Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise?
Autor(a) principal: | |
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Data de Publicação: | 2009 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNIFESP |
Texto Completo: | http://repositorio.unifesp.br/handle/11600/31316 http://dx.doi.org/10.1186/1471-2199-10-7 |
Resumo: | Background: A major effort of the scientific community has been to obtain complete pictures of the genomes of many organisms. This has been accomplished mainly by annotation of structural and functional elements in the genome sequence, a process that has been centred in the gene concept and, as a consequence, biased toward protein coding sequences. Recently, the explosion of transcriptome data generated and the discovery of many functional non-protein coding RNAs have painted a more detailed and complex scenario for the genome. Here we analyzed the mouse carboxypeptidase M locus in this broader perspective in order to define the mouse CPM gene structure and evaluate the existence of other transcripts from the same genomic region.Results: Bioinformatic analysis of nucleotide sequences that map to the mouse CPM locus suggests that, in addition to the mouse CPM mRNA, it expresses at least 33 different transcripts, many of which seem to be non-coding RNAs. We randomly chose to evaluate experimentally four of these extra transcripts. They are expressed in a tissue specific manner, indicating that they are not artefacts or transcriptional noise. Furthermore, one of these four extra transcripts shows expression patterns that differed considerably from the other ones and from the mouse CPM gene, suggesting that there may be more than one transcriptional unit in this locus. in addition, we have confirmed the mouse CPM gene RefSeq sequence by rapid amplification of cDNA ends (RACE) and directional cloning.Conclusion: This study supports the recent view that the majority of the genome is transcribed and that many of the resulting transcripts seem to be non-coding RNAs from introns of genes or from independent transcriptional units. Although some of the information on the transcriptome of many organisms may actually be artefacts or transcriptional noise, we argue that it can be experimentally evaluated and used to find and define biological functional elements on the genome. Furthermore, the transcription of other functional RNAs besides the protein coding RNA from a specific genomic locus imposes extra care when designing and interpreting experiments involving genetic manipulations or expression detection and quantification. |
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Guimarães, Alessander de Oliveira [UNIFESP]Motta, Fabiana Louise Teixeira [UNIFESP]Alves, Viviane S. [UNIFESP]Castilho, Beatriz Amaral de [UNIFESP]Pesquero, João Bosco [UNIFESP]Universidade Federal de São Paulo (UNIFESP)2016-01-24T13:52:16Z2016-01-24T13:52:16Z2009-02-08Bmc Molecular Biology. London: Biomed Central Ltd, v. 10, 14 p., 2009.1471-2199http://repositorio.unifesp.br/handle/11600/31316http://dx.doi.org/10.1186/1471-2199-10-7WOS000264206600001.pdf10.1186/1471-2199-10-7WOS:000264206600001Background: A major effort of the scientific community has been to obtain complete pictures of the genomes of many organisms. This has been accomplished mainly by annotation of structural and functional elements in the genome sequence, a process that has been centred in the gene concept and, as a consequence, biased toward protein coding sequences. Recently, the explosion of transcriptome data generated and the discovery of many functional non-protein coding RNAs have painted a more detailed and complex scenario for the genome. Here we analyzed the mouse carboxypeptidase M locus in this broader perspective in order to define the mouse CPM gene structure and evaluate the existence of other transcripts from the same genomic region.Results: Bioinformatic analysis of nucleotide sequences that map to the mouse CPM locus suggests that, in addition to the mouse CPM mRNA, it expresses at least 33 different transcripts, many of which seem to be non-coding RNAs. We randomly chose to evaluate experimentally four of these extra transcripts. They are expressed in a tissue specific manner, indicating that they are not artefacts or transcriptional noise. Furthermore, one of these four extra transcripts shows expression patterns that differed considerably from the other ones and from the mouse CPM gene, suggesting that there may be more than one transcriptional unit in this locus. in addition, we have confirmed the mouse CPM gene RefSeq sequence by rapid amplification of cDNA ends (RACE) and directional cloning.Conclusion: This study supports the recent view that the majority of the genome is transcribed and that many of the resulting transcripts seem to be non-coding RNAs from introns of genes or from independent transcriptional units. Although some of the information on the transcriptome of many organisms may actually be artefacts or transcriptional noise, we argue that it can be experimentally evaluated and used to find and define biological functional elements on the genome. Furthermore, the transcription of other functional RNAs besides the protein coding RNA from a specific genomic locus imposes extra care when designing and interpreting experiments involving genetic manipulations or expression detection and quantification.