102206, China
- College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Qingqing Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Huanyu Zhou
- National Institute of Biological Sciences, Beijing 102206, China
| | - Fangrui Ni
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xueying Wu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yijun Qi
- National Institute of Biological Sciences, Beijing 102206, China
- Address correspondence to
| |
Collapse
|
221
|
Algal lipid bodies: stress induction, purification, and biochemical characterization in wild-type and starchless Chlamydomonas reinhardtii. EUKARYOTIC CELL 2009; 8:1856-68. [PMID: 19880756 DOI: 10.1128/ec.00272-09] [Citation(s) in RCA: 340] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
When the unicellular green soil alga Chlamydomonas reinhardtii is deprived of nitrogen after entering stationary phase in liquid culture, the cells produce abundant cytoplasmic lipid bodies (LBs), as well as abundant starch, via a pathway that accompanies a regulated autophagy program. After 48 h of N starvation in the presence of acetate, the wild-type LB content has increased 15-fold. When starch biosynthesis is blocked in the sta6 mutant, the LB content increases 30-fold, demonstrating that genetic manipulation can enhance LB production. The use of cell wall-less strains permitted development of a rapid "popped-cell" microscopic assay to quantitate the LB content per cell and permitted gentle cell breakage and LB isolation. The highly purified LBs contain 90% triacylglycerol (TAG) and 10% free fatty acids (FFA). The fatty acids associated with the TAGs are approximately 50% saturated (C(16) and C(18)) fatty acids and approximately 50% unsaturated fatty acids, half of which are in the form of oleic acid (C(18:1)). The FFA are approximately 50% C(16) and approximately 50% C(18). The LB-derived TAG yield from a liter of sta6 cells at 10(7) cells/ml after starvation for 48 h is calculated to approach 400 mg. The LB fraction also contains low levels of charged glycerolipids, with the same profile as whole-cell charged glycerolipids, that presumably form LB membranes; chloroplast-specific neutral glycerolipids (galactolipids) are absent. Very low levels of protein are also present, but all matrix-assisted laser desorption ionization-identified species are apparent contaminants. Nitrogen stress-induced LB production in C. reinhardtii has the hallmarks of a discrete pathway that should be amenable to additional genetic and culture condition manipulation.
Collapse
|
222
|
Zhang Z, Yu J, Li D, Zhang Z, Liu F, Zhou X, Wang T, Ling Y, Su Z. PMRD: plant microRNA database. Nucleic Acids Res 2009; 38:D806-13. [PMID: 19808935 PMCID: PMC2808885 DOI: 10.1093/nar/gkp818] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNA) are approximately 21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Glycine max, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, Arabidopsis, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD. We expect PMRD to be a useful tool for scientists in the miRNA field in order to study the function of miRNAs and their target genes, especially in model plants and major crops.
Collapse
Affiliation(s)
- Zhenhai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry and State Key Laboratory for Agricultural Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | | | | | | | | | | | | | | | | |
Collapse
|
223
|
Bioinformatic analysis of microRNA biogenesis and function related proteins in eleven animal genomes. J Genet Genomics 2009; 36:591-601. [DOI: 10.1016/s1673-8527(08)60151-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 05/13/2009] [Accepted: 05/19/2009] [Indexed: 01/20/2023]
|
224
|
Zhang YQ, Chen DL, Tian HF, Zhang BH, Wen JF. Genome-wide computational identification of microRNAs and their targets in the deep-branching eukaryote Giardia lamblia. Comput Biol Chem 2009; 33:391-6. [DOI: 10.1016/j.compbiolchem.2009.07.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 07/05/2009] [Accepted: 07/16/2009] [Indexed: 12/29/2022]
|
225
|
Jian X, Zhang L, Li G, Zhang L, Wang X, Cao X, Fang X, Chen F. Identification of novel stress-regulated microRNAs from Oryza sativa L. Genomics 2009; 95:47-55. [PMID: 19796675 DOI: 10.1016/j.ygeno.2009.08.017] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 08/20/2009] [Accepted: 08/23/2009] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are a type of small non-coding RNA found in eukaryotes. They play a key role in gene expression by down-regulating gene expression and are involved in the environment stress response in plants. Although a large number of miRNAs have been identified from Arabidopsis, few studies have focused on Oryza sativa miRNAs, especially on stress-related miRNAs. Five cDNA libraries of small RNAs from rice seedlings treated with cold, dehydration, salinity, and abscisic acid (ABA), as well as wild-type seedlings, were constructed. Seven rice novel miRNAs were identified by Northern analysis, and their expression patterns under different stress treatments were determined. Results showed that the expression of several novel miRNAs was regulated by one or more stress treatments. Our identification of novel stress-related miRNAs in rice suggests that these miRNAs might be involved in rice stress response pathways.
