Research article
Comprehensive analysis of the base composition around the transcription start site in Metazoa
-
* Corresponding author: Stein Aerts stein.aerts@esat.kuleuven.ac.be
1 Department of Electrical Engineering (ESAT-SCD), Katholieke Universiteit Leuven, Belgium
2 Laboratory of Transcription Regulation, Nencki Institute, Warsaw, Poland
3 On leave at Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, Lyngby, Denmark
BMC Genomics 2004, 5:34 doi:10.1186/1471-2164-5-34
Published: 1 June 2004Abstract
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.