G4 Structures in Control of Replication and Transcription of rRNA Genes.

Kateřina Havlová,Jiří Fajkus

doi:10.3389/fpls.2020.593692

Abstract

Genes encoding 45S ribosomal RNA (rDNA) are known for their abundance within eukaryotic genomes and for their unstable copy numbers in response to changes in various genetic and epigenetic factors. Commonly, we understand as epigenetic factors (affecting gene expression without a change in DNA sequence), namely DNA methylation, histone posttranslational modifications, histone variants, RNA interference, nucleosome remodeling and assembly, and chromosome position effect. All these were actually shown to affect activity and stability of rDNA. Here, we focus on another phenomenon – the potential of DNA containing shortly spaced oligo-guanine tracts to form quadruplex structures (G4). Interestingly, sites with a high propensity to form G4 were described in yeast, animal, and plant rDNAs, in addition to G4 at telomeres, some gene promoters, and transposons, suggesting the evolutionary ancient origin of G4 as a regulatory module. Here, we present examples of rDNA promoter regions with extremely high potential to form G4 in two model plants, Arabidopsis thaliana and Physcomitrella patens. The high G4 potential is balanced by the activity of G4-resolving enzymes. The ability of rDNA to undergo these “structural gymnastics” thus represents another layer of the rich repertoire of epigenetic regulations, which is pronounced in rDNA due to its highly repetitive character.

Highlights

Among many potential reasons to become interested in genes encoding ribosomal RNA is the possibility to study the wide range of regulatory mechanisms used to control their expression and genomic stability
E.g., S. cerevisiae (Bayev et al, 1980) or the moss Physcomitrella patens (Goffova et al, 2019), ribosomal DNA (rDNA) units comprise 5S ribosomal RNA (rRNA) genes inserted in the intergenic spacers between individual 18S-5.8S-25S transcription units. 5S rRNA is not present in the primary RNA Pol I transcript but is transcribed by RNA Pol III
Besides RNA Pol I and – in some cases – RNA Pol III promoters, intergenic spacers show the presence of additional promoters, which may promote transcription by RNA Pol I or II, giving rise to non-codingRNAs affecting rRNA expression (Doelling et al, 1993; Mayer et al, 2006; Cesarini et al, 2010; Earley et al, 2010; