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GC-compositional strand bias around transcription start sites in plants and fungi

BioMed Central
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  • Biology

Abstract ral ss BioMed CentBMC Genomics Open AcceResearch article GC-compositional strand bias around transcription start sites in plants and fungi Shigeo Fujimori1,2, Takanori Washio*1,3 and Masaru Tomita1,4 Address: 1Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan, 2Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan, 3Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan and 4Department of Environmental Information, Keio University, Fujisawa, Kanagawa 252-8520, Japan Email: Shigeo Fujimori - [email protected]; Takanori Washio* - [email protected]; Masaru Tomita - [email protected] * Corresponding author Abstract 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, re

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