BACKGROUND: A GC-compositional strand bias or GC-skew (=(C-G)/(C+G)), where C 
and G denote the numbers of cytosine and guanine residues, was recently reported 
near the transcription start sites (TSS) of Arabidopsis genes. However, it is 
unclear whether other eukaryotic species have equally prominent GC-skews, and 
the biological meaning of this trait remains unknown.
RESULTS: Our study confirmed a significant GC-skew (C > G) in the TSS of Oryza 
sativa (rice) genes. The full-length cDNAs and genomic sequences from 
Arabidopsis and rice were compared using statistical analyses. Despite marked 
differences in the G+C content around the TSS in the two plants, the degrees of 
bias were almost identical. Although slight GC-skew peaks, including opposite 
skews (C < G), were detected around the TSS of genes in human and Drosophila, 
they were qualitatively and quantitatively different from those identified in 
plants. However, plant-like GC-skew in regions upstream of the translation 
initiation sites (TIS) in some fungi was identified following analyses of the 
expressed sequence tags and/or genomic sequences from other species. On the 
basis of our dataset, we estimated that > 70 and 68% of Arabidopsis and rice 
genes, respectively, had a strong GC-skew (> 0.33) in a 100-bp window (that is, 
the number of C residues was more than double the number of G residues in a 
+/-100-bp window around the TSS). The mean GC-skew value in the TSS of 
highly-expressed genes in Arabidopsis was significantly greater than that of 
genes with low expression levels. Many of the GC-skew peaks were preferentially 
located near the TSS, so we examined the potential value of GC-skew as an index 
for TSS identification. Our results confirm that the GC-skew can be used to 
assist the TSS prediction in plant genomes.
CONCLUSION: The GC-skew (C > G) around the TSS is strictly conserved between 
monocot and eudicot plants (ie. angiosperms in general), and a similar skew has 
been observed in some fungi. Highly-expressed Arabidopsis genes had overall a 
more marked GC-skew in the TSS compared to genes with low expression levels. We 
therefore propose that the GC-skew around the TSS in some plants and fungi is 
related to transcription. It might be caused by mutations during transcription 
initiation or the frequent use of transcription factor-biding sites having a 
strand preference. In addition, GC-skew is a good candidate index for TSS 
prediction in plant genomes, where there is a lack of correlation among CpG 
islands and genes.