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Mehrabadi M, Hussain M, Asgari S. MicroRNAome of Spodoptera frugiperda cells (Sf9) and its alteration following baculovirus infection. J Gen Virol 2013; 94:1385-1397. [DOI: 10.1099/vir.0.051060-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) as small non-coding RNAs play important roles in many biological processes such as development, cell signalling and immune response. Studies also suggest that miRNAs are important in host–virus interactions where the host limits virus infection by differentially expressing miRNAs that target essential viral genes. Here, we identified conserved and new miRNAs from Spodoptera frugiperda cells (Sf9) using a combination of deep sequencing and bioinformatics as well as experimental approaches. S. frugiperda miRNAs share common features of miRNAs in other organisms, such as uracil (U) at the 5′ end of miRNA. The 5′ ends of the miRNAs were more conserved than the 3′ ends, revealing evolutionary protection of the seed region in miRNAs. The predominant miRNAs were found to be conserved among arthropods. The majority of homologous miRNAs were found in Bombyx mori, with 76 of the 90 identified miRNAs. We found that seed shifting and arm switching have happened in this insect's miRNAs. Expression levels of the majority of miRNAs changed following baculovirus infection. Results revealed that baculovirus infection mainly led to an overall suppression of cellular miRNAs. We found four different genes being regulated by sfr-miR-184 at the post-transcriptional level. The data presented here further support conservation of miRNAs in insects and other organisms. In addition, the results reveal a differential expression of host miRNAs upon baculovirus infection, suggesting their potential roles in host–virus interactions. Seed shifting and arm switching happened during evolution of miRNAs in different insects and caused miRNA diversification, which led to changes in the target repository of miRNAs.
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Affiliation(s)
- Mohammad Mehrabadi
- Department of Plant Protection, University of Tehran, Karaj 31584, Iran
- School of Biological Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Mazhar Hussain
- School of Biological Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Sassan Asgari
- School of Biological Sciences, University of Queensland, St. Lucia, QLD 4072, Australia
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Wu W, Ren Q, Li C, Wang Y, Sang M, Zhang Y, Li B. Characterization and comparative profiling of MicroRNAs in a sexual dimorphism insect, Eupolyphaga sinensis Walker. PLoS One 2013; 8:e59016. [PMID: 23620723 PMCID: PMC3631196 DOI: 10.1371/journal.pone.0059016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/09/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND MicroRNAs are now recognized as key post-transcriptional regulators in animal ontogenesis and phenotypic diversity. Eupolyphaga sinensis Walker (Blattaria) is a sexually dimorphic insect, which is also an important source of material used in traditional Chinese medicine. The male E. sinensis have shorter lifecycles and go through fewer instars than the female. Furthermore, the males have forewings, while the females are totally wingless. RESULTS We used the Illumina/Solexa deep sequencing technology to sequence small RNA libraries prepared from the fourth-instar larvae of male and female E. sinensis. 19,097,799 raw reads were yielded in total: 7,817,445 reads from the female library and 11,280,354 from the male, respectively. As a result, we identified 168 known miRNAs belonging to 55 families as well as 204 novel miRNAs. Moreover, 45 miRNAs showed significantly different expression between the female and the male fourth-instar larvae, and we validated 10 of them by Stem-loop qRT-PCR. Some of these differentially expressed miRNAs are related to metamorphosis, development and phenotypic diversity. CONCLUSIONS/SIGNIFICANCE This is the first comprehensive description of miRNAs in E. sinensis. The results provide a useful resource for further in-depth study on molecular regulation and evolution of miRNAs. These findings not only enrich miRNAs for hemimetabolans but also lay the foundation for the study of post-transcriptional regulation on the phenomena of sexual dimorphism.
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Affiliation(s)
- Wei Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chengjun Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yanyun Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ming Sang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yi Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- * E-mail:
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Guo Q, Tao YL, Chu D. Characterization and comparative profiling of miRNAs in invasive Bemisia tabaci (Gennadius) B and Q. PLoS One 2013; 8:e59884. [PMID: 23527280 PMCID: PMC3603954 DOI: 10.1371/journal.pone.0059884] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/19/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small, conserved, non-coding RNAs that post-transcriptionally regulate gene expression. Bemisia tabaci (Gennadius) B and Q are two invasive and dominant whiteflies, and B. tabaci Q has been displacing B in China. Differences in biological traits (fecundity, host range, resistance to insecticides, etc.) as affected by miRNAs might be involved in the displacement. In this study, we performed high-throughput sequencing to identify miRNAs in B. tabaci B and Q. RESULTS We identified 170 conserved miRNAs and 15 novel candidates, and found significant differences in the expression of miRNAs between B. tabaci B and Q. CONCLUSION Expression levels of miRNAs differ in B. tabaci B vs. Q. Additional research is needed to determine whether these differences are related to differences in the biology of B. tabaci B and Q, and whether these differences help explain why B. tabaci Q is displacing B in China.
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Affiliation(s)
- Qiang Guo
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Yun-Li Tao
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong Province, China
- * E-mail:
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54
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Li J, Wang XP, Wang MQ, Ma WH, Hua HX. Advances in the use of the RNA interference technique in Hemiptera. INSECT SCIENCE 2013; 20:31-9. [PMID: 23955823 DOI: 10.1111/j.1744-7917.2012.01550.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
RNA interference (RNAi) suppresses the expression of target genes by post-transcriptional regulation. Because double-stranded RNA (dsRNA) mediated gene silencing is a conserved mechanism in many eukaryotes, RNAi has become a valuable tool for unveiling gene function in many model insects. Recent research has also shown that RNAi can also be effective in the downregulation of target genes in Hemiptera. In this review, we discuss the use of the RNAi technique in gene functional analysis in hemipterans, highlighting the methods of dsRNA uptake by these insects and discuss the knock-down efficiency of these techniques. Although the RNAi technique has disadvantages, our primary goal here is to determine whether it can be exploited further in the discovery of new gene functions, and as a pest control strategy, in some important Hemipteran pests.
