In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.

Detalhes bibliográficos
Autor(a) principal: Vasconcelos, Elton José Rosas de
Data de Publicação: 2012
Outros Autores: Terrão, Mônica Cristina, Ruiz, Jeronimo Conceição, Vêncio, Ricardo Zorzetto Nicoliello, Cruz, Angela Kaysel
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
DOI: 10.1016/j.molbiopara.2012.02.009
Texto Completo: https://arca.fiocruz.br/handle/icict/7992
Resumo: Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos. Ribeirão Preto, SP, Brazil
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spelling Vasconcelos, Elton José Rosas deTerrão, Mônica CristinaRuiz, Jeronimo ConceiçãoVêncio, Ricardo Zorzetto NicolielloCruz, Angela Kaysel2014-07-17T19:07:31Z2014-07-17T19:07:31Z2012VASCONCELOS, Elton José Rosas de et al. In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements. Molecular and Biochemical Parasitology. 2012, vol.183, pp. 140-1500166-6851https://arca.fiocruz.br/handle/icict/799210.1016/j.molbiopara.2012.02.009engElsevier/North-Holland Biomedical PressIn silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos. Ribeirão Preto, SP, BrazilUniversidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos. Ribeirão Preto, SP, BrazilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Belo Horizonte, MG, BrazilUniversidade de São Paulo. Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto. Departamento de Computação e Matemática. Ribeirão Preto, SP, Brazil.Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos. Ribeirão Preto, SP, BrazilIn silico analyses of Leishmania spp. genome data are a powerful resource to improve the understanding of these pathogens' biology. Trypanosomatids such as Leishmania spp. have their protein-coding genes grouped in long polycistronic units of functionally unrelated genes. The control of gene expression happens by a variety of posttranscriptional mechanisms. The high degree of synteny among Leishmania species is accompanied by highly conserved coding sequences (CDS) and poorly conserved intercoding untranslated sequences. To identify the elements involved in the control of gene expression, we conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L. major, L. infantum, and L. braziliensis. We used a combination of computational tools, such as Linux-Shell, PERL and R languages, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms to construct a pipeline which was able to: (i) search for conservation in target-regions, (ii) eliminate CICS redundancy and mask repeat elements, (iii) predict the mRNA's extremities, (iv) analyze the distribution of orthologous genes within the generated LeishCICS-clusters, (v) assign GO terms to the LeishCICS-clusters, and (vi) provide statistical support for the gene-enrichment annotation. We associated the LeishCICS-cluster data, generated at the end of the pipeline, with the expression profile of L. donovani genes during promastigote-amastigote differentiation, as previously evaluated by others (GEO accession: GSE21936). A Pearson's correlation coefficient greater than 0.5 was observed for 730 LeishCICS-clusters containing from 2 to 17 genes. The designed computational pipeline is a useful tool and its application identified potential regulatory cis elements and putative regulons in Leishmania.Base SequenceComputational BiologyLeishmania/geneticsSequence AnalysisDNAProtozoaninfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZORIGINALIn silico identification of conserved intercoding sequences in Leishmania genomes.pdfIn silico identification of conserved intercoding sequences in Leishmania genomes.pdfapplication/pdf2797406https://arca.fiocruz.br/bitstreams/abd96e9b-008e-44a9-9d9b-d366bfed609a/download6aaabc0ee7ff5f0336d8a74694789247MD51trueAnonymousREADLICENSElicense.txtlicense.txttext/plain; charset=utf-81914https://arca.fiocruz.br/bitstreams/a30b3c0e-86a6-4221-989f-ed37cc89530b/download7d48279ffeed55da8dfe2f8e81f3b81fMD52falseAnonymousREADTEXTIn silico identification of conserved intercoding sequences in Leishmania genomes.pdf.txtIn silico identification of conserved intercoding sequences in Leishmania genomes.pdf.txtExtracted texttext/plain22https://arca.fiocruz.br/bitstreams/0493f57e-5b08-46ea-82f9-0d4f2350c09c/download6cccda74febad7705949cb89ee2669ddMD55falseAnonymousREADTHUMBNAILIn silico identification of conserved intercoding sequences in Leishmania genomes.pdf.jpgIn silico identification of conserved intercoding sequences in Leishmania genomes.pdf.jpgGenerated Thumbnailimage/jpeg5541https://arca.fiocruz.br/bitstreams/d814b431-4f60-4e3c-81ec-81aaeea68547/downloadde497454ebceb19df053c9c2cd43199aMD56falseAnonymousREADicict/79922025-07-29 21:30:19.094open.accessoai:arca.fiocruz.br:icict/7992https://arca.fiocruz.brRepositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352025-07-30T00:30:19Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)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
dc.title.none.fl_str_mv In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.
title In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.
spellingShingle In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.
Vasconcelos, Elton José Rosas de
Base Sequence
Computational Biology
Leishmania/genetics
Sequence Analysis
DNA
Protozoan
title_short In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.
title_full In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.
title_fullStr In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.
title_full_unstemmed In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.
title_sort In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.
author Vasconcelos, Elton José Rosas de
author_facet Vasconcelos, Elton José Rosas de
Terrão, Mônica Cristina
Ruiz, Jeronimo Conceição
Vêncio, Ricardo Zorzetto Nicoliello
Cruz, Angela Kaysel
author_role author
author2 Terrão, Mônica Cristina
Ruiz, Jeronimo Conceição
Vêncio, Ricardo Zorzetto Nicoliello
Cruz, Angela Kaysel
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Vasconcelos, Elton José Rosas de
Terrão, Mônica Cristina
Ruiz, Jeronimo Conceição
Vêncio, Ricardo Zorzetto Nicoliello
Cruz, Angela Kaysel
dc.subject.en.none.fl_str_mv Base Sequence
Computational Biology
Leishmania/genetics
Sequence Analysis
DNA
Protozoan
topic Base Sequence
Computational Biology
Leishmania/genetics
Sequence Analysis
DNA
Protozoan
description Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos. Ribeirão Preto, SP, Brazil
publishDate 2012
dc.date.issued.fl_str_mv 2012
dc.date.accessioned.fl_str_mv 2014-07-17T19:07:31Z
dc.date.available.fl_str_mv 2014-07-17T19:07:31Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
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status_str publishedVersion
dc.identifier.citation.fl_str_mv VASCONCELOS, Elton José Rosas de et al. In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements. Molecular and Biochemical Parasitology. 2012, vol.183, pp. 140-150
dc.identifier.uri.fl_str_mv https://arca.fiocruz.br/handle/icict/7992
dc.identifier.issn.none.fl_str_mv 0166-6851
dc.identifier.doi.none.fl_str_mv 10.1016/j.molbiopara.2012.02.009
identifier_str_mv VASCONCELOS, Elton José Rosas de et al. In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements. Molecular and Biochemical Parasitology. 2012, vol.183, pp. 140-150
0166-6851
10.1016/j.molbiopara.2012.02.009
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