Collapse
Affiliation(s)
- Xinyu Jian
- National Centre for Plant Gene Research, Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, P.O. Box 2707, South 1-3, Zhongguancun, Beijing 100080, P.R. China
| | | | | | | | | | | | | | | |
Collapse
|
226
|
Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 2009; 10:135-51. [PMID: 19715439 DOI: 10.1146/annurev-genom-082908-145957] [Citation(s) in RCA: 340] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcriptome analysis has been a key area of biological inquiry for decades. Over the years, research in the field has progressed from candidate gene-based detection of RNAs using Northern blotting to high-throughput expression profiling driven by the advent of microarrays. Next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution.
Collapse
Affiliation(s)
- Olena Morozova
- BC Cancer Agency, Genome Sciences Center, Vancouver, BC V5Z 4S6, Canada.
| | | | | |
Collapse
|
227
|
Lelandais-Brière C, Naya L, Sallet E, Calenge F, Frugier F, Hartmann C, Gouzy J, Crespi M. Genome-wide Medicago truncatula small RNA analysis revealed novel microRNAs and isoforms differentially regulated in roots and nodules. THE PLANT CELL 2009; 21:2780-96. [PMID: 19767456 PMCID: PMC2768930 DOI: 10.1105/tpc.109.068130] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 07/09/2009] [Accepted: 07/26/2009] [Indexed: 05/18/2023]
Abstract
Posttranscriptional regulation of a variety of mRNAs by small 21- to 24-nucleotide RNAs, notably the microRNAs (miRNAs), is emerging as a novel developmental mechanism. In legumes like the model Medicago truncatula, roots are able to develop a de novo meristem through the symbiotic interaction with nitrogen-fixing rhizobia. We used deep sequencing of small RNAs from root apexes and nodules of M. truncatula to identify 100 novel candidate miRNAs encoded by 265 hairpin precursors. New atypical precursor classes producing only specific 21- and 24-nucleotide small RNAs were found. Statistical analysis on sequencing reads abundance revealed specific miRNA isoforms in a same family showing contrasting expression patterns between nodules and root apexes. The differentially expressed conserved and nonconserved miRNAs may target a large variety of mRNAs. In root nodules, which show diverse cell types ranging from a persistent meristem to a fully differentiated central region, we discovered miRNAs spatially enriched in nodule meristematic tissues, vascular bundles, and bacterial infection zones using in situ hybridization. Spatial regulation of miRNAs may determine specialization of regulatory RNA networks in plant differentiation processes, such as root nodule formation.
Collapse
Affiliation(s)
- Christine Lelandais-Brière
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
- Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
| | - Loreto Naya
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
| | - Erika Sallet
- Laboratoire des Interactions Plantes Micro-organismes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique–Institut National de la Recherche Agronomique 2594/441, F- 31320 Castanet Tolosan, France
- Plateforme Bioinformatique du Génopole Toulouse Midi-Pyrénées, Groupement d'Intérêt Scientifique Toulouse Genopole, F-31320 Castanet Tolosan, France
| | - Fanny Calenge
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
- Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
| | - Florian Frugier
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
| | - Caroline Hartmann
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
- Université Paris Diderot-Paris 7, 75205 Paris Cedex 13, France
| | - Jérome Gouzy
- Laboratoire des Interactions Plantes Micro-organismes, Unité Mixte de Recherche, Centre National de la Recherche Scientifique–Institut National de la Recherche Agronomique 2594/441, F- 31320 Castanet Tolosan, France
| | - Martin Crespi
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, F-91198 Gif-sur-Yvette Cedex, France
| |
Collapse
|
228
|
Couvillion MT, Lee SR, Hogstad B, Malone CD, Tonkin LA, Sachidanandam R, Hannon GJ, Collins K. Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila. Genes Dev 2009; 23:2016-32. [PMID: 19656801 DOI: 10.1101/gad.1821209] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PAZ/PIWI domain (PPD) proteins carrying small RNAs (sRNAs) function in gene and genome regulation. The ciliate Tetrahymena thermophila encodes numerous PPD proteins exclusively of the Piwi clade. We show that the three Tetrahymena Piwi family proteins (Twis) preferentially expressed in growing cells differ in their genetic essentiality and subcellular localization. Affinity purification of all eight distinct Twi proteins revealed unique properties of their bound sRNAs. Deep sequencing of Twi-bound and total sRNAs in strains disrupted for various silencing machinery uncovered an unanticipated diversity of 23- to 24-nt sRNA classes in growing cells, each with distinct genetic requirements for accumulation. Altogether, Twis distinguish sRNAs derived from loci of pseudogene families, three types of DNA repeats, structured RNAs, and EST-supported loci with convergent or paralogous transcripts. Most surprisingly, Twi7 binds complementary strands of unequal length, while Twi10 binds a specific permutation of the guanosine-rich telomeric repeat. These studies greatly expand the structural and functional repertoire of endogenous sRNAs and RNPs.