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Affiliation(s)
- Jie Li
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, Huazhong Agricultural University, Wuhan, China
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55
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Chilana P, Sharma A, Arora V, Bhati J, Rai A. Computational identification and characterization of putative miRNAs in Heliothis virescens. Bioinformation 2013; 9:79-83. [PMID: 23390350 PMCID: PMC3563402 DOI: 10.6026/97320630009079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 11/24/2012] [Indexed: 12/19/2022] Open
Abstract
Heliothis virescens, a polyphagous pest, is one of the most destructive pests of many crops and vegetables. Various insecticides and
pesticides are used by agriculturalists to stop the growth and development of this pest. RNA interference is a new area for the
management of pests/insects by inhibiting the growth related RNAs. This involves the miRNAs identification and its
characterization. In the present study, computational approach is applied to predict putative miRNA candidates along with their
possible target(s) in the Heliothis virescens. A total of 63,662 ESTs were downloaded from dbEST database and processed, trimmed
and masked through EGassembler. The H. virescens contigs database obtained after assembly was now used to find the putative
miRNA candidates by performing a local BLAST with the miRNAs of insects retrieved from miRBase. We have predicted putative
miRNA candidates by homology search against all the reported insect miRNAs. These putative miRNAs candidates were further
validated and filtered by different features. In addition, we have also attempted to predict the putative targets of these filtered
miRNAs, by making use of 3' untranslated regions of mRNAs from B. mori. These miRNAs and their targets in H. virescens will
help in improved understanding of molecular mechanisms of miRNA and development of novel and more precise techniques for
better understanding some post transcriptional gene silencing.
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Affiliation(s)
- Poonam Chilana
- Centre for Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi - 110012
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Lucas K, Raikhel AS. Insect microRNAs: biogenesis, expression profiling and biological functions. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:24-38. [PMID: 23165178 PMCID: PMC3534889 DOI: 10.1016/j.ibmb.2012.10.009] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/24/2012] [Accepted: 10/28/2012] [Indexed: 05/09/2023]
Abstract
MicroRNAs (miRNA) are a class of endogenous regulatory RNA molecules 21-24 nucleotides in length that modulate gene expression at the post-transcriptional level via base pairing to target sites within messenger RNAs (mRNA). Typically, the miRNA "seed sequence" (nucleotides 2-8 at the 5' end) binds complementary seed match sites within the 3' untranslated region of mRNAs, resulting in either translational inhibition or mRNA degradation. MicroRNAs were first discovered in Caenorhabditis elegans and were shown to be involved in the timed regulation of developmental events. Since their discovery in the 1990s, thousands of potential miRNAs have since been identified in various organisms through small RNA cloning methods and/or computational prediction, and have been shown to play functionally important roles of gene regulation in invertebrates, vertebrates, plants, fungi and viruses. Numerous functions of miRNAs identified in Drosophila melanogaster have demonstrated a great significance of these regulatory molecules. However, elucidation of miRNA roles in non-drosophilid insects presents a challenging and important task.
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Affiliation(s)
- Keira Lucas
- Department of Entomology, University of California Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, U.S.A
- Graduate Program in Genetics, Genomics and Bioinformatics, University of California Riverside, Riverside, CA 92521, U.S.A
| | - Alexander S. Raikhel
- Department of Entomology, University of California Riverside, Riverside, CA 92521, U.S.A
- Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA 92521, U.S.A
- Corresponding author. Department of Entomology, University of California, Riverside, Riverside, CA 92521, U.S.A. Tel. +1 951 827 2129. (Keira Lucas); (Alexander S. Raikhel)
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57
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Ge X, Zhang Y, Jiang J, Zhong Y, Yang X, Li Z, Huang Y, Tan A. Identification of microRNAs in Helicoverpa armigera and Spodoptera litura based on deep sequencing and homology analysis. Int J Biol Sci 2012; 9:1-15. [PMID: 23289012 PMCID: PMC3535529 DOI: 10.7150/ijbs.5249] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 11/21/2012] [Indexed: 12/19/2022] Open
Abstract
The current identification of microRNAs (miRNAs) in insects is largely dependent on genome sequences. However, the lack of available genome sequences inhibits the identification of miRNAs in various insect species. In this study, we used a miRNA database of the silkworm Bombyx mori as a reference to identify miRNAs in Helicoverpa armigera and Spodoptera litura using deep sequencing and homology analysis. Because all three species belong to the Lepidoptera, the experiment produced reliable results. Our study identified 97 and 91 conserved miRNAs in H. armigera and S. litura, respectively. Using the genome of B. mori and BAC sequences of H. armigera as references, 1 novel miRNA and 8 novel miRNA candidates were identified in H. armigera, and 4 novel miRNA candidates were identified in S. litura. An evolutionary analysis revealed that most of the identified miRNAs were insect-specific, and more than 20 miRNAs were Lepidoptera-specific. The investigation of the expression patterns of miR-2a, miR-34, miR-2796-3p and miR-11 revealed their potential roles in insect development. miRNA target prediction revealed that conserved miRNA target sites exist in various genes in the 3 species. Conserved miRNA target sites for the Hsp90 gene among the 3 species were validated in the mammalian 293T cell line using a dual-luciferase reporter assay. Our study provides a new approach with which to identify miRNAs in insects lacking genome information and contributes to the functional analysis of insect miRNAs.
