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Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants

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Title Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants
 
Creator Garg, Rohini
Aggarwal, Jyoti
Thakkar, Bijal
 
Subject Abiotic
Secondary metabolism
Plant molecular biology
 
Description Accepted date: 18 May 2016
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.
This work was financially supported by the Department of Biotechnology, Government of India, New Delhi under the Innovative Young Biotechnologist Award scheme (BT/06/IYBA/2012). We are thankful to Dr. Mukesh Jain, Jawaharlal Nehru University, for helpful suggestions. We acknowledge Advanced Instrumentation Research Facility at Jawaharlal Nehru University for CD spectroscopy experiments.
 
Date 2016-06-23T11:04:48Z
2016-06-23T11:04:48Z
2016
 
Type Article
 
Identifier Scientific Reports, 6: 28211
2045-2322
http://172.16.0.77:8080/jspui/handle/123456789/663
http://www.nature.com/articles/srep28211
10.1038/srep28211
 
Language en_US
 
Publisher Nature Publishing Group