Collapse
Affiliation(s)
- Mary T Couvillion
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | | | | | | | | | | | | | | |
Collapse
|
229
|
Smith KE, Linser PJ. Silencing of carbonic anhydrase in an Anopheles gambiae larval cell line, Ag55. JOURNAL OF RNAI AND GENE SILENCING : AN INTERNATIONAL JOURNAL OF RNA AND GENE TARGETING RESEARCH 2009; 5:345-50. [PMID: 19771232 PMCID: PMC2737235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 03/29/2009] [Accepted: 04/08/2009] [Indexed: 10/25/2022]
Abstract
RNAi has been used extensively to down-regulate proteins in adult mosquitoes; however, it is not well adapted for use in larvae. Larval mosquitoes can generate a pH as high as 10.5 in the anterior region of their midgut. The mechanisms responsible for the generation and maintenance of this pH are not entirely understood, but members of the carbonic anhydrase (CA) family of enzymes have been implicated. Here we use an An. gambiae larval cell line, Ag55 cells, to demonstrate that application of full-length double-stranded RNA specific to one CA, AgCA9, is sufficient to silence AgCA9 mRNA and down-regulate the corresponding protein. This is a first step towards determining the role(s) of these enzymes in pH regulation.
Collapse
Affiliation(s)
| | - Paul J Linser
- Correspondence to: Paul Linser, , Tel: +904 4614036, Fax: +904 4614010
| |
Collapse
|
230
|
Wei B, Cai T, Zhang R, Li A, Huo N, Li S, Gu YQ, Vogel J, Jia J, Qi Y, Mao L. Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Funct Integr Genomics 2009; 9:499-511. [PMID: 19499258 DOI: 10.1007/s10142-009-0128-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 05/17/2009] [Indexed: 12/31/2022]
Abstract
The small RNA transcriptomes of bread wheat and its emerging model Brachypodium distachyon were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNAs) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of expressed sequence tags, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' rapid amplification of complementary DNA ends experiments demonstrated their capability to cleave predicted target genes including three disease-resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in B. distachyon.
Collapse
Affiliation(s)
- Bo Wei
- National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, Pr China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
231
|
Li H, Zhang Z, Huang F, Chang L, Ma Y. MicroRNA expression profiles in conventional and micropropagated strawberry (Fragaria x ananassa Duch.) plants. PLANT CELL REPORTS 2009; 28:891-902. [PMID: 19277667 DOI: 10.1007/s00299-009-0693-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 02/18/2009] [Accepted: 02/19/2009] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs which play a critical role in plant growth and development. To detect strawberry miRNAs and discover the expression difference between conventional and micropropagated strawberry plants, we carried out the detection and quantification of strawberry miRNAs by microarray. The main findings were that 74 miRNAs were checked in strawberry plants and four miRNA genes displayed clear expression difference between conventional and micropropagated strawberry plants, including two up-regulated genes (miR535 and miR390) and two down-regulated genes (miR169a and miR169d). The ratios of conventionally propagated strawberry plant/micropropagated strawberry plant for miR535, miR390, miR169a and miR169d were 2.6884, 2.2673, 0.2496 and 0.3814, respectively. Quantitative reverse transcription polymerase chain reaction applied to the two up-regulated genes (miR535 and miR390) validated the microarray result. This is the first report on differential expression of miRNAs in conventional and micropropagated plants.