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Affiliation(s)
- Xie Ge
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, P.R. China
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Expression of small RNA in Aphis gossypii and its potential role in the resistance interaction with melon. PLoS One 2012; 7:e48579. [PMID: 23173035 PMCID: PMC3500242 DOI: 10.1371/journal.pone.0048579] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/03/2012] [Indexed: 02/05/2023] Open
Abstract
Background The regulatory role of small RNAs (sRNAs) in various biological processes is an active area of investigation; however, there has been limited information available on the role of sRNAs in plant-insect interactions. This study was designed to identify sRNAs in cotton-melon aphid (Aphis gossypii) during the Vat-mediated resistance interaction with melon (Cucumis melo). Methodology/Principal Findings The role of miRNAs was investigated in response to aphid herbivory, during both resistant and susceptible interactions. sRNA libraries made from A. gossypii tissues feeding on Vat+ and Vat− plants revealed an unexpected abundance of 27 nt long sRNA sequences in the aphids feeding on Vat+ plants. Eighty-one conserved microRNAs (miRNAs), twelve aphid-specific miRNAs, and nine novel candidate miRNAs were also identified. Plant miRNAs found in the aphid libraries were most likely ingested during phloem feeding. The presence of novel miRNAs was verified by qPCR experiments in both resistant Vat+ and susceptible Vat− interactions. The comparative analyses revealed that novel miRNAs were differentially regulated during the resistant and susceptible interactions. Gene targets predicted for the miRNAs identified in this study by in silico analyses revealed their involvement in morphogenesis and anatomical structure determination, signal transduction pathways, cell differentiation and catabolic processes. Conclusion/Significance In this study, conserved and novel miRNAs were reported in A. gossypii. Deep sequencing data showed differences in the abundance of miRNAs and piRNA-like sequences in A. gossypii. Quantitative RT-PCR revealed that A. gossypii miRNAs were differentially regulated during resistant and susceptible interactions. Aphids can also ingest plant miRNAs during phloem feeding that are stable in the insect.
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Sripada L, Tomar D, Prajapati P, Singh R, Singh AK, Singh R. Systematic analysis of small RNAs associated with human mitochondria by deep sequencing: detailed analysis of mitochondrial associated miRNA. PLoS One 2012; 7:e44873. [PMID: 22984580 PMCID: PMC3439422 DOI: 10.1371/journal.pone.0044873] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 08/09/2012] [Indexed: 01/02/2023] Open
Abstract
Mitochondria are one of the central regulators of many cellular processes beyond its well established role in energy metabolism. The inter-organellar crosstalk is critical for the optimal function of mitochondria. Many nuclear encoded proteins and RNA are imported to mitochondria. The translocation of small RNA (sRNA) including miRNA to mitochondria and other sub-cellular organelle is still not clear. We characterized here sRNA including miRNA associated with human mitochondria by cellular fractionation and deep sequencing approach. Mitochondria were purified from HEK293 and HeLa cells for RNA isolation. The sRNA library was generated and sequenced using Illumina system. The analysis showed the presence of unique population of sRNA associated with mitochondria including miRNA. Putative novel miRNAs were characterized from unannotated sRNA sequences. The study showed the association of 428 known, 196 putative novel miRNAs to mitochondria of HEK293 and 327 known, 13 putative novel miRNAs to mitochondria of HeLa cells. The alignment of sRNA to mitochondrial genome was also studied. The targets were analyzed using DAVID to classify them in unique networks using GO and KEGG tools. Analysis of identified targets showed that miRNA associated with mitochondria regulates critical cellular processes like RNA turnover, apoptosis, cell cycle and nucleotide metabolism. The six miRNAs (counts >1000) associated with mitochondria of both HEK293 and HeLa were validated by RT-qPCR. To our knowledge, this is the first systematic study demonstrating the associations of sRNA including miRNA with mitochondria that may regulate site-specific turnover of target mRNA important for mitochondrial related functions.
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Affiliation(s)
- Lakshmi Sripada
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, India
| | - Dhanendra Tomar
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, India
| | - Paresh Prajapati
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, India
| | - Rochika Singh
- Department of Human Health and Disease, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, India
| | - Arun Kumar Singh
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, India
| | - Rajesh Singh
- Department of Cell Biology, School of Biological Sciences and Biotechnology, Indian Institute of Advanced Research, Gandhinagar, India
- * E-mail:
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Yang L, Lu X, Liu Y, Lv Z, Chen J, Yu W, Zhang Y, Nie Z. Expression analysis of miRNAs in BmN cells. Gene 2012; 505:240-5. [PMID: 22713175 DOI: 10.1016/j.gene.2012.06.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 06/09/2012] [Accepted: 06/11/2012] [Indexed: 10/28/2022]
Abstract
MicroRNAs (miRNAs) are the family of noncoding single-strand RNA molecules of 21-25 nucleotides in length and play a broad and key regulation role in various physiological and pathological processes including differentiation, apoptosis, proliferation, and tumorigenesis. In Bombyx mori, a total of 487 pre-miRNAs and 562 mature miRNAs were identified by experimental or computational approaches, but their functions remain unknown. To carry out the research of gain-of-function of miRNAs in BmN cells, we firstly identified the endogenous expression of miRNAs in BmN cells by microarray and found that only 73 miRNAs could be detected by miRNA microarray. Then three low abundance or undetected miRNAs, pri-mir-1a, pri-mir-8 and pri-mir-133, were selected to express in BmN cells. The eukaryotic expression vector pIEx-1 harboring baculovirus ie1 promoter and hr5 enhancer was screened and used for expressing miRNA in BmN cells. Three miRNA expression vectors pIEx-1-EGFP-pri-mir-1a/8/133 were constructed, which contained the three corresponding pri-miRNA sequences, respectively. The constructed miRNA vectors were successfully transfected into BmN cells and the qRT-PCR analysis showed that relative abundance of bmo-mir-1a, bmo-mir-8 and bmo-mir-133 in BmN cells transfected with the pIEx-1-EGFP-pri-mir-1a/8/133 is as 32, 4.4 and 904 times as that in BmN cells transfected with the control vector pIEx-1-EGFP, respectively. The present work lays a foundation for the further functional studies of miRNAs in silkworm.
