G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing

Abstract

Despite their central role in transcription, it has been difficult to define universal sequences associated to eukaryotic promoters. Within chromatin context, recruitment of the transcriptional machinery requires opening of the promoter but how DNA elements could contribute to this process has remained elusive. Here, we show that G-quadruplex (G4) secondary structures are highly enriched mammalian core promoter elements. G4s are located at the deepest point of nucleosome exclusion at promoters and correlate with maximum promoter activity. We found that experimental G4s exclude nucleosomes both in vivo and in vitro and display a strong positioning potential. At model promoters, impairing G4s affected both transcriptional activity and chromatin opening. G4 destabilization also resulted in an inactive promoter state and affected transition to effective RNA production in live imaging experiments. Finally, G4 stabilization resulted in global reduction of proximal promoter pausing. Altogether, our data introduce G4s as bona fide promoter elements allowing nucleosome exclusion and facilitating pause release by the RNA Polymerase II.

3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes

“…DNA G4s are stable four-stranded non-canonical structures that are highly related to promoters and transcription activation [23][24][25][26] . Further, a recent publication based on integrative analysis of multi-omics studies have provided comprehensive mechanistic insights into the function of G4s as promoter elements that reduce nucleosome density, increase the levels of active histone marks (H3K4me3 and H3K27ac), generate nucleosome arrays by positioning nucleosomes at a periodic distance to each other and facilitate pause release of Poll II into effective RNA production resulting in enhanced transcriptional activity 29 . Even though similar chromatin features were described to be induced by G4s at promoter-distal regulatory elements, such as SE 58 , no mechanistic insights were provided prior to our study elucidating the role of G4s in chromatin looping mediating longrange enhancer-promoter interactions.…”

“…A G4 is a stable nucleic acid secondary structure formed by square planes, in which four guanines located in the same plane stabilized by a monovalent cation 20,21 . While the early work about G4s mainly focused on their roles in telomeres 22 , recent studies demonstrated that G4s are both, enriched at promoters 23,24 and related to increased gene expression [25][26][27][28][29] . On the other hand, G4s were also located in gene bodies and related to reduced gene expression by inhibiting elongation of RNA polymerase 30,31 .…”

Abundance of G-Quadruplex Forming Sequences in the Hepatitis Delta Virus Genomes

“…PQS appearing at higher thresholds have a higher propensity to fold into G4s and form very stable structures. 17 The raw data for all genomes analyzed are in Supporting Information 01, which also provides information on NCBI accession numbers, length, GC count, percentage GC genome content, and the number and frequency of PQS.…”