Collapse
Affiliation(s)
- He Li
- College of Horticulture, Shenyang Agricultural University, Dongling Road 120, 110161, Shenyang, Liaoning, People's Republic of China
| | | | | | | | | |
Collapse
|
232
|
Dai Z, Chen Z, Ye H, Zhou L, Cao L, Wang Y, Peng S, Chen L. Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution. Evol Dev 2009; 11:41-9. [PMID: 19196332 DOI: 10.1111/j.1525-142x.2008.00301.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cephalochordates, urochordates, and vertebrates comprise the three extant groups of chordates. Although higher morphological and developmental similarity exists between cephalochordates and vertebrates, molecular phylogeny studies have instead suggested that the morphologically simplified urochordates are the closest relatives to vertebrates. MicroRNAs (miRNAs) are regarded as the major factors driving the increase of morphological complexity in early vertebrate evolution, and are extensively characterized in vertebrates and in a few species of urochordates. However, the comprehensive set of miRNAs in the basal chordates, namely the cephalochordates, remains undetermined. Through extensive sequencing of a small RNA library and genomic homology searches, we characterized 100 miRNAs from the cephalochordate amphioxus, Branchiostoma japonicum, and B. floridae. Analysis of the evolutionary history of the cephalochordate miRNAs showed that cephalochordates possess 54 miRNA families homologous to those of vertebrates, which is threefold higher than those shared between urochordates and vertebrates. The miRNA contents demonstrated a clear correlation between the extent of miRNA overlapping and morphological similarity among the three chordate groups, providing a strong evidence of miRNAs being the major genetic factors driving morphological complexity in early chordate evolution.
Collapse
Affiliation(s)
- Zhonghua Dai
- Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | | | | | | | | | | |
Collapse
|
233
|
Beer LL, Boyd ES, Peters JW, Posewitz MC. Engineering algae for biohydrogen and biofuel production. Curr Opin Biotechnol 2009; 20:264-71. [DOI: 10.1016/j.copbio.2009.06.002] [Citation(s) in RCA: 230] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Revised: 06/02/2009] [Accepted: 06/03/2009] [Indexed: 01/11/2023]
|
234
|
Gene dysregulation in Huntington's disease: REST, microRNAs and beyond. Neuromolecular Med 2009; 11:183-99. [PMID: 19458943 DOI: 10.1007/s12017-009-8063-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 04/17/2009] [Indexed: 02/06/2023]
Abstract
Huntington's disease (HD) is an incurable, fatal neurodegenerative disorder that is caused by a polyglutamine expansion in the huntingtin (Htt) protein. Neuronal death in the striatum-the most obvious manifestation of the disease-is likely to result from widespread dysregulation of gene expression in various brain regions. To date, several potential mechanisms for this have been discovered, including one involving REST (RE1-Silencing Transcription Factor), a master regulator of neuronal genes. Recently, independent studies have demonstrated that post-transcriptional gene regulation by microRNAs is also disrupted in HD. Expression of key neuronal microRNAs-including mir-9/9*, mir-124 and mir-132-is repressed in the brains of human HD patients and mouse models. These changes occur downstream of REST, and are likely to result in major disruption of mRNA regulation and neuronal function. In this study we will discuss these findings and their implications for our understanding of HD. Using updated bioinformatic analysis, we predict 21 new candidate microRNAs in HD. We propose future strategies for unifying large-scale transcriptional and microRNA datasets with the aim of explaining HD aetiology. By way of example, we show how available genomic datasets can be integrated to provide independent, analytical validation for dysregulation of REST and microRNA mir-124 in HD. As a consequence, gene ontology analysis indicates that HD is characterised by a broad-based depression of neural genes in the caudate and motor cortex. Thus, we propose that a combination of REST, microRNAs and possibly other non-coding RNAs profoundly affect the neuronal transcriptome in HD.
Collapse
|
235
|
Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. Genome Biol 2009; 10:R50. [PMID: 19432952 PMCID: PMC2718516 DOI: 10.1186/gb-2009-10-5-r50] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 03/23/2009] [Accepted: 05/11/2009] [Indexed: 11/10/2022] Open
Abstract
Signals for microRNA targeting and ubiquitination are enriched in intrinsically disordered proteins, but some highly disordered proteins can escape rapid degradation. Background Disordered proteins need to be expressed to carry out specified functions; however, their accumulation in the cell can potentially cause major problems through protein misfolding and aggregation. Gene expression levels, mRNA decay rates, microRNA (miRNA) targeting and ubiquitination have critical roles in the degradation and disposal of human proteins and transcripts. Here, we describe a study examining these features to gain insights into the regulation of disordered proteins. Results In comparison with ordered proteins, disordered proteins have a greater proportion of predicted ubiquitination sites. The transcripts encoding disordered proteins also have higher proportions of predicted miRNA target sites and higher mRNA decay rates, both of which are indicative of the observed lower gene expression levels. The results suggest that the disordered proteins and their transcripts are present in the cell at low levels and/or for a short time before being targeted for disposal. Surprisingly, we find that for a significant proportion of highly disordered proteins, all four of these trends are reversed. Predicted estimates for miRNA targets, ubiquitination and mRNA decay rate are low in the highly disordered proteins that are constitutively and/or highly expressed. Conclusions Mechanisms are in place to protect the cell from these potentially dangerous proteins. The evidence suggests that the enrichment of signals for miRNA targeting and ubiquitination may help prevent the accumulation of disordered proteins in the cell. Our data also provide evidence for a mechanism by which a significant proportion of highly disordered proteins (with high expression levels) can escape rapid degradation to allow them to successfully carry out their function.
