Identification of Schistosoma mansoni microRNAs

Detalhes bibliográficos
Autor(a) principal: Simões, Mariana Crivellari Machado
Data de Publicação: 2011
Outros Autores: Lee, Jonathan, Djikeng, Appolinaire, Cerqueira, Gustavo Coutinho, Zerlotini, Adhemar, Pereira, Rosiane Aparecida da Silva, Dalby, Andrew R, LoVerde, Phillip Thomas, El-Sayed, Najib M, Oliveira, Guilherme Corrêa
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/9349
Resumo: Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brazil/Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais. Centro de Excelência em Bioinformática. Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil
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spelling Simões, Mariana Crivellari MachadoLee, JonathanDjikeng, AppolinaireCerqueira, Gustavo CoutinhoZerlotini, AdhemarPereira, Rosiane Aparecida da SilvaDalby, Andrew RLoVerde, Phillip ThomasEl-Sayed, Najib MOliveira, Guilherme Corrêa2015-01-08T15:58:05Z2015-01-08T15:58:05Z2011SIMÕES, Mariana Crivellari Machado et al. Identification of Schistosoma mansoni micrornas. BMC Genomics, vol. 12, p. 47, 2011.1471-2164https://www.arca.fiocruz.br/handle/icict/934910.1186/1471-2164-12-47engBioMed CentralIdentification of Schistosoma mansoni microRNAsinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUniversidade Federal de Minas Gerais. Belo Horizonte, MG, Brazil/Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais. Centro de Excelência em Bioinformática. Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, BrazilPeter Medawar Building. Department of Statistics South Parks Road. Oxford, UKJ Craig Venter Institute. Medical Center Drive. Rockville, MD, USA/International Livestock Research Institute. Biosciences eastern and central Africa. Nairobi, KenyaUniversity of Maryland. Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology. College Park, MD, USA/University of Maryland. School of Medicine. Institute for Genome Sciences Baltimore, MD, USAUniversidade Federal de Minas Gerais. Belo Horizonte, MG, Brazil/Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais. Centro de Excelência em Bioinformática. Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, BrazilInstituto Nacional de Ciência e Tecnologia em Doenças Tropicais. Centro de Excelência em Bioinformática. Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, BrazilPeter Medawar Building. Department of Statistics South Parks Road. Oxford, UKUniversity of Texas Health Science Center. San Antonio, TX, USAUniversity of Maryland. Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology. College Park, MD, USAInstituto Nacional de Ciência e Tecnologia em Doenças Tropicais. Centro de Excelência em Bioinformática. Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, BrazilBackground MicroRNAs (miRNAs) constitute a class of single-stranded RNAs which play a crucial role in regulating development and controlling gene expression by targeting mRNAs and triggering either translation repression or messenger RNA (mRNA) degradation. miRNAs are widespread in eukaryotes and to date over 14,000 miRNAs have been identified by computational and experimental approaches. Several miRNAs are highly conserved across species. In Schistosoma, the full set of miRNAs and their expression patterns during development remain poorly understood. Here we report on the development and implementation of a homology-based detection strategy to search for miRNA genes in Schistosoma mansoni. In addition, we report results on the experimental detection of miRNAs by means of cDNA cloning and sequencing of size-fractionated RNA samples. Results Homology search using the high-throughput pipeline was performed with all known miRNAs in miRBase. A total of 6,211 mature miRNAs were used as reference sequences and 110 unique S. mansoni sequences were returned by BLASTn analysis. The existing mature miRNAs that produced these hits are reported, as well as the locations of the homologous sequences in the S. mansoni genome. All BLAST hits aligned with at least 95% of the miRNA sequence, resulting in alignment lengths of 19-24 nt. Following several filtering steps, 15 potential miRNA candidates were identified using this approach. By sequencing small RNA cDNA libraries from adult worm pairs, we identified 211 novel miRNA candidates in the S. mansoni genome. Northern blot analysis was used to detect the expression of the 30 most frequent sequenced miRNAs and to compare the expression level of these miRNAs between the lung stage schistosomula and adult worm stages. Expression of 11 novel miRNAs was confirmed by northern blot analysis and some presented a stage-regulated expression pattern. Three miRNAs previously identified from S. japonicum were also present in S. mansoni. Conclusion Evidence for the presence of miRNAs in S. mansoni is presented. The number of miRNAs detected by