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Oliveira JV, de Brito AF, Braconi CT, de Melo Freire CC, Iamarino A, de Andrade Zanotto PM. Modularity and evolutionary constraints in a baculovirus gene regulatory network. BMC SYSTEMS BIOLOGY 2013; 7:87. [PMID: 24006890 PMCID: PMC3879405 DOI: 10.1186/1752-0509-7-87] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 08/15/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression. RESULTS We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization. CONCLUSIONS Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks.
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Affiliation(s)
- Juliana Velasco Oliveira
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas Caixa Postal 6170, 13083-970, Brazil
| | - Anderson Fernandes de Brito
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
| | - Caio César de Melo Freire
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
| | - Atila Iamarino
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Department of Microbiology, Institute of Biomedical Sciences – ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo – USP, São Paulo, SP, Brazil
- Departamento de Microbiologia, Instituto de Ciências Biomédicas - ICB II, Laboratório de Evolução Molecular e Bioinformática, Universidade de São Paulo - USP, Av. Prof. Lineu Prestes, 1374, São Paulo CEP: 05508-900, Brasil
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Katsuma S, Kang W, Shin-i T, Ohishi K, Kadota K, Kohara Y, Shimada T. Mass identification of transcriptional units expressed from the Bombyx mori nucleopolyhedrovirus genome. J Gen Virol 2010; 92:200-3. [PMID: 20881086 DOI: 10.1099/vir.0.025908-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In order to identify the transcriptional units expressed from an entire nucleopolyhedrovirus (NPV) genome during infection, we constructed a full-length-enriched cDNA library from Bombyx mori NPV (BmNPV)-infected BmN cells. We randomly sequenced 11,520 clones from both ends to obtain a total of 4679 BmNPV-derived transcriptional units. The data revealed a number of novel transcripts, including putative non-coding RNAs, most of which are expressed from recognized baculovirus early or late promoter motifs. These findings provide new insights into the complex transcriptional regulation of an NPV genome and suggest roles for as-yet-uncharacterized transcripts.
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Affiliation(s)
- Susumu Katsuma
- Department of Agricultural and Environmental Biology, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
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Use of genomic DNA as reference in DNA microarrays. Methods Mol Biol 2009. [PMID: 19488717 DOI: 10.1007/978-1-59745-483-4_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
DNA microarray has become a mainstream technology to explore gene expression profiles, identify novel genes involved in a biological process of interest and predict their function, and determine biomarkers that are relevant to a given phenotype or disease. Typical two-channel microarray studies use an experimental design called the complementary DNA (cDNA) reference method, in which samples from test and control conditions are compared directly on a microarray slide. A substantial limitation of this strategy is that it is nearly impossible to compare data between experiments because the reference sample composition is subjected to changes at the level of experimental design and thereby not consistent from one experiment to another. Using genomic DNA as common reference will effectively overcome this limitation. This chapter describes detailed methods to prepare genomic DNA of high quality, label with fluorescent dye, co-hybridize with cDNA samples, and the subsequent data analyses. In addition, notes are provided to help the readers to obtain optimal results using the procedure.
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Földes-Papp Z. Viral Chip Technology in Genomic Medicine. GENOMIC AND PERSONALIZED MEDICINE 2009. [PMCID: PMC7149707 DOI: 10.1016/b978-0-12-369420-1.00048-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference. BMC Genomics 2008; 9 Suppl 2:S5. [PMID: 18831796 PMCID: PMC2559895 DOI: 10.1186/1471-2164-9-s2-s5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results using this method. To explain it, we hypothesize that data processing is a critical element that impacts the data quality. Results Microarray experiments were performed in a γ-proteobacterium Shewanella oneidensis. Pair-wise comparison of three experimental conditions was obtained either with two labeled cDNA samples co-hybridized to the same array, or by employing Shewanella genomic DNA as a standard reference. Various data processing techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that data quality was significantly improved by imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses. Conclusion These findings demonstrate that data processing significantly influences data quality, which provides an explanation for the conflicting evaluation in the literature. This work could serve as a guideline for microarray data analysis using genomic DNA as a standard reference.
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Pasquini G, Barba M, Hadidi A, Faggioli F, Negri R, Sobol I, Tiberini A, Caglayan K, Mazyad H, Anfoka G, Ghanim M, Zeidan M, Czosnek H. Oligonucleotide microarray-based detection and genotyping of Plum pox virus. J Virol Methods 2008; 147:118-26. [DOI: 10.1016/j.jviromet.2007.08.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 08/03/2007] [Accepted: 08/22/2007] [Indexed: 10/22/2022]
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