Collapse
|
236
|
Soares AR, Pereira PM, Santos B, Egas C, Gomes AC, Arrais J, Oliveira JL, Moura GR, Santos MAS. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics 2009; 10:195. [PMID: 19397817 PMCID: PMC2684549 DOI: 10.1186/1471-2164-10-195] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Accepted: 04/27/2009] [Indexed: 12/19/2022] Open
Abstract
Background MicroRNAs (miRNAs) are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes, namely developmental timing, cell differentiation, cell proliferation, immune response and infection. For this reason, their identification is essential to understand eukaryotic biology. Their small size, low abundance and high instability complicated early identification, however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. Results We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish (Danio rerio). For this, a series of cDNA libraries were prepared from miRNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics. Twenty five novel miRNAs were predicted, 107 miRNA star sequences and also 41 candidate miRNA targets were identified. A miRNA expression profile built on the basis of pyrosequencing read numbers showed high expression of most miRNAs throughout zebrafish development and identified tissue specific miRNAs. Conclusion This study increases the number of zebrafish miRNAs from 192 to 217 and demonstrates that a single DNA mini-chip pyrosequencing run is effective in miRNA identification in zebrafish. This methodology also produced sufficient information to elucidate miRNA expression patterns during development and in differentiated organs. Moreover, some zebrafish miRNA star sequences were more abundant than their corresponding miRNAs, suggesting a functional role for the former in gene expression control in this vertebrate model organism.
Collapse
Affiliation(s)
- Ana R Soares
- RNA Biology Laboratory, Department of Biology & CESAM, University of Aveiro, Aveiro 3810-193, Portugal.
| | | | | | | | | | | | | | | | | |
Collapse
|
237
|
Ahmed F, Ansari HR, Raghava GPS. Prediction of guide strand of microRNAs from its sequence and secondary structure. BMC Bioinformatics 2009; 10:105. [PMID: 19358699 PMCID: PMC2676257 DOI: 10.1186/1471-2105-10-105] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 04/09/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are produced by the sequential processing of a long hairpin RNA transcript by Drosha and Dicer, an RNase III enzymes, and form transitory small RNA duplexes. One strand of the duplex, which incorporates into RNA-induced silencing complex (RISC) and silences the gene expression is called guide strand, or miRNA; while the other strand of duplex is degraded and called the passenger strand, or miRNA*. Predicting the guide strand of miRNA is important for better understanding the RNA interference pathways. RESULTS This paper describes support vector machine (SVM) models developed for predicting the guide strands of miRNAs. All models were trained and tested on a dataset consisting of 329 miRNA and 329 miRNA* pairs using five fold cross validation technique. Firstly, models were developed using mono-, di-, and tri-nucleotide composition of miRNA strands and achieved the highest accuracies of 0.588, 0.638 and 0.596 respectively. Secondly, models were developed using split nucleotide composition and achieved maximum accuracies of 0.553, 0.641 and 0.602 for mono-, di-, and tri-nucleotide respectively. Thirdly, models were developed using binary pattern and achieved the highest accuracy of 0.708. Furthermore, when integrating the secondary structure features with binary pattern, an accuracy of 0.719 was seen. Finally, hybrid models were developed by combining various features and achieved maximum accuracy of 0.799 with sensitivity 0.781 and specificity 0.818. Moreover, the performance of this model was tested on an independent dataset that achieved an accuracy of 0.80. In addition, we also compared the performance of our method with various siRNA-designing methods on miRNA and siRNA datasets. CONCLUSION In this study, first time a method has been developed to predict guide miRNA strands, of miRNA duplex. This study demonstrates that guide and passenger strand of miRNA precursors can be distinguished using their nucleotide sequence and secondary structure. This method will be useful in understanding microRNA processing and can be implemented in RNA silencing technology to improve the biological and clinical research. A web server has been developed based on SVM models described in this study (http://crdd.osdd.net:8081/RISCbinder/).