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Affiliation(s)
- Lancui Yang
- Institute of Biochemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China
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61
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Zhang X, Zheng Y, Jagadeeswaran G, Ren R, Sunkar R, Jiang H. Identification and developmental profiling of conserved and novel microRNAs in Manduca sexta. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 42:381-95. [PMID: 22406339 PMCID: PMC3340478 DOI: 10.1016/j.ibmb.2012.01.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 01/08/2012] [Accepted: 01/26/2012] [Indexed: 05/09/2023]
Abstract
MicroRNAs (miRNAs) are a group of small RNAs involved in translation inhibition or mRNA degradation. Due to its large size, Manduca sexta has long been used as a model to study insect physiology and biochemistry. While transcriptome studies have greatly enriched our knowledge on M. sexta structural genes, little is known about posttranscriptional regulation by miRNAs in this lepidopteran species. We constructed four small RNA libraries from embryos, 4th instar feeding larvae, pupae, and adults, obtained 21 million reads of 18-31 nucleotides by Illumina sequencing, and found 163 conserved and 13 novel miRNAs. By searching the M. sexta genome assembly, we identified precursors of 82 conserved miRNAs, 76 of which had mapped reads in one or more of these libraries. After normalization, we compared numbers of miRNA and miRNA-star reads in these libraries and observed abundance changes during development. Interestingly, mse-miR-281-star, mse-miR-31-star, mse-miR-965-star, mse-miR-9a-star, mse-miR-9b-star, mse-miR-2a-star, mse-miR-92b-star and mse-miR-279c-star are either more abundant or maintained at similar levels compared to respective mature miRNA strand. Expression profiling of the first set of miRNAs provided insights to their possible involvement in developmental regulation. This study will aid in the annotation of miRNA genes in the genome.
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Affiliation(s)
- Xiufeng Zhang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA.
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A new strategy for identification of highly conserved microRNAs in non-model insect, Spodoptera litura. Int J Mol Sci 2012; 13:612-627. [PMID: 22312275 PMCID: PMC3269709 DOI: 10.3390/ijms13010612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/23/2011] [Accepted: 12/28/2011] [Indexed: 12/19/2022] Open
Abstract
The indigenous small non-coding RNAs, known as microRNAs (miRNAs), are important regulators of gene expression and many of them are evolutionarily conserved. Whether stem-loop RT-PCR, as a sensitive method, could be utilized to clone conserved miRNAs from non-model insects lacks information. Here, three miRNAs, sli-miR-14, sli-miR-2a and sli-bantam, were cloned from Spodoptera litura by stem-loop RT-PCR. Two groups of primers were designed, and one of them performed especially well and proved stable. The sequences of two highly conserved miRNAs, sli-miR-14 and sli-miR-2a were identical to those in Drosophila melanogaster. To validate the reliability of this strategy, pre-miR-14 and pre-miR-2a in S. litura as representatives were given as well; this shared high homology with those in D. melanogaster and Bombyx mori, and both mature sequences of sli-miR-14 and sli-miR-2a in their precursors shared 100% identity to the results shown by stem-loop RT-PCR. Moreover, expression patterns of these miRNAs were investigated by real-time quantitative PCR. Sli-miR-14 and sli-miR-2a could be detected successfully and their expression patterns showed similar characteristics with those in model insects, further suggesting stem-loop RT-PCR technology can be used for identification of highly conserved miRNAs in non-model insects. These results provide a simplified and efficient strategy for studying the structure and function of highly conserved miRNAs, especially some critical miRNAs in non-model insects.
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Huang Y, Zou Q, Wang SP, Tang SM, Zhang GZ, Shen XJ. Construction and detection of expression vectors of microRNA-9a in BmN cells. J Zhejiang Univ Sci B 2011; 12:527-33. [PMID: 21726059 DOI: 10.1631/jzus.b1000296] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
MicroRNAs (miRNAs) are small endogenous RNAs molecules, approximately 21-23 nucleotides in length, which regulate gene expression by base-pairing with 3' untranslated regions (UTRs) of target mRNAs. However, the functions of only a few miRNAs in organisms are known. Recently, the expression vector of artificial miRNA has become a promising tool for gene function studies. Here, a method for easy and rapid construction of eukaryotic miRNA expression vector was described. The cytoplasmic actin 3 (A3) promoter and flanked sequences of miRNA-9a (miR-9a) precursor were amplified from genomic DNA of the silkworm (Bombyx mori) and was inserted into pCDNA3.0 vector to construct a recombinant plasmid. The enhanced green fluorescent protein (EGFP) gene was used as reporter gene. The Bombyx mori N (BmN) cells were transfected with recombinant miR-9a expression plasmid and were harvested 48 h post transfection. Total RNAs of BmN cells transfected with recombinant vectors were extracted and the expression of miR-9a was evaluated by reverse transcriptase polymerase chain reaction (RT-PCR) and Northern blot. Tests showed that the recombinant miR-9a vector was successfully constructed and the expression of miR-9a with EGFP was detected.
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Affiliation(s)
- Yong Huang
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Jiangsu University of Science and Technology, Zhenjiang 212018, China
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Fu Y, Shi Z, Wu M, Zhang J, Jia L, Chen X. Identification and differential expression of microRNAs during metamorphosis of the Japanese flounder (Paralichthys olivaceus). PLoS One 2011; 6:e22957. [PMID: 21818405 PMCID: PMC3144956 DOI: 10.1371/journal.pone.0022957] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 07/02/2011] [Indexed: 01/26/2023] Open
Abstract
Background MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs of 20–25 nucleotides that play a key role in diverse biological processes. Japanese flounder undergo dramatic metamorphosis in their early development. The metamorphosis is characterized by morphological transformation from a bilaterally symmetrical to an asymmetrical body shape concomitant with extensive morphological and physiological remodeling of organs. So far, only a few miRNAs have been identified in fish and there are very few reports about the Japanese flounder miRNA. Methodology/Principal Findings Solexa sequencing technology was used to perform high throughput sequencing of the small RNA library from the metamorphic period of Japanese flounder. Subsequently, aligning these sequencing data with metazoan known miRNAs, we characterized 140 conserved miRNAs and 57 miRNA: miRNA* pairs from the small RNA library. Among these 57 miRNA: miRNA* pairs, twenty flounder miRNA precursors were amplified from genomic DNA. We also demonstrated evolutionary conservation of Japanese flounder miRNAs and miRNA* in the animal evolution process. Using miRNA microarrays, we identified 66 differentially expressed miRNAs at two metamorphic stages (17 and 29 days post hatching) of Japanese flounder. The results show that miRNAs might play a key role in regulating gene expression during Japanese flounder metamorphosis. Conclusions/Significance We identified a large number of miRNAs during flounder metamorphosis, some of which are differentially expressed at two different metamorphic stages. The study provides an opportunity for further understanding of miRNA function in the regulation of flounder metamorphosis and gives us clues for further studies of the mechanisms of metamorphosis in Japanese flounder.
