Please use this identifier to cite or link to this item: https://www.arca.fiocruz.br/handle/icict/7992
Title: In silico identification of conserved intercoding sequences in Leishmania genomes: unraveling putative cis-regulatory elements.
Authors: Vasconcelos, Elton José Rosas de
Terrão, Mônica Cristina
Ruiz, Jerônimo Conceição
Vêncio, Ricardo Zorzetto Nicoliello
Cruz, Angela Kaysel
Affilliation: Universidade de São Paulo. Faculdade de Medicina de Ribeirão Preto. Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos. 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, Brazil
Fundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Belo Horizonte, MG, Brazil
Universidade 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, Brazil
Abstract: In 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.
Keywords: Base Sequence
Computational Biology
Leishmania/genetics
Sequence Analysis
DNA
Protozoan
Issue Date: 2012
Publisher: Elsevier/North-Holland Biomedical Press
Citation: 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
DOI: 10.1016/j.molbiopara.2012.02.009
ISSN: 0166-6851
Copyright: open access
Appears in Collections:MG - IRR - Artigos de Periódicos

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