Genome-wide identification of G-quadruplex forming regions in Arabidopsis: Unraveling the role of Pif1 like helicase (AtPLH1) in gene regulation

G-quadruplexes (GQSes) are highly stable DNA secondary structures, which exist as knots in the genome during different cellular processes like replication, transcription and translation. Although several studies have shown the role of Pif1-helicases regulating several cellular processes in yeast and human, the involvement of these helicases in GQS-mediated gene regulation remains largely unexplored in plants. In this study, we identified GQS-enriched regions by DNA affinity purification followed by sequencing from Arabidopsis Pif1-like helicase 1 (Atplh1) mutant. Differentially enriched peaks (DEPs) in the mutant showed preferential distribution in the exonic and promoter regions. The genes involved in various processes like transcriptional regulation, UDP-glycosylation, response to abiotic stress, ethylene biosynthesis and response to carbohydrate stimulus, were found to be differentially expressed (DEGs) between control and mutant plants. These DEGs showed enrichment of binding sites of ERF, WRKY, BBM and BIM transcription factors. Further, the DEGs harboring DEPs were found associated with response to wounding and salt stress, response to unfolded protein, heat stress response and UDP-glycosyl transferase activity. In addition, the mutants exhibited lesser growth inhibition under cold stress. Overall, our study identified genome-wide GQSes in Arabidopsis and altered gene expression regulated by AtPLH1.