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Affiliation(s)
- Yuanshuai Fu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, People's Republic of China
| | - Zhiyi Shi
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, People's Republic of China
- * E-mail:
| | - Minglin Wu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, People's Republic of China
| | - Junling Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, People's Republic of China
| | - Liang Jia
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, People's Republic of China
| | - Xiaowu Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, People's Republic of China
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Huang Y, Shen XJ, Zou Q, Huang JS, Tang SM. Genomic analysis of silkworm microRNA promoters and clusters. Mol Biol 2011. [DOI: 10.1134/s0026893310061068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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66
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Terenius O, Papanicolaou A, Garbutt JS, Eleftherianos I, Huvenne H, Kanginakudru S, Albrechtsen M, An C, Aymeric JL, Barthel A, Bebas P, Bitra K, Bravo A, Chevalier F, Collinge DP, Crava CM, de Maagd RA, Duvic B, Erlandson M, Faye I, Felföldi G, Fujiwara H, Futahashi R, Gandhe AS, Gatehouse HS, Gatehouse LN, Giebultowicz JM, Gómez I, Grimmelikhuijzen CJP, Groot AT, Hauser F, Heckel DG, Hegedus DD, Hrycaj S, Huang L, Hull JJ, Iatrou K, Iga M, Kanost MR, Kotwica J, Li C, Li J, Liu J, Lundmark M, Matsumoto S, Meyering-Vos M, Millichap PJ, Monteiro A, Mrinal N, Niimi T, Nowara D, Ohnishi A, Oostra V, Ozaki K, Papakonstantinou M, Popadic A, Rajam MV, Saenko S, Simpson RM, Soberón M, Strand MR, Tomita S, Toprak U, Wang P, Wee CW, Whyard S, Zhang W, Nagaraju J, Ffrench-Constant RH, Herrero S, Gordon K, Swevers L, Smagghe G. RNA interference in Lepidoptera: an overview of successful and unsuccessful studies and implications for experimental design. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:231-45. [PMID: 21078327 DOI: 10.1016/j.jinsphys.2010.11.006] [Citation(s) in RCA: 540] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/03/2010] [Accepted: 11/04/2010] [Indexed: 05/03/2023]
Abstract
Gene silencing through RNA interference (RNAi) has revolutionized the study of gene function, particularly in non-model insects. However, in Lepidoptera (moths and butterflies) RNAi has many times proven to be difficult to achieve. Most of the negative results have been anecdotal and the positive experiments have not been collected in such a way that they are possible to analyze. In this review, we have collected detailed data from more than 150 experiments including all to date published and many unpublished experiments. Despite a large variation in the data, trends that are found are that RNAi is particularly successful in the family Saturniidae and in genes involved in immunity. On the contrary, gene expression in epidermal tissues seems to be most difficult to silence. In addition, gene silencing by feeding dsRNA requires high concentrations for success. Possible causes for the variability of success in RNAi experiments in Lepidoptera are discussed. The review also points to a need to further investigate the mechanism of RNAi in lepidopteran insects and its possible connection to the innate immune response. Our general understanding of RNAi in Lepidoptera will be further aided in the future as our public database at http://insectacentral.org/RNAi will continue to gather information on RNAi experiments.
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Affiliation(s)
- Olle Terenius
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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67
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Surridge AK, Lopez-Gomollon S, Moxon S, Maroja LS, Rathjen T, Nadeau NJ, Dalmay T, Jiggins CD. Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. BMC Genomics 2011; 12:62. [PMID: 21266089 PMCID: PMC3039609 DOI: 10.1186/1471-2164-12-62] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 01/26/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Heliconius butterflies are an excellent system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. miRNAs could act as regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races. RESULTS We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs were differentially represented in the libraries between colour pattern races. These candidates were tested further using Northern blots, showing that differences in expression were primarily due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified hme-miR-193 and hme-miR-2788; located 2380 bp apart in an intergenic region. These two miRNAs are expressed in wings and show an upregulation between 24 and 72 hours post-pupation, indicating a potential role in butterfly wing development. A search for miRNAs in all available H. melpomene BAC sequences (~2.5 Mb) did not reveal any other miRNAs and no novel miRNAs were predicted. CONCLUSIONS Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages and may have important functions in butterfly wing development. Two miRNAs were located in the HmYb region and were expressed in developing pupal wings. Future work will examine the expression of these miRNAs in different colour pattern races and identify miRNA targets among wing patterning genes.
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Affiliation(s)
- Alison K Surridge
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, UK
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68
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Li D, Wang Y, Zhang K, Jiao Z, Zhu X, Skogerboe G, Guo X, Chinnusamy V, Bi L, Huang Y, Dong S, Chen R, Kan Y. Experimental RNomics and genomic comparative analysis reveal a large group of species-specific small non-message RNAs in the silkworm Bombyx mori. Nucleic Acids Res 2011; 39:3792-805. [PMID: 21227919 PMCID: PMC3089462 DOI: 10.1093/nar/gkq1317] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Accumulating evidences show that small non-protein coding RNAs (ncRNAs) play important roles in development, stress response and other cellular processes. The silkworm is an important model for studies on insect genetics and control of lepidopterous pests. Here, we have performed the first systematic identification and analysis of intermediate size ncRNAs (50–500 nt) in the silkworm. We identified 189 novel ncRNAs, including 141 snoRNAs, six snRNAs, three tRNAs, one SRP and 38 unclassified ncRNAs. Forty ncRNAs showed significantly altered expression during silkworm development or across specific stage transitions. Genomic comparisons revealed that 123 of these ncRNAs are potentially silkworm-specific. Analysis of the genomic organization of the ncRNA loci showed that 32.62% of the novel snoRNA loci are intergenic, and that all the intronic snoRNAs follow the pattern of one-snoRNA-per-intron. Target site analysis predicted a total of 95 2′-O-methylation and pseudouridylation modification sites of rRNAs, snRNAs and tRNAs. Together, these findings provide new clues for future functional study of ncRNA during insect development and evolution.