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Universidade Federal de São Paulo, Dept Biofis, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol & Imunol, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Biofis, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Microbiol & Imunol, São Paulo, BrazilWeb of Science14engBiomed Central LtdBmc Molecular BiologyMultiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise?info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da UNIFESPinstname:Universidade Federal de São Paulo (UNIFESP)instacron:UNIFESPORIGINALWOS000264206600001.pdfapplication/pdf2222554${dspace.ui.url}/bitstream/11600/31316/1/WOS000264206600001.pdf5bcf02a3639b2a581ade6f36d1151d76MD51open accessTEXTWOS000264206600001.pdf.txtWOS000264206600001.pdf.txtExtracted texttext/plain61088${dspace.ui.url}/bitstream/11600/31316/2/WOS000264206600001.pdf.txta2fe9383517f15faedd981e7e6143224MD52open access11600/313162022-06-02 09:02:09.975open accessoai:repositorio.unifesp.br:11600/31316Repositório InstitucionalPUBhttp://www.repositorio.unifesp.br/oai/requestopendoar:34652022-06-02T12:02:09Repositório Institucional da UNIFESP - Universidade Federal de São Paulo (UNIFESP)false |
dc.title.en.fl_str_mv |
Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise? |
title |
Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise? |
spellingShingle |
Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise? Guimarães, Alessander de Oliveira [UNIFESP] |
title_short |
Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise? |
title_full |
Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise? |
title_fullStr |
Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise? |
title_full_unstemmed |
Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise? |
title_sort |
Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise? |
author |
Guimarães, Alessander de Oliveira [UNIFESP] |
author_facet |
Guimarães, Alessander de Oliveira [UNIFESP] Motta, Fabiana Louise Teixeira [UNIFESP] Alves, Viviane S. [UNIFESP] Castilho, Beatriz Amaral de [UNIFESP] Pesquero, João Bosco [UNIFESP] |
author_role |
author |
author2 |
Motta, Fabiana Louise Teixeira [UNIFESP] Alves, Viviane S. [UNIFESP] Castilho, Beatriz Amaral de [UNIFESP] Pesquero, João Bosco [UNIFESP] |
author2_role |
author author author author |
dc.contributor.institution.none.fl_str_mv |
Universidade Federal de São Paulo (UNIFESP) |
dc.contributor.author.fl_str_mv |
Guimarães, Alessander de Oliveira [UNIFESP] Motta, Fabiana Louise Teixeira [UNIFESP] Alves, Viviane S. [UNIFESP] Castilho, Beatriz Amaral de [UNIFESP] Pesquero, João Bosco [UNIFESP] |
description |
Background: A major effort of the scientific community has been to obtain complete pictures of the genomes of many organisms. This has been accomplished mainly by annotation of structural and functional elements in the genome sequence, a process that has been centred in the gene concept and, as a consequence, biased toward protein coding sequences. Recently, the explosion of transcriptome data generated and the discovery of many functional non-protein coding RNAs have painted a more detailed and complex scenario for the genome. Here we analyzed the mouse carboxypeptidase M locus in this broader perspective in order to define the mouse CPM gene structure and evaluate the existence of other transcripts from the same genomic region.Results: Bioinformatic analysis of nucleotide sequences that map to the mouse CPM locus suggests that, in addition to the mouse CPM mRNA, it expresses at least 33 different transcripts, many of which seem to be non-coding RNAs. We randomly chose to evaluate experimentally four of these extra transcripts. They are expressed in a tissue specific manner, indicating that they are not artefacts or transcriptional noise. Furthermore, one of these four extra transcripts shows expression patterns that differed considerably from the other ones and from the mouse CPM gene, suggesting that there may be more than one transcriptional unit in this locus. in addition, we have confirmed the mouse CPM gene RefSeq sequence by rapid amplification of cDNA ends (RACE) and directional cloning.Conclusion: This study supports the recent view that the majority of the genome is transcribed and that many of the resulting transcripts seem to be non-coding RNAs from introns of genes or from independent transcriptional units. Although some of the information on the transcriptome of many organisms may actually be artefacts or transcriptional noise, we argue that it can be experimentally evaluated and used to find and define biological functional elements on the genome. Furthermore, the transcription of other functional RNAs besides the protein coding RNA from a specific genomic locus imposes extra care when designing and interpreting experiments involving genetic manipulations or expression detection and quantification. |
publishDate |
2009 |
dc.date.issued.fl_str_mv |
2009-02-08 |
dc.date.accessioned.fl_str_mv |
2016-01-24T13:52:16Z |
dc.date.available.fl_str_mv |
2016-01-24T13:52:16Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
Bmc Molecular Biology. London: Biomed Central Ltd, v. 10, 14 p., 2009. |
dc.identifier.uri.fl_str_mv |
http://repositorio.unifesp.br/handle/11600/31316 http://dx.doi.org/10.1186/1471-2199-10-7 |
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1471-2199 |
dc.identifier.file.none.fl_str_mv |
WOS000264206600001.pdf |
dc.identifier.doi.none.fl_str_mv |
10.1186/1471-2199-10-7 |
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WOS:000264206600001 |
identifier_str_mv |
Bmc Molecular Biology. London: Biomed Central Ltd, v. 10, 14 p., 2009. 1471-2199 WOS000264206600001.pdf 10.1186/1471-2199-10-7 WOS:000264206600001 |
url |
http://repositorio.unifesp.br/handle/11600/31316 http://dx.doi.org/10.1186/1471-2199-10-7 |
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Biomed Central Ltd |
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Biomed Central Ltd |
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