Collapse
Affiliation(s)
- Firoz Ahmed
- Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India.
| | | | | |
Collapse
|
238
|
Molnar A, Bassett A, Thuenemann E, Schwach F, Karkare S, Ossowski S, Weigel D, Baulcombe D. Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:165-74. [PMID: 19054357 DOI: 10.1111/j.1365-313x.2008.03767.x] [Citation(s) in RCA: 220] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are small RNAs, 21 to 22 nucleotides long, with important regulatory roles. They are processed from longer RNA molecules with imperfectly matched foldback regions and they function in modulating the stability and translation of mRNA. Recently, we and others have demonstrated that the unicellular alga Chlamydomonas reinhardtii, like diverse multicellular organisms, contains miRNAs. These RNAs resemble the miRNAs of land plants in that they direct site-specific cleavage of target mRNA with miRNA-complementary motifs and, presumably, act as regulatory molecules in growth and development. Utilizing these findings we have developed a novel artificial miRNA system based on ligation of DNA oligonucleotides that can be used for specific high-throughput gene silencing in green algae.
Collapse
Affiliation(s)
- Attila Molnar
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | | | | | | | | | | | | | | |
Collapse
|
239
|
Zhao T, Wang W, Bai X, Qi Y. Gene silencing by artificial microRNAs in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:157-64. [PMID: 19054364 DOI: 10.1111/j.1365-313x.2008.03758.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular green alga. It is a model system for studying functions of the chloroplast, basal body and flagella. The completion of the Chlamydomonas genome sequence makes it possible to use reverse genetic approaches in this organism. Chlamydomonas contains a set of endogenous microRNAs (miRNAs) that down-regulate their target gene expression through mRNA cleavage. Here we developed an artificial miRNA-based strategy to knock down gene expression in Chlamydomonas. Using an endogenous Chlamydomonas miRNA precursor as the backbone, we constructed two artificial miRNAs (amiRNAs) targeting the MAA7 and RBCS1/2 genes, respectively. When overexpressed, these two amiRNAs could cleave their respective targets precisely at the predicted sites, resulting in greatly decreased accumulation of MAA7 and RBCS1/2 transcripts and expected mutant phenotypes. We further showed that the two amiRNAs could be produced simultaneously from a dimeric amiRNA precursor. We anticipate that the amiRNA technology developed in this study will be very useful in assessing the functions of individual genes and in genome-wide approaches.
Collapse
Affiliation(s)
- Tao Zhao
- National Institute of Biological Sciences, No.7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
| | | | | | | |
Collapse
|
240
|
Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF. Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res 2009; 37:1602-15. [PMID: 19151082 PMCID: PMC2655684 DOI: 10.1093/nar/gkn1084] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 12/22/2008] [Accepted: 12/23/2008] [Indexed: 02/06/2023] Open
Abstract
A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs--in particular rRNAs, tRNAs and some snRNAs--we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome.
Collapse
Affiliation(s)
- Jana Hertel
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Danielle de Jong
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Manja Marz
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Dominic Rose
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Hakim Tafer
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Andrea Tanzer
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Bernd Schierwater
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| |
Collapse
|
241
|
Zhang Y, Zhou X, Ge X, Jiang J, Li M, Jia S, Yang X, Kan Y, Miao X, Zhao G, Li F, Huang Y. Insect-Specific microRNA Involved in the Development of the Silkworm Bombyx mori. PLoS One 2009; 4:e4677. [PMID: 19262741 PMCID: PMC2650705 DOI: 10.1371/journal.pone.0004677] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 01/05/2009] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous non-coding genes that participate in post-transcription regulation by either degrading mRNA or blocking its translation. It is considered to be very important in regulating insect development and metamorphosis. We conducted a large-scale screening for miRNA genes in the silkworm Bombyx mori using sequence-by-synthesis (SBS) deep sequencing of mixed RNAs from egg, larval, pupal, and adult stages. Of 2,227,930 SBS tags, 1,144,485 ranged from 17 to 25 nt, corresponding to 256,604 unique tags. Among these non-redundant tags, 95,184 were matched to the silkworm genome. We identified 3,750 miRNA candidate genes using a computational pipeline combining RNAfold and TripletSVM algorithms. We confirmed 354 miRNA genes using miRNA microarrays and then performed expression profile analysis on these miRNAs for all developmental stages. While 106 miRNAs were expressed in all stages, 248 miRNAs were egg- and pupa-specific, suggesting that insect miRNAs play a significant role in embryogenesis and metamorphosis. We selected eight miRNAs for quantitative RT-PCR analysis; six of these were consistent with our microarray results. In addition, we searched for orthologous miRNA genes in mammals, a nematode, and other insects and found that most silkworm miRNAs are conserved in insects, whereas only a small number of silkworm miRNAs has orthologs in mammals and the nematode. These results suggest that there are many miRNAs unique to insects.