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Affiliation(s)
- Dandan Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture, Nanjing 210095, China
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Jia Q, Lin K, Liang J, Yu L, Li F. Discovering conserved insect microRNAs from expressed sequence tags. JOURNAL OF INSECT PHYSIOLOGY 2010; 56:1763-1769. [PMID: 20655920 DOI: 10.1016/j.jinsphys.2010.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 07/13/2010] [Accepted: 07/15/2010] [Indexed: 05/29/2023]
Abstract
MicroRNAs (miRNA) participate in regulating diverse biological pathways by translational repression in animals. They have attracted increasing attention recently. However, little work has been done on the miRNA genes in agriculturally important pests. Because the transcripts of most miRNA genes are the products of type-II RNA polymerase, pri-miRNA has a poly(A) tail and appears in expressed sequence tags (EST). We developed a computational pipeline to identify miRNA genes from insect ESTs. First, 980,697 ESTs from 63 insects were collected and used to search the nr database. The ESTs which did not share significant similarities with any known protein-coding genes were treated as non-coding ESTs. Next, known mature miRNAs were used to align with non-coding ESTs. The ESTs which contain the sequence of mature miRNA were treated as candidate ESTs. Finally, putative precursors were extracted flanking the mature miRNA region in candidate ESTs and evaluated by the Triplet-SVM algorithm. As a result, 86 miRNAs from 30 insect species were found based on a strict criterion while 330 miRNAs from 51 species were found based on a loose criterion. Evolution analysis indicated that mir-467, mir-297 and mir-466 were the highest conserved miRNA families in insects. To confirm the reliability of putative insect miRNAs, the expression profile of nine predicted miRNAs in Locusta migratoria was investigated. Eight miRNAs were successfully detected by RT-PCR. Most miRNAs were expressed ubiquitously at all examined tissues and developmental stages whereas Lmi-mir-509 was specifically expressed in the thorax of the 2nd, 4th and 5th instars and adult locust. In all, our work reported an efficient computational strategy for predicting miRNA genes from insect ESTs and presented tens of miRNAs in diverse insect species which are expected to participate in many important physiological processes.
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Affiliation(s)
- Qidong Jia
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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70
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Czech A, Fedyunin I, Zhang G, Ignatova Z. Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations. MOLECULAR BIOSYSTEMS 2010; 6:1767-72. [PMID: 20617253 DOI: 10.1039/c004796c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations that alter the amino acid sequence are known to potentially exert deleterious effects on protein function, whereas substitutions of nucleotides without amino acid change are assumed to be neutral for the protein's functionality. However, cumulative evidence suggests that synonymous substitutions might also induce phenotypic variability by affecting splicing accuracy, translation fidelity, and conformation and function of proteins. tRNA isoacceptors mediate the translation of codons to amino acids, and asymmetric tRNA abundance causes variations in the rate of translation of each single triplet. Consequently, the effect of a silent point mutation in the coding region could be significant due to differential abundances of the cognate tRNA(s), emphasizing the importance of precise assessment of tRNA composition. Here, we provide an overview of the methods used to quantitatively determine the concentrations of tRNA species and discuss synonymous mutations in the context of tRNA composition of the cell, thus providing a new twist on the detrimental impact of the silent mutations.
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Affiliation(s)
- Andreas Czech
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14467 Potsdam-Golm, Germany
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71
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Legeai F, Rizk G, Walsh T, Edwards O, Gordon K, Lavenier D, Leterme N, Méreau A, Nicolas J, Tagu D, Jaubert-Possamai S. Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum. BMC Genomics 2010; 11:281. [PMID: 20444247 PMCID: PMC2880305 DOI: 10.1186/1471-2164-11-281] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Accepted: 05/05/2010] [Indexed: 12/21/2022] Open
Abstract
Background Post-transcriptional regulation in eukaryotes can be operated through microRNA (miRNAs) mediated gene silencing. MiRNAs are small (18-25 nucleotides) non-coding RNAs that play crucial role in regulation of gene expression in eukaryotes. In insects, miRNAs have been shown to be involved in multiple mechanisms such as embryonic development, tissue differentiation, metamorphosis or circadian rhythm. Insect miRNAs have been identified in different species belonging to five orders: Coleoptera, Diptera, Hymenoptera, Lepidoptera and Orthoptera. Results We developed high throughput Solexa sequencing and bioinformatic analyses of the genome of the pea aphid Acyrthosiphon pisum in order to identify the first miRNAs from a hemipteran insect. By combining these methods we identified 149 miRNAs including 55 conserved and 94 new miRNAs. Moreover, we investigated the regulation of these miRNAs in different alternative morphs of the pea aphid by analysing the expression of miRNAs across the switch of reproduction mode. Pea aphid microRNA sequences have been posted to miRBase: http://microrna.sanger.ac.uk/sequences/ Conclusions Our study has identified candidates as putative regulators involved in reproductive polyphenism in aphids and opens new avenues for further functional analyses.
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Affiliation(s)
- Fabrice Legeai
- INRA, UMR1099 BiO3P, Domaine de la Motte, F-35653 Le Rheu, France
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Microarray analysis of the gene expression profile in the midgut of silkworm infected with cytoplasmic polyhedrosis virus. Mol Biol Rep 2010; 38:333-41. [PMID: 20349281 DOI: 10.1007/s11033-010-0112-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 03/16/2010] [Indexed: 12/16/2022]
Abstract
In order to obtain an overall view on silkworm response to Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection, a microarray system comprising 22,987 oligonucluotide 70-mer probes was employed to compare differentially expressed genes in the midguts of BmCPV-infected and normal silkworm larvae. At 72 h post-inoculation, 258 genes exhibited at least 2.0-fold differences in expression level. Out of these, 135 genes were up-regulated, while 123 genes were down-regulated. According to gene ontology (GO), 140 genes were classified into GO categories. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicates that 35 genes were involved in 10 significant (P<0.05) KEGG pathways. The expressions of genes related to valine, leucine, and isoleucine degradation, retinol metabolism, and vitamin B6 metabolism were all down-regulated. The expressions of genes involved in ribosome and proteasome pathway were all up-regulated. Quantitative real-time polymerase chain reaction was performed to validate the expression patterns of 13 selected genes of interest. The results suggest that BmCPV infection resulted in the disturbance of protein and amino acid metabolism and a series of major physiological and pathological changes in silkworm. Our results provide new insights into the molecular mechanism of BmCPV infection and host cell response.
