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Open Access Highly Accessed Research article

GC3 biology in corn, rice, sorghum and other grasses

Tatiana V Tatarinova12*, Nickolai N Alexandrov3, John B Bouck3 and Kenneth A Feldmann34

Author Affiliations

1 Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia, 30332, USA

2 Division of Mathematics and Statistics, University of Glamorgan, Pontypridd, CF37 1DL, UK

3 Ceres, Inc, 1535 Rancho Conejo Rd, Thousand Oaks, CA, 91320, USA

4 School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA

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BMC Genomics 2010, 11:308  doi:10.1186/1471-2164-11-308

Published: 16 May 2010

Abstract

Background

The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates.

Results

Here we demonstrate that in certain organisms the amount of GC at the wobble position (GC3) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC3 content: they (1) provide more targets for methylation, (2) exhibit more variable expression, (3) more frequently possess upstream TATA boxes, (4) are predominant in certain classes of genes (e.g., stress responsive genes) and (5) have a GC3 content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC3 bimodality in grasses.

Conclusions

Our findings suggest that high levels of GC3 typify a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC3 bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation.