Jorge E S de Souza

Publications (3)17.59 Total impact

• Source

  Available from: Pedro A. F. Galante

  Article: Alternative splicing and genetic diversity: silencers are more frequently modified by SNVs associated with alternative exon/intron borders.

  Jorge E S de Souza, Rodrigo F Ramalho, Pedro A F Galante, Diogo Meyer, Sandro J de Souza
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  ABSTRACT: With the availability of a large amount of genomic data it is expected that the influence of single nucleotide variations (SNVs) in many biological phenomena will be elucidated. Here, we approached the problem of how SNVs affect alternative splicing. First, we observed that SNVs and exonic splicing regulators (ESRs) independently show a biased distribution in alternative exons. More importantly, SNVs map more frequently in ESRs located in alternative exons than in ESRs located in constitutive exons. By looking at SNVs associated with alternative exon/intron borders (by their common presence in the same cDNA molecule), we observed that a specific type of ESR, the exonic splicing silencers (ESSs), are more frequently modified by SNVs. Our results establish a clear association between genetic diversity and alternative splicing involving ESSs.
  Nucleic Acids Research 03/2011; 39(12):4942-8. · 8.03 Impact Factor
• Article: The impact of SNPs on the interpretation of SAGE and MPSS experimental data.

  Ana Paula M Silva, Jorge E S De Souza, Pedro A F Galante, Gregory J Riggins, Sandro J De Souza, Anamaria A Camargo
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  ABSTRACT: Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) are powerful techniques for gene expression analysis. A crucial step in analyzing SAGE and MPSS data is the assignment of experimentally obtained tags to a known transcript. However, tag to transcript assignment is not a straightforward process since alternative tags for a given transcript can also be experimentally obtained. Here, we have evaluated the impact of Single Nucleotide Polymorphisms (SNPs) on the generation of alternative SAGE and MPSS tags. This was achieved through the construction of a reference database of SNP-associated alternative tags, which has been integrated with SAGE Genie. A total of 2020 SNP-associated alternative tags were catalogued in our reference database and at least one SNP-associated alternative tag was observed for approximately 8.6% of all known human genes. A significant fraction (61.9%) of these alternative tags matched a list of experimentally obtained tags, validating their existence. In addition, the origin of four out of five SNP-associated alternative MPSS tags was experimentally confirmed through the use of the GLGI-MPSS protocol (Generation of Long cDNA fragments for Gene Identification). The availability of our SNP-associated alternative tag database will certainly improve the interpretation of SAGE and MPSS experiments.
  Nucleic Acids Research 02/2004; 32(20):6104-10. · 8.03 Impact Factor
• Article: ORESTES are enriched in rare exon usage variants affecting the encoded proteins.

  Noboru Jo Sakabe, Jorge E S de Souza, Pedro A F Galante, Paulo S L de Oliveira, Fábio Passetti, Helena Brentani, Elisson C Osório, André C Zaiats, Maarten R Leerkes, João Paulo Kitajima, Ricardo R Brentani, Robert L Strausberg, Andrew J G Simpson, Sandro José de Souza
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  ABSTRACT: A significant fraction of the variability found in the human transcriptome is due to alternative splicing, including alternative exon usage (AEU), intron retention and use of cryptic splice sites. We present a comparison of a large-scale analysis of AEU in the human transcriptome through genome mapping of Open Reading Frame ESTs (ORESTES) and conventional ESTs. It is shown here that ORESTES probe low abundant messages more efficiently. In addition, most of the variants detected by ORESTES affect the structure of the corresponding proteins.
  Comptes Rendus Biologies 326(10-11):979-85. · 1.53 Impact Factor