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2015 ; 31
(19
): 3081-4
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GC3-biased gene domains in mammalian genomes
#MMPMID26019240
Shen W
; Wang D
; Ye B
; Shi M
; Ma L
; Zhang Y
; Zhao Z
Bioinformatics
2015[Oct]; 31
(19
): 3081-4
PMID26019240
show ga
MOTIVATION: Synonymous codon usage bias has been shown to be correlated with many
genomic features among different organisms. However, the biological significance
of codon bias with respect to gene function and genome organization remains
unclear. RESULTS: Guanine and cytosine content at the third codon position (GC3)
could be used as a good indicator of codon bias. Here, we used relative GC3 bias
values to compare the strength of GC3 bias of genes in human and mouse. We
reported, for the first time, that GC3-rich and GC3-poor gene products might have
distinct sub-cellular spatial distributions. Moreover, we extended the view of
genomic gene domains and identified conserved GC3 biased gene domains along
chromosomes. Our results indicated that similar GC3 biased genes might be
co-translated in specific spatial regions to share local translational
machineries, and that GC3 could be involved in the organization of genome
architecture. AVAILABILITY AND IMPLEMENTATION: Source code is available upon
request from the authors. CONTACT: zhaozh@nic.bmi.ac.cn or zany1983@gmail.com
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics
online.
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