Collapse
Affiliation(s)
- Yong Zhang
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Xue Zhou
- Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
| | - Xie Ge
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Jianhao Jiang
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Muwang Li
- Sericultural Research Institute, Chinese Academy of Agriculture Sciences, Zhengjiang, People's Republic of China
| | - Shihai Jia
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Xiaonan Yang
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Yunchao Kan
- Nan Yang Normal University, Nanyang, Henan Province, People's Republic of China
| | - Xuexia Miao
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Guoping Zhao
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Fei Li
- Nanjing Agricultural University, Nanjing, Jiangsu Province, People's Republic of China
- * E-mail: (FL); (YH)
| | - Yongping Huang
- Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, People's Republic of China
- * E-mail: (FL); (YH)
| |
Collapse
|
242
|
Abstract
MicroRNAs (miRNAs) are key posttranscriptional regulators of eukaryotic gene expression. Plants use highly conserved as well as more recently evolved, species-specific miRNAs to control a vast array of biological processes. This Review discusses current advances in our understanding of the origin, biogenesis, and mode of action of plant miRNAs and draws comparisons with their metazoan counterparts.
Collapse
Affiliation(s)
- Olivier Voinnet
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357-Université de Strasbourg, 67084 Strasbourg, France.
| |
Collapse
|
243
|
Abstract
Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. There is a growing realization that, despite their differences, these distinct small RNA pathways are interconnected, and that small RNA pathways compete and collaborate as they regulate genes and protect the genome from external and internal threats.
Collapse
Affiliation(s)
- Megha Ghildiyal
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
| | | |
Collapse
|
244
|
Matzke M, Kanno T, Daxinger L, Huettel B, Matzke AJM. RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 2009; 21:367-76. [PMID: 19243928 DOI: 10.1016/j.ceb.2009.01.025] [Citation(s) in RCA: 371] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2008] [Accepted: 01/23/2009] [Indexed: 11/18/2022]
Abstract
Plants have evolved an elaborate transcriptional machinery dedicated to eliciting sequence-specific, chromatin-based gene silencing. Two Pol II-related, plant-specific RNA polymerases, named Pol IV and Pol V, collaborate with proteins of the RNA interference machinery to generate long and short noncoding RNAs involved in epigenetic regulation. As revealed by a variety of genetic, molecular, and genomic technologies, these RNAs are used extensively in plants to direct the establishment, spread, and removal of DNA cytosine methylation throughout their genomes. RNA-mediated chromatin-level silencing is increasingly implicated in development, stress responses, and natural epigenetic variation that may promote phenotypic diversity, physiological plasticity, and evolutionary change.
Collapse
Affiliation(s)
- Marjori Matzke
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
| | | | | | | | | |
Collapse
|
245
|
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.
Collapse
|
246
|
Perspectives of DNA microarray and next-generation DNA sequencing technologies. ACTA ACUST UNITED AC 2009; 52:7-16. [PMID: 19152079 DOI: 10.1007/s11427-009-0012-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 10/08/2008] [Indexed: 10/21/2022]
Abstract
DNA microarray and next-generation DNA sequencing technologies are important tools for high-throughput genome research, in revealing both the structural and functional characteristics of genomes. In the past decade the DNA microarray technologies have been widely applied in the studies of functional genomics, systems biology and pharmacogenomics. The next-generation DNA sequencing method was first introduced by the 454 Company in 2003, immediately followed by the establishment of the Solexa and Solid techniques by other biotech companies. Though it has not been long since the first emergence of this technology, with the fast and impressive improvement, the application of this technology has extended to almost all fields of genomics research, as a rival challenging the existing DNA microarray technology. This paper briefly reviews the working principles of these two technologies as well as their application and perspectives in genome research.
