Analysis of alternative splicing by using expressed sequence data / Análise de splicing alternativo utilizando dados de sequências expressas

AUTOR(ES)

Ulises Maximiliano Mancini Villagra

DATA DE PUBLICAÇÃO

2009

RESUMO

Alternative splicing is a process by which the exons of the primary gene transcript are linked in different ways during RNA processing resulting in distinctive proteins. It is an important mechanism in eukaryotic gene expression that enhances proteome diversity and, therefore, the coding capacity of the genome. Different mechanisms seem affect alternative splicing regulation, including metabolic stresses. In the present study, a detailed informatics analysis of ORESTES sequences from head and neck tissues was performed. This in silico analysis revealed that gain of exon sequences is more frequent than exon skipping and GT/AG rule is predominant in splice sites. We observed that alternative splicing usually does not alter the reading frame but may disrupt a protein domain and remove or add new phosphorylation and glycosylation sites. Repetitive and potential regulator elements were frequent in the alternative sequences or in their neighbors. The expression of putative splicing isoforms was investigated in different tissues, including upon stress conditions. We validated approximately 50 new splicing events in normal and tumor cells. Several variants, such as those from HNRNPK, ACTN1, BAT3, CEP192, MPV17, PDK1, PRKAR1A, RAG1AP1 and TRIP6 genes showed distinctive expression pattern in different cell types, in normal and cancer samples from head and neck carcinoma patients and, in some cases, in different tumor stages. We also validated a new transcript of RIPK2 gene, which codes a serine/threonine kinase that activates the NF-kB pathway, and observed a shift in the expression of this variant as a response to temperature stress in vitro. It is currently not clear whether alternative splicing is the cause or the consequence of the neoplastic process. Our data add new information to this topic and provide some examples on the importance of RNA processing in gene expression regulation, both in normal and disease conditions.

ASSUNTO(S)

alternative splicing transcritoma transcriptome splicing alternativo

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