Cargando…

Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing

We analyzed diversity of mRNA produced as a result of alternative splicing in order to evaluate gene function. First, we predicted the number of human genes transcribed into protein-coding mRNAs by using the sequence information of full-length cDNAs and 5′-ESTs and obtained 23 241 of such human gene...

Descripción completa

Detalles Bibliográficos
Autores principales: Wakamatsu, Ai, Kimura, Kouichi, Yamamoto, Jun-ichi, Nishikawa, Tetsuo, Nomura, Nobuo, Sugano, Sumio, Isogai, Takao
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780955/
https://www.ncbi.nlm.nih.gov/pubmed/19880432
http://dx.doi.org/10.1093/dnares/dsp022
_version_ 1782174541608386560
author Wakamatsu, Ai
Kimura, Kouichi
Yamamoto, Jun-ichi
Nishikawa, Tetsuo
Nomura, Nobuo
Sugano, Sumio
Isogai, Takao
author_facet Wakamatsu, Ai
Kimura, Kouichi
Yamamoto, Jun-ichi
Nishikawa, Tetsuo
Nomura, Nobuo
Sugano, Sumio
Isogai, Takao
author_sort Wakamatsu, Ai
collection PubMed
description We analyzed diversity of mRNA produced as a result of alternative splicing in order to evaluate gene function. First, we predicted the number of human genes transcribed into protein-coding mRNAs by using the sequence information of full-length cDNAs and 5′-ESTs and obtained 23 241 of such human genes. Next, using these genes, we analyzed the mRNA diversity and consequently sequenced and identified 11 769 human full-length cDNAs whose predicted open reading frames were different from other known full-length cDNAs. Especially, 30% of the cDNAs we identified contained variation in the transcription start site (TSS). Our analysis, which particularly focused on multiple variable first exons (FEVs) formed due to the alternative utilization of TSSs, led to the identification of 261 FEVs expressed in the tissue-specific manner. Quantification of the expression profiles of 13 genes by real-time PCR analysis further confirmed the tissue-specific expression of FEVs, e.g. OXR1 had specific TSS in brain and tumor tissues, and so on. Finally, based on the results of our mRNA diversity analysis, we have created the FLJ Human cDNA Database. From our result, it has been understood mechanisms that one gene produces suitable protein-coding transcripts responding to the situation and the environment.
format Text
id pubmed-2780955
institution National Center for Biotechnology Information
language English
publishDate 2009
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-27809552009-11-23 Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing Wakamatsu, Ai Kimura, Kouichi Yamamoto, Jun-ichi Nishikawa, Tetsuo Nomura, Nobuo Sugano, Sumio Isogai, Takao DNA Res Full Papers We analyzed diversity of mRNA produced as a result of alternative splicing in order to evaluate gene function. First, we predicted the number of human genes transcribed into protein-coding mRNAs by using the sequence information of full-length cDNAs and 5′-ESTs and obtained 23 241 of such human genes. Next, using these genes, we analyzed the mRNA diversity and consequently sequenced and identified 11 769 human full-length cDNAs whose predicted open reading frames were different from other known full-length cDNAs. Especially, 30% of the cDNAs we identified contained variation in the transcription start site (TSS). Our analysis, which particularly focused on multiple variable first exons (FEVs) formed due to the alternative utilization of TSSs, led to the identification of 261 FEVs expressed in the tissue-specific manner. Quantification of the expression profiles of 13 genes by real-time PCR analysis further confirmed the tissue-specific expression of FEVs, e.g. OXR1 had specific TSS in brain and tumor tissues, and so on. Finally, based on the results of our mRNA diversity analysis, we have created the FLJ Human cDNA Database. From our result, it has been understood mechanisms that one gene produces suitable protein-coding transcripts responding to the situation and the environment. Oxford University Press 2009-12 2009-10-30 /pmc/articles/PMC2780955/ /pubmed/19880432 http://dx.doi.org/10.1093/dnares/dsp022 Text en © The Author 2009. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Full Papers
Wakamatsu, Ai
Kimura, Kouichi
Yamamoto, Jun-ichi
Nishikawa, Tetsuo
Nomura, Nobuo
Sugano, Sumio
Isogai, Takao
Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing
title Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing
title_full Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing
title_fullStr Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing
title_full_unstemmed Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing
title_short Identification and Functional Analyses of 11 769 Full-length Human cDNAs Focused on Alternative Splicing
title_sort identification and functional analyses of 11 769 full-length human cdnas focused on alternative splicing
topic Full Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780955/
https://www.ncbi.nlm.nih.gov/pubmed/19880432
http://dx.doi.org/10.1093/dnares/dsp022
work_keys_str_mv AT wakamatsuai identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing
AT kimurakouichi identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing
AT yamamotojunichi identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing
AT nishikawatetsuo identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing
AT nomuranobuo identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing
AT suganosumio identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing
AT isogaitakao identificationandfunctionalanalysesof11769fulllengthhumancdnasfocusedonalternativesplicing