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Genomic distribution and possible functional roles of putative G-quadruplex motifs in two subspecies of Oryza sativa

Paper ID Volume ID Publish Year Pages File Format Full-Text
15063 1370 2015 9 PDF Available
Title
Genomic distribution and possible functional roles of putative G-quadruplex motifs in two subspecies of Oryza sativa
Abstract

•The research on G-quadrulexes has blossomed for the recent years, but it is fewer in plants by far.•Novel rules were used to analyze putative G-quadruplex motifs in plant genomes.•The putative G-quadruplex motif is prevailed in this genome and related on many kinds of biological process.

G-quadruplex is a stable, four-stranded DNA or RNA structure formed from guanine-rich regions and implicated in telomere maintenance, replication, gene regulation at transcription level or translation level, etc. Based on bioinformatics methods, we analyzed different putative G-quadruplex motifs (PGQMs) patterns in various genomic regions of two subspecies (indica and japonica) of Oryza sativa and the whole genomes of other 8 species. In total, in the 10 species we discussed, the PGQMs densities in monocots were higher than dicots. 40,483 and 31,795 PGQMs were identified with a density of 108.46 and 84.89 PGQMs/Mb, respectively, in japonica and indica genomes, 10,655 and 5420 loci were found to contain at least one PGQM in their gene bodies (with a percentage of 19% and 14%) indicating a wide distribution of G-quadruplex motifs in O. sativa genome. They preferred to locate in transcription start sites proximal regions and 5′-UTR with relative high enrichment. This phenomenon supports the hypothesis that PGQMs are involved in gene transcription and translation. In addition, we analyzed the distribution of different loop length in G-quadruplex and found the density of long loop PGQMs was less than short loop in indica’s intron but it was similar in japonica. Meanwhile, we focused on the loci with PGQMs and conducted gene ontology (GO) analysis of them. As a result, many GO terms were identified and significantly correlated with the loci containing at least one PGQM. The GO analysis in the two subspecies of rice may be helpful for elucidating the functional roles of G-quadruplexes.

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Keywords
Bioinformatics; G-quadruplex; 5'-UTR; TSS-proximal region
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Genomic distribution and possible functional roles of putative G-quadruplex motifs in two subspecies of Oryza sativa
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 56, June 2015, Pages 122–130
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us