homology-based computational methods in S. mansoni is limited due to the lack of close relatives in the miRNA repository. In spite of this, the computational approach described here can likely be applied to the identification of pre-miRNA hairpins in other organisms. Construction and analysis of a small RNA library led to the experimental identification of 14 novel miRNAs from S. mansoni through a combination of molecular cloning, DNA sequencing and expression studies. Our results significantly expand the set of known miRNAs in multicellular parasites and provide a basis for understanding the structural and functional evolution of miRNAs in these metazoan parasites.Computational BiologyGenomeHelminth/geneticsMicroRNAs/geneticsSchistosoma mansoni/geneticsinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-81914https://www.arca.fiocruz.br/bitstream/icict/9349/1/license.txt7d48279ffeed55da8dfe2f8e81f3b81fMD51ORIGINALIdentification of Schistosoma mansoni microRNAs - 1471-2164-12-47.pdfIdentification of Schistosoma mansoni microRNAs - 1471-2164-12-47.pdfapplication/pdf7050303https://www.arca.fiocruz.br/bitstream/icict/9349/2/Identification%20of%20Schistosoma%20mansoni%20microRNAs%20-%201471-2164-12-47.pdf052c4ae3b0784bff33135f710af6ea3fMD52TEXTIdentification of Schistosoma mansoni microRNAs - 1471-2164-12-47.pdf.txtIdentification of Schistosoma mansoni microRNAs - 1471-2164-12-47.pdf.txtExtracted texttext/plain3977https://www.arca.fiocruz.br/bitstream/icict/9349/3/Identification%20of%20Schistosoma%20mansoni%20microRNAs%20-%201471-2164-12-47.pdf.txtc4bef29f837c8e06c8e1265f5f11514cMD53icict/93492019-06-19 10:05:43.354oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352019-06-19T13:05:43Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.pt_BR.fl_str_mv Identification of Schistosoma mansoni microRNAs
title Identification of Schistosoma mansoni microRNAs
spellingShingle Identification of Schistosoma mansoni microRNAs
Simões, Mariana Crivellari Machado
Computational Biology
Genome
Helminth/genetics
MicroRNAs/genetics
Schistosoma mansoni/genetics
title_short Identification of Schistosoma mansoni microRNAs
title_full Identification of Schistosoma mansoni microRNAs
title_fullStr Identification of Schistosoma mansoni microRNAs
title_full_unstemmed Identification of Schistosoma mansoni microRNAs
title_sort Identification of Schistosoma mansoni microRNAs
author Simões, Mariana Crivellari Machado
author_facet Simões, Mariana Crivellari Machado
Lee, Jonathan
Djikeng, Appolinaire
Cerqueira, Gustavo Coutinho
Zerlotini, Adhemar
Pereira, Rosiane Aparecida da Silva
Dalby, Andrew R
LoVerde, Phillip Thomas
El-Sayed, Najib M
Oliveira, Guilherme Corrêa
author_role author
author2 Lee, Jonathan
Djikeng, Appolinaire
Cerqueira, Gustavo Coutinho
Zerlotini, Adhemar
Pereira, Rosiane Aparecida da Silva
Dalby, Andrew R
LoVerde, Phillip Thomas
El-Sayed, Najib M
Oliveira, Guilherme Corrêa
author2_role author
author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Simões, Mariana Crivellari Machado
Lee, Jonathan
Djikeng, Appolinaire
Cerqueira, Gustavo Coutinho
Zerlotini, Adhemar
Pereira, Rosiane Aparecida da Silva
Dalby, Andrew R
LoVerde, Phillip Thomas
El-Sayed, Najib M
Oliveira, Guilherme Corrêa
dc.subject.en.pt_BR.fl_str_mv Computational Biology
Genome
Helminth/genetics
MicroRNAs/genetics
Schistosoma mansoni/genetics
topic Computational Biology
Genome
Helminth/genetics
MicroRNAs/genetics
Schistosoma mansoni/genetics
description Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brazil/Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais. Centro de Excelência em Bioinformática. Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Laboratório de Parasitologia Celular e Molecular. Belo Horizonte, MG, Brazil
publishDate 2011
dc.date.issued.fl_str_mv 2011
dc.date.accessioned.fl_str_mv 2015-01-08T15:58:05Z
dc.date.available.fl_str_mv 2015-01-08T15:58:05Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.citation.fl_str_mv SIMÕES, Mariana Crivellari Machado et al. Identification of Schistosoma mansoni micrornas. BMC Genomics, vol. 12, p. 47, 2011.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/9349
dc.identifier.issn.none.fl_str_mv 1471-2164
dc.identifier.doi.none.fl_str_mv 10.1186/1471-2164-12-47
identifier_str_mv SIMÕES, Mariana Crivellari Machado et al. Identification of Schistosoma mansoni micrornas. BMC Genomics, vol. 12, p. 47, 2011.
1471-2164
10.1186/1471-2164-12-47
url https://www.arca.fiocruz.br/handle/icict/9349
dc.language.iso.fl_str_mv eng
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dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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instname:Fundação Oswaldo Cruz (FIOCRUZ)
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collection Repositório Institucional da FIOCRUZ (ARCA)
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