Collapse
|
247
|
Naqvi AR, Islam MN, Choudhury NR, Haq QMR. The fascinating world of RNA interference. Int J Biol Sci 2009; 5:97-117. [PMID: 19173032 PMCID: PMC2631224 DOI: 10.7150/ijbs.5.97] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 11/02/2008] [Indexed: 12/14/2022] Open
Abstract
Micro- and short-interfering RNAs represent small RNA family that are recognized as critical regulatory species across the eukaryotes. Recent high-throughput sequencing have revealed two more hidden players of the cellular small RNA pool. Reported in mammals and Caenorhabditis elegans respectively, these new small RNAs are named piwi-interacting RNAs (piRNAs) and 21U-RNAs. Moreover, small RNAs including miRNAs have been identified in unicellular alga Chlamydomonas reinhardtii, redefining the earlier concept of multi-cellularity restricted presence of these molecules. The discovery of these species of small RNAs has allowed us to understand better the usage of genome and the number of genes present but also have complicated the situation in terms of biochemical attributes and functional genesis of these molecules. Nonetheless, these new pools of knowledge have opened up avenues for unraveling the finer details of the small RNA mediated pathways.
Collapse
Affiliation(s)
- Afsar Raza Naqvi
- Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi - 110 025, India
| | | | | | | |
Collapse
|
248
|
Xiong H, Qian J, He T, Li F. Independent transcription of miR-281 in the intron of ODA in Drosophila melanogaster. Biochem Biophys Res Commun 2008; 378:883-9. [PMID: 19073139 DOI: 10.1016/j.bbrc.2008.12.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 12/03/2008] [Indexed: 02/09/2023]
Abstract
MicroRNAs (miRNAs) have recently received much interest for their role in post-transcriptional regulation. However, the study of miRNA transcription lags behind that of gene cloning and functional analysis. The MiR-281 in Drosophila melanogaster is located in the first intron of isoform RA of the ornithine decarboxylase antizyme (ODA) gene. ODA has three isoforms because of alternative transcription start sites (TSSs). Expression profile analysis indicated that miR-281 is not co-expressed with any ODA isoform. We amplified the primary transcripts of miR-281 using the RACE technique. The pri-miRNA is 2149bp with a poly (A) tail and a canonical polyadenylation signal (AATAAA). Chromatin immunoprecipitation analysis confirmed the binding of hypophosphorylated Pol-II and the transcription factor Myc at the core miR-281 promoter region. The abundance of miR-281 does not correlate, either positively or negatively, with the expression of any ODA isoform, indicating that ODA has little influence on the transcription of miR-281.
Collapse
Affiliation(s)
- Huiping Xiong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | | | | | | |
Collapse
|
249
|
Abstract
MicroRNAs (miRNAs) play important roles in eukaryotes, plants and some viruses. It is increasingly clear that miRNAs-encoded by viruses can affect the viral life cycle and host physiology. Viral miRNAs could repress the innate and adaptive host immunity, modulate cellular signaling pathways, and regulate the expression of cellular and viral genes. These functions facilitate viral acute and persistent infections, and have profound effects on the host cell survival and disease progression. Here, we discuss the miRNAs encoded by herpesviruses, and their regulatory roles involved in virus-host interactions.
Collapse
|
250
|
Nakayashiki H, Nguyen QB. RNA interference: roles in fungal biology. Curr Opin Microbiol 2008; 11:494-502. [PMID: 18955156 DOI: 10.1016/j.mib.2008.10.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2008] [Revised: 09/26/2008] [Accepted: 10/01/2008] [Indexed: 12/30/2022]
Abstract
The discovery of RNA interference (RNAi) has been the major recent breakthrough in biology. Only a few years after its discovery, RNAi has rapidly become a powerful reverse genetic tool, especially in organisms where gene targeting is inefficient and/or time-consuming. In filamentous fungi, RNAi is not currently used as widely as is gene targeting by homologous recombination that works with practical efficiencies in most model fungal species. However, to explore gene function in filamentous fungi, RNAi has the potential to offer new, efficient tools that gene disruption methods cannot provide. In this review, possible advantages and disadvantages of RNAi for fungal biology in the postgenomics era will be discussed. In addition, we will briefly review recent discoveries on RNAi-related biological phenomena (RNA silencing) in fungi.
Collapse
Affiliation(s)
- Hitoshi Nakayashiki
- Laboratory of Plant Pathology, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan.
| | | |
Collapse
|