Genome-wide discovery of G-quadruplexes in barley

Authors: CAGIRICI, BUSRA - Orise Fellow; BUDAK, HIKMET - Montana Bioagriculture Inc; Sen, Taner

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2021
Publication Date: 4/12/2021
Citation: Cagirici, B.H., Budak, H., Sen, T.Z. 2021. Genome-wide discovery of G-quadruplexes in barley. Scientific Reports. 11. Article 7876. https://doi.org/10.1038/s41598-021-86838-3.
DOI: https://doi.org/10.1038/s41598-021-86838-3

Interpretive Summary: G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar shapes in genomes that were implicated in genome stability and cellular regulation. In this study, we analyzed the distributions of G4 elements across chromosomes in the reference genome of barley. We then compared these distributions against those for maize, Arabidopsis, and other plants. We studied the G4 distribution in the upstream of genes and the effects of smoothening in the calculation of G4s. We compared the functional annotations between genes with and without G4s. Finally, we focused on specific classes of disease resistance genes and examined the presence/absence of G4 motifs.

Technical Abstract: G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar shapes. Aberrant formation of G4 structures has been associated with genomic instability, functional similarities of the G4s in transcription, replication, and translation have been observed in related species. However, most plant species are lacking comprehensive studies of G4 structures. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. G4 motifs peaked around the 5' untranslated region (5’ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distribution around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions like transcription initiation and hydrolase activity. Additionally, single-nucleotide polymorphisms (SNPs) was shown to be depleted in G4 motifs in comparison to the promoter region.