DNA:RNA hybrid G-quadruplex formation upstream of transcription start site

• Published in: Scientific reports Vol. 10; no. 1; p. 7429
• Main Authors: Zhang, Jia-yu, Xia, Ye, Hao, Yu-hua, Tan, Zheng
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 04.05.2020; Nature Publishing Group
• Subjects: 631/45/147; 631/92/147; Base Sequence; Computational Biology; Deoxyribonucleic acid; DNA; DNA - genetics; DNA-Directed RNA Polymerases - genetics; G-Quadruplexes; Genomes; Guanine; Guanine - chemistry; Humanities and Social Sciences; Humans; multidisciplinary; Nucleic Acid Conformation; Nucleotide sequence; Oligonucleotides - genetics; Positive selection; Ribonucleic acid; RNA; RNA - genetics; Science; Science (multidisciplinary); Supercoiling; Transcription; Transcription Initiation Site; Transcription, Genetic
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-020-64117-x

Bioinformatic analysis reveals an enrichment of putative DNA:RNA hybrid G-quadruplex-forming sequences (PHQS) on both sides of the transcription start sites (TSSs) in the genome of warm-blooded animals, suggesting a positive selection of PHQSs in evolution and functional role of DNA:RNA hybrid G-quadruplexes (HQs) in transcription. The formation of HQs downstream of TSS in transcribed DNA has been documented under in vitro conditions; however, it is still not known if such HQs can form at the upstream side of TSSs. In this study, we report that such HQs can form in transcription in DNA with two to three guanine tracts if RNA carrying the required number of G-tracts is supplied. We also show that the formation of such HQs is dependent on the negative supercoiling generated by RNA polymerases. These results suggest that HQs may also form at the upstream side of TSSs in vivo and play a role in transcription since the two requirements are satisfied in cells.