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The majority of long non-stop reading frames on the antisense strand can be explained by biased codon usage
1Institut für Molekularbiologie II, Universität Zürich, Switzerland.
Gene
|July 18, 1997
Summary
Long antisense non-stop reading frames (aNRFs) are more common than expected, particularly in heat-shock protein 70 kDa (Hsp70) genes. Codon usage bias, influenced by GC content, explains the prevalence of these aNRFs.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Recent studies suggest an unexpected frequency of long reading frames on the antisense strand of open reading frames (ORFs).
- Antisense non-stop reading frames (aNRFs) overlapping known coding regions are of particular interest.
- The heat-shock protein 70 kDa (Hsp70) family is frequently implicated in these observations.
Purpose of the Study:
- To investigate the occurrence and characteristics of long antisense non-stop reading frames (aNRFs) in vertebrate DNA.
- To determine the relationship between aNRFs and codon usage bias, especially in the Hsp70 gene family.
- To explore the potential role of codon usage bias in explaining the presence of long aNRFs.
Main Methods:
- Searched the vertebrate DNA database for long (greater than 900 bp) aNRFs overlapping known coding regions.
- Analyzed the DNA sequences for characteristics such as GC content at the third codon position of sense ORFs.
- Investigated codon usage bias in both specific Hsp70 genes and a general species-wide context.
Main Results:
- Long aNRFs were predominantly found in DNA with high GC content at the third codon position of sense ORFs.
- The heat-shock protein 70 kDa (Hsp70) family was the major class of sequences identified containing long aNRFs.
- These long Hsp70 aNRFs were observed across diverse species, including fish, flies, fungi, and bacteria.
- Codon usage bias, driven by GC content and sometimes high gene expression, was shown to explain the presence of long aNRFs, including those in the Hsp70 family.
Conclusions:
- The prevalence of long antisense non-stop reading frames (aNRFs), even in the Hsp70 family, can be attributed to codon usage bias on the sense strand.
- Codon usage bias is primarily influenced by GC content at the third codon position of sense ORFs and, in some cases, by gene expression levels.
- While codon usage bias provides an explanation, the possibility of some aNRFs being transcribed and translated cannot be ruled out.