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Registro Completo |
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Biblioteca(s): |
Embrapa Agricultura Digital. |
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Data corrente: |
15/12/2009 |
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Data da última atualização: |
13/10/2016 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
HERAI, R. H.; YAMAGISHI, M. E. B. |
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Afiliação: |
ROBERTO HIROCHI HERAI, CNPTIA; MICHEL EDUARDO BELEZA YAMAGISHI, CNPTIA. |
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Título: |
Detection of human interchromosomal trans-splicing in sequence databanks. |
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Ano de publicação: |
2010 |
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Fonte/Imprenta: |
Briefings in Bioinformatics, London, v. 2, n. 2, p. 198-209, 2010. |
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DOI: |
10.1093/bib/bbp041 |
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Idioma: |
Inglês |
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Conteúdo: |
Trans-splicing is a common phenomenon in nematodes and kinetoplastids, and it has also been reported in other organisms, including humans. Up to now, all in silico strategies to find evidence of trans-splicing in humans have required that the candidate sequences follow the consensus splicing site rules (spliceosome-mediated mechanism). However, this criterion is not supported by the best human experimental evidence, which, except in a single case, do not follow canonical splicing sites. Moreover, recent findings describe a novel alternative tRNA mediated trans-splicing mechanism, which prescinds the spliceosome machinery. In order to answer the question, ?Are there hybrid mRNAs in sequence databanks, whose characteristics resemble those of the best human experimental evidence??, we have developed a methodology that successfully identified 16 hybrid mRNAs which might be instances of interchromosomal trans-splicing. Each hybrid mRNA is formed by a trans-spliced region (TSR), which was successfully mapped either onto known genes or onto a human endogenous retrovirus (HERV-K) transcript which supports their transcription. The existence of these hybrid mRNAs indicates that trans-splicing may be more widespread than believed. Furthermore, non-canonical splice site patterns suggest that infrequent splicing sites may occur under special conditions, or that an alternative trans-splicing mechanism is involved. Finally, our candidates are supposedly from normal tissue, and a recent study has reported that trans-splicing may occur not only in malignant tissues, but in normal tissues as well. Our methodology can be applied to 5'-UTR, coding sequences and 3'-UTR in order to find new candidates for a posteriori experimental confirmation. MenosTrans-splicing is a common phenomenon in nematodes and kinetoplastids, and it has also been reported in other organisms, including humans. Up to now, all in silico strategies to find evidence of trans-splicing in humans have required that the candidate sequences follow the consensus splicing site rules (spliceosome-mediated mechanism). However, this criterion is not supported by the best human experimental evidence, which, except in a single case, do not follow canonical splicing sites. Moreover, recent findings describe a novel alternative tRNA mediated trans-splicing mechanism, which prescinds the spliceosome machinery. In order to answer the question, ?Are there hybrid mRNAs in sequence databanks, whose characteristics resemble those of the best human experimental evidence??, we have developed a methodology that successfully identified 16 hybrid mRNAs which might be instances of interchromosomal trans-splicing. Each hybrid mRNA is formed by a trans-spliced region (TSR), which was successfully mapped either onto known genes or onto a human endogenous retrovirus (HERV-K) transcript which supports their transcription. The existence of these hybrid mRNAs indicates that trans-splicing may be more widespread than believed. Furthermore, non-canonical splice site patterns suggest that infrequent splicing sites may occur under special conditions, or that an alternative trans-splicing mechanism is involved. Finally, our candidates are supposedly from normal tissue, and a recent stu... Mostrar Tudo |
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Palavras-Chave: |
Banco de dados; Bioinformática; Inter-chromosomal trans-splicing; Non-canonical splicing sites; TRNA-mediatedtrans-splicing. |
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Thesaurus Nal: |
Bioinformatics. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/148693/1/AP-Brief-Bioinform-2010-Herai-198-209.pdf
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Marc: |
LEADER 02445naa a2200217 a 4500
001 1577947
005 2016-10-13
008 2010 bl uuuu u00u1 u #d
024 7 $a10.1093/bib/bbp041$2DOI
100 1 $aHERAI, R. H.
245 $aDetection of human interchromosomal trans-splicing in sequence databanks.$h[electronic resource]
260 $c2010
520 $aTrans-splicing is a common phenomenon in nematodes and kinetoplastids, and it has also been reported in other organisms, including humans. Up to now, all in silico strategies to find evidence of trans-splicing in humans have required that the candidate sequences follow the consensus splicing site rules (spliceosome-mediated mechanism). However, this criterion is not supported by the best human experimental evidence, which, except in a single case, do not follow canonical splicing sites. Moreover, recent findings describe a novel alternative tRNA mediated trans-splicing mechanism, which prescinds the spliceosome machinery. In order to answer the question, ?Are there hybrid mRNAs in sequence databanks, whose characteristics resemble those of the best human experimental evidence??, we have developed a methodology that successfully identified 16 hybrid mRNAs which might be instances of interchromosomal trans-splicing. Each hybrid mRNA is formed by a trans-spliced region (TSR), which was successfully mapped either onto known genes or onto a human endogenous retrovirus (HERV-K) transcript which supports their transcription. The existence of these hybrid mRNAs indicates that trans-splicing may be more widespread than believed. Furthermore, non-canonical splice site patterns suggest that infrequent splicing sites may occur under special conditions, or that an alternative trans-splicing mechanism is involved. Finally, our candidates are supposedly from normal tissue, and a recent study has reported that trans-splicing may occur not only in malignant tissues, but in normal tissues as well. Our methodology can be applied to 5'-UTR, coding sequences and 3'-UTR in order to find new candidates for a posteriori experimental confirmation.
650 $aBioinformatics
653 $aBanco de dados
653 $aBioinformática
653 $aInter-chromosomal trans-splicing
653 $aNon-canonical splicing sites
653 $aTRNA-mediatedtrans-splicing
700 1 $aYAMAGISHI, M. E. B.
773 $tBriefings in Bioinformatics, London$gv. 2, n. 2, p. 198-209, 2010.
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Embrapa Agricultura Digital (CNPTIA) |
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