Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants.
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.
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
Rohini
R
Garg
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
Jyoti
J
Aggarwal
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.
Bijal
B
Thakkar
D000818:Animals; D018744:DNA, Plant / Q000235:genetics*; D054856:G-Quadruplexes; D005786:Gene Expression Regulation; D018745:Genome, Plant / Q000235:genetics; D006801:Humans; D007438:Introns / Q000235:genetics; D015394:Molecular Structure; D010944:Plants / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics
D018744:DNA, Plant