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Comprehensive analysis of the base composition around the transcription start site in Metazoa

BACKGROUND: The transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site...

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Autores principales: Aerts, Stein, Thijs, Gert, Dabrowski, Michal, Moreau, Yves, De Moor, Bart
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2004
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC436054/
https://www.ncbi.nlm.nih.gov/pubmed/15171795
http://dx.doi.org/10.1186/1471-2164-5-34
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author Aerts, Stein
Thijs, Gert
Dabrowski, Michal
Moreau, Yves
De Moor, Bart
author_facet Aerts, Stein
Thijs, Gert
Dabrowski, Michal
Moreau, Yves
De Moor, Bart
author_sort Aerts, Stein
collection PubMed
description BACKGROUND: The transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site for all annotated genes across multiple genomes. RESULTS: The most prominent feature in the base compositions is a significant local variation in G+C content over a large region around the transcription start site. The change is present in all animal phyla but the extent of variation is different between distinct classes of vertebrates, and the shape of the variation is completely different between vertebrates and arthropods. Furthermore, the height of the variation correlates with CpG frequencies in vertebrates but not in invertebrates and it also correlates with gene expression, especially in mammals. We also detect GC and AT skews in all clades (where %G is not equal to %C or %A is not equal to %T respectively) but these occur in a more confined region around the transcription start site and in the coding region. CONCLUSIONS: The dramatic changes in nucleotide composition in humans are a consequence of CpG nucleotide frequencies and of gene expression, the changes in Fugu could point to primordial CpG islands, and the changes in the fly are of a totally different kind and unrelated to dinucleotide frequencies.
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spelling pubmed-4360542004-06-26 Comprehensive analysis of the base composition around the transcription start site in Metazoa Aerts, Stein Thijs, Gert Dabrowski, Michal Moreau, Yves De Moor, Bart BMC Genomics Research Article BACKGROUND: The transcription start site of a metazoan gene remains poorly understood, mostly because there is no clear signal present in all genes. Now that several sequenced metazoan genomes have been annotated, we have been able to compare the base composition around the transcription start site for all annotated genes across multiple genomes. RESULTS: The most prominent feature in the base compositions is a significant local variation in G+C content over a large region around the transcription start site. The change is present in all animal phyla but the extent of variation is different between distinct classes of vertebrates, and the shape of the variation is completely different between vertebrates and arthropods. Furthermore, the height of the variation correlates with CpG frequencies in vertebrates but not in invertebrates and it also correlates with gene expression, especially in mammals. We also detect GC and AT skews in all clades (where %G is not equal to %C or %A is not equal to %T respectively) but these occur in a more confined region around the transcription start site and in the coding region. CONCLUSIONS: The dramatic changes in nucleotide composition in humans are a consequence of CpG nucleotide frequencies and of gene expression, the changes in Fugu could point to primordial CpG islands, and the changes in the fly are of a totally different kind and unrelated to dinucleotide frequencies. BioMed Central 2004-06-01 /pmc/articles/PMC436054/ /pubmed/15171795 http://dx.doi.org/10.1186/1471-2164-5-34 Text en Copyright © 2004 Aerts et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.
spellingShingle Research Article
Aerts, Stein
Thijs, Gert
Dabrowski, Michal
Moreau, Yves
De Moor, Bart
Comprehensive analysis of the base composition around the transcription start site in Metazoa
title Comprehensive analysis of the base composition around the transcription start site in Metazoa
title_full Comprehensive analysis of the base composition around the transcription start site in Metazoa
title_fullStr Comprehensive analysis of the base composition around the transcription start site in Metazoa
title_full_unstemmed Comprehensive analysis of the base composition around the transcription start site in Metazoa
title_short Comprehensive analysis of the base composition around the transcription start site in Metazoa
title_sort comprehensive analysis of the base composition around the transcription start site in metazoa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC436054/
https://www.ncbi.nlm.nih.gov/pubmed/15171795
http://dx.doi.org/10.1186/1471-2164-5-34
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