GC3 biology in corn, rice, sorghum and other grasses.
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.
Tatarinova
Tatiana V
TV
Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. tvtatari@glam.ac.uk
Alexandrov
Nickolai N
NN
Bouck
John B
JB
Feldmann
Kenneth A
KA
D001482:Base Composition; D003062:Codon / Q000737:chemistry* / Q000235:genetics*; D019175:DNA Methylation; D005785:Gene Conversion; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D023281:Genomics; D007438:Introns / Q000235:genetics; D012275:Oryza / Q000235:genetics; D006109:Poaceae / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D045868:Sorghum / Q000235:genetics; D016385:TATA Box / Q000235:genetics; D003313:Zea mays / Q000235:genetics
D003062:Codon
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