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Cai Y, Yu X, Zhou Q, Yu C, Hu H, Liu J, Lin H, Yang J, Zhang B, Cui P, Hu S, Yu J. Novel microRNAs in silkworm (Bombyx mori). Funct Integr Genomics 2010; 10:405-15. [DOI: 10.1007/s10142-010-0162-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 01/18/2010] [Accepted: 01/31/2010] [Indexed: 11/30/2022]
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Liu S, Gao S, Zhang D, Yin J, Xiang Z, Xia Q. MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori. BMC Genomics 2010; 11:85. [PMID: 20122259 PMCID: PMC2835664 DOI: 10.1186/1471-2164-11-85] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Accepted: 02/02/2010] [Indexed: 12/19/2022] Open
Abstract
Background MicroRNAs (miRNAs) repress target genes at the post-transcriptional level, and function in the development and cell-lineage pathways of host species. Tissue-specific expression of miRNAs is highly relevant to their physiological roles in the corresponding tissues. However, to date, few miRNAs have been spatially identified in the silkworm. Results We establish for the first time the spatial expression patterns of nearly 100 miRNAs in multiple normal tissues (organs) of Bombyx mori females and males using microarray and Northern-blotting analyses. In all, only 10 miRNAs were universally distributed (including bmo-let-7 and bmo-bantam), while the majority were expressed exclusively or preferentially in specific tissue types (e.g., bmo-miR-275 and bmo-miR-1). Additionally, we examined the developmental patterns of miRNA expression during metamorphosis of the body wall, silk glands, midgut and fat body. In total, 63 miRNAs displayed significant alterations in abundance in at least 1 tissue during the developmental transition from larvae to pupae (e.g., bmo-miR-263b and bmo-miR-124). Expression patterns of five miRNAs were significantly increased during metamorphosis in all four tissues (e.g., bmo-miR-275 and bmo-miR-305), and two miRNA pairs, bmo-miR-10b-3p/5p and bmo-miR-281-3p/5p, showed coordinate expression. Conclusions In this study, we conducted preliminary spatial measurements of several miRNAs in the silkworm. Periods of rapid morphological change were associated with alterations in miRNA expression patterns in the body wall, silk glands, midgut and fat body during metamorphosis. Accordingly, we propose that corresponding ubiquitous or tissue-specific expression of miRNAs supports their critical roles in tissue specification. These results should facilitate future functional analyses.
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Affiliation(s)
- Shiping Liu
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, PR China
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75
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Jagadeeswaran G, Zheng Y, Sumathipala N, Jiang H, Arrese EL, Soulages JL, Zhang W, Sunkar R. Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 2010. [PMID: 20089182 DOI: 10.1186/1471‐2164‐11‐52] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In eukaryotes, microRNAs (miRNAs) have emerged as critical regulators of gene expression. The Silkworm (Bombyx mori L.) is one of the most suitable lepidopteran insects for studying the molecular aspects of metamorphosis because of its large size, availability of mutants and genome sequence. Besides, this insect also has been amply studied from a physiological and biochemical perspective. Deep sequencing of small RNAs isolated from different stages of silkworm is a powerful tool not only for measuring the changes in miRNA profile but also for discovering novel miRNAs. RESULTS We generated small RNA libraries from feeding larvae, spinning larvae, pupae and adults of B. mori and obtained approximately 2.5 million reads of 18-30 nt. Sequence analysis identified 14 novel and 101 conserved miRNAs. Most novel miRNAs are preferentially expressed in pupae, whereas more than 95% of the conserved miRNAs are dynamically regulated during different developmental stages. Remarkably, the miRNA-star (miR*) of four miRNAs are expressed at much higher levels than their corresponding miRNAs, and their expression profiles are distinct from their corresponding miRNA profiles during different developmental stages. Additionally, we detected two antisense miRNA loci (miR-263-S and miR-263-AS; miR-306-S and miR-306-AS) that are expressed in sense and antisense directions. Interestingly, miR-263 and miR-306 are preferentially and abundantly expressed in pupae and adults, respectively. CONCLUSIONS We identified 101 homologs of conserved miRNAs, 14 species-specific and two antisense miRNAs in the silkworm. Our results provided deeper insights into changes in conserved and novel miRNA and miRNA* accumulation during development.
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Affiliation(s)
- Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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76
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Jagadeeswaran G, Zheng Y, Sumathipala N, Jiang H, Arrese EL, Soulages JL, Zhang W, Sunkar R. Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics 2010; 11:52. [PMID: 20089182 PMCID: PMC2824724 DOI: 10.1186/1471-2164-11-52] [Citation(s) in RCA: 153] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 01/20/2010] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In eukaryotes, microRNAs (miRNAs) have emerged as critical regulators of gene expression. The Silkworm (Bombyx mori L.) is one of the most suitable lepidopteran insects for studying the molecular aspects of metamorphosis because of its large size, availability of mutants and genome sequence. Besides, this insect also has been amply studied from a physiological and biochemical perspective. Deep sequencing of small RNAs isolated from different stages of silkworm is a powerful tool not only for measuring the changes in miRNA profile but also for discovering novel miRNAs. RESULTS We generated small RNA libraries from feeding larvae, spinning larvae, pupae and adults of B. mori and obtained approximately 2.5 million reads of 18-30 nt. Sequence analysis identified 14 novel and 101 conserved miRNAs. Most novel miRNAs are preferentially expressed in pupae, whereas more than 95% of the conserved miRNAs are dynamically regulated during different developmental stages. Remarkably, the miRNA-star (miR*) of four miRNAs are expressed at much higher levels than their corresponding miRNAs, and their expression profiles are distinct from their corresponding miRNA profiles during different developmental stages. Additionally, we detected two antisense miRNA loci (miR-263-S and miR-263-AS; miR-306-S and miR-306-AS) that are expressed in sense and antisense directions. Interestingly, miR-263 and miR-306 are preferentially and abundantly expressed in pupae and adults, respectively. CONCLUSIONS We identified 101 homologs of conserved miRNAs, 14 species-specific and two antisense miRNAs in the silkworm. Our results provided deeper insights into changes in conserved and novel miRNA and miRNA* accumulation during development.
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Affiliation(s)
- Guru Jagadeeswaran
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
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Abstract
How does a juvenile insect transform into an adult? This question, which sums up the wonder of insect metamorphosis, has fascinated mankind since ancient times. Modern physiology has established the endocrine basis regulating these transformations, which mainly depend on two hormone types: ecdysteroids, which promote molts, and juvenile hormones, which repress the transformation into the adult stage. The interplay of these two hormones regulates the genes involved in juvenile and adult programs and the shift from one to the other. microRNAs (miRNAs) are small noncoding RNAs, which participate in many biological processes, and we wondered whether they might be also involved in insect metamorphosis. In insects, Dicer-1 ribonuclease transforms miRNA precursors into mature miRNAs. Thus, using systemic RNA interference (RNAi) to silence the expression of Dicer-1 in the hemimetabolan insect Blattella germanica, we depleted miRNA contents in the last instar nymph. This practically inhibited metamorphosis after the next molt, as the resulting specimens showed nymphoid features and were able to molt again. The experiments show that miRNAs play a key role in hemimetabolan metamorphosis, perhaps regulating genes that are juvenile hormone targets.
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78
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Computational identification and characteristics of novel microRNAs from the silkworm (Bombyx mori L.). Mol Biol Rep 2009; 37:3171-6. [DOI: 10.1007/s11033-009-9897-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Accepted: 10/02/2009] [Indexed: 10/20/2022]
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79
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Liu S, Zhang L, Li Q, Zhao P, Duan J, Cheng D, Xiang Z, Xia Q. MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori). BMC Genomics 2009; 10:455. [PMID: 19785751 PMCID: PMC2761947 DOI: 10.1186/1471-2164-10-455] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 09/28/2009] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are expressed by a wide range of eukaryotic organisms, and function in diverse biological processes. Numerous miRNAs have been identified in Bombyx mori, but the temporal expression profiles of miRNAs corresponding to each stage transition over the entire life cycle of the silkworm remain to be established. To obtain a comprehensive overview of the correlation between miRNA expression and stage transitions, we performed a whole-life test and subsequent stage-by-stage examinations on nearly one hundred miRNAs in the silkworm. RESULTS Our results show that miRNAs display a wide variety of expression profiles over the whole life of the silkworm, including continuous expression from embryo to adult (miR-184), up-regulation over the entire life cycle (let-7 and miR-100), down-regulation over the entire life cycle (miR-124), expression associated with embryogenesis (miR-29 and miR-92), up-regulation from early 3rd instar to pupa (miR-275), and complementary pulses in expression between miR-34b and miR-275. Stage-by-stage examinations revealed further expression patterns, such as emergence at specific time-points during embryogenesis and up-regulation of miRNA groups in late embryos (miR-1 and bantam), expression associated with stage transition between instar and molt larval stages (miR-34b), expression associated with silk gland growth and spinning activity (miR-274), continuous high expression from the spinning larval to pupal and adult stages (miR-252 and miR-31a), a coordinate expression trough in day 3 pupae of both sexes (miR-10b and miR-281), up-regulation in pupal metamorphosis of both sexes (miR-29b), and down-regulation in pupal metamorphosis of both sexes (miR-275). CONCLUSION We present the full-scale expression profiles of miRNAs throughout the life cycle of Bombyx mori. The whole-life expression profile was further investigated via stage-by-stage analysis. Our data provide an important resource for more detailed functional analysis of miRNAs in this animal.
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Affiliation(s)
- Shiping Liu
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Liang Zhang
- National Engineering Center for Beijing Biochip Technology, Life Science Parkway, Changping District, Beijing 102206, PR China
| | - Qibin Li
- Beijing Genomics Institute at Shenzhen, Shenzhen 518083, PR China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100000, PR China
| | - Ping Zhao
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Jun Duan
- Institute of Agricultural and Life Sciences, Chongqing University, Chongqing, 400030, PR China
| | - Daojun Cheng
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Zhonghuai Xiang
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, PR China
| | - Qingyou Xia
- The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, PR China
- Institute of Agricultural and Life Sciences, Chongqing University, Chongqing, 400030, PR China
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Yu X, Zhou Q, Cai Y, Luo Q, Lin H, Hu S, Yu J. A discovery of novel microRNAs in the silkworm (Bombyx mori) genome. Genomics 2009; 94:438-44. [PMID: 19699294 DOI: 10.1016/j.ygeno.2009.08.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 06/28/2009] [Accepted: 08/11/2009] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are pivotal regulators involved in various physiological and pathological processes via their post-transcriptional regulation of gene expressions. We sequenced 14 libraries of small RNAs constructed from samples spanning the life cycle of silkworms, and discovered 50 novel miRNAs previously not known in animals and verified 43 of them using stem-loop RT-PCR. Our genome-wide analyses of 27 species-specific miRNAs suggest they arise from transposable elements, protein-coding genes duplication/transposition and random foldback sequences; which is consistent with the idea that novel animal miRNAs may evolve from incomplete self-complementary transcripts and become fixed in the process of co-adaptation with their targets. Computational prediction suggests that the silkworm-specific miRNAs may have a preference of regulating genes that are related to life-cycle-associated traits, and these genes can serve as potential targets for subsequent studies of the modulating networks in the development of Bombyx mori.
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Affiliation(s)
- Xiaomin Yu
- Key Laboratory of Genome Information and Sciences, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
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