Co-transcriptional formation of DNA:RNA hybrid G-quadruplex and potential function as constitutional cis element for transcription control

Abstract

G-quadruplex formation in genomic DNA is considered to regulate transcription. Previous investigations almost exclusively focused on intramolecular G-quadruplexes formed by DNA carrying four or more G-tracts, and structure formation has rarely been studied in physiologically relevant processes. Here, we report an almost entirely neglected, but actually much more prevalent form of G-quadruplexes, DNA:RNA hybrid G-quadruplexes (HQ) that forms in transcription. HQ formation requires as few as two G-tracts instead of four on a non-template DNA strand. Potential HQ sequences (PHQS) are present in >97% of human genes, with an average of 73 PHQSs per gene. HQ modulates transcription under both in vitro and in vivo conditions. Transcriptomal analysis of human tissues implies that maximal gene expression may be limited by the number of PHQS in genes. These features suggest that HQs may play fundamental roles in transcription regulation and other transcription-mediated processes.

Human Origin Recognition Complex Binds Preferentially to G-quadruplex-preferable RNA and Single-stranded DNA

“…Nevertheless, it is worth thinking that the possibility that G4 structure, which can be induced by transcription (42), may modulate the ORC function in replication and/or other nuclear functions.…”

RNA G-Quadruplexes in Biology: Principles and Molecular Mechanisms

“…Formation of such hybrid G4 requires as few as two tandem G-tracks (guanine-rich sequences) on the nascent RNA transcript and a non-template DNA strand instead of four or more G-tracks required for formation of canonical intramolecular G4s (Figure 3B). Bioinformatic analysis identified that putative hybrid G4s are enriched within regions downstream of transcription start sites and are found in >97% of human genes, with an average of 73 putative hybrid G4s per gene 122; 123 . Formation of hybrid G4s was confirmed using T7 RNA polymerase in vitro transcription 123; 124; 125 , in vitro crosslinking, site-specific mutagenesis and transfection studies using luciferase reporters 123 .…”

“…Bioinformatic analysis identified that putative hybrid G4s are enriched within regions downstream of transcription start sites and are found in >97% of human genes, with an average of 73 putative hybrid G4s per gene 122; 123 . Formation of hybrid G4s was confirmed using T7 RNA polymerase in vitro transcription 123; 124; 125 , in vitro crosslinking, site-specific mutagenesis and transfection studies using luciferase reporters 123 . Results from these studies suggest that hybrid G4s inhibit transcription in vitro and represent cis –elements that are built into a gene and activated co-transcriptionally.…”

RNA G-quadruplexes and their potential regulatory roles in translation

“…Recently, it was discovered by performing nascent strand sequencing that G4 sequences may also position nucleosomes at a subset of human replication origins 37 . Moreover, it was reported that Potential DNA:RNA Hybrid G-Quadruplex Sequences (PHQS) are present in > 97% of human genes, and these PHQS may modulate transcription 38 . Additional studies show that helicases, which are the molecular motors to unwind DNA and RNA, are involved in the active resolution of G4s.…”