Abstract
DNA, in addition to the canonical B-form, can acquire a variety of alternate structures, such as G-quadruplexes. These structures have been implicated in several cellular processes in animals. In this study, we identified different types of G-quadruplex forming sequences (GQSes) in 15 sequenced plants and analyzed their distribution in various genomic features, including gene body, coding, intergenic and promoter regions. G2-type GQSes were most abundant in all the plant species analyzed. A strong association of G3-type GQSes with intergenic, promoter and intronic regions was found. However, G2-type GQSes were enriched in genic, CDS, exonic and untranslated regions. Further, we identified GQSes present in the conserved genes among monocots and dicots. The genes involved in development, cell growth and size, transmembrane transporter, and regulation of gene expression were found to be significantly enriched. In the promoter region, we detected strong co-occurrence of Telobox, ERF, MYB, RAV1B and E2F motifs with GQSes. Further, we validated the structure formation of several plant GQSes, demonstrated their effect on stalling in-vitro replication and revealed their interaction with plant nuclear proteins. Our data provide insights into the prevalence of GQSes in plants, establish their association with different genomic features and functional relevance.
Highlights
DNA, in addition to the canonical B-form, can acquire a variety of alternate structures, such as
G2L1-4 type G-quadruplex forming sequences (GQSes) were highest in all the plant species analyzed
More than 90% of the GQSes identified were of G2-type, whereas G3-type constituted less than 5% of the total GQSes identified in each of the plant species
Summary
DNA, in addition to the canonical B-form, can acquire a variety of alternate structures, such as. We identified different types of G-quadruplex forming sequences (GQSes) in 15 sequenced plants and analyzed their distribution in various genomic features, including gene body, coding, intergenic and promoter regions. A strong association of G3-type GQSes with intergenic, promoter and intronic regions was found. Our data provide insights into the prevalence of GQSes in plants, establish their association with different genomic features and functional relevance. G-quadruplex is one of the non-canonical four-stranded structure made up of multiple Hoogsteen base-paired G-quartets stacked on top of each other[2]. These have been found to be enriched in functional regions of the genome, such as genes, promoters, telomeres and untranslated regions (UTRs) of mRNA3–9. Recent experiments with human cell lines have established the formation of G-quadruplexes in DNA and RNA in eukaryotic cells[16,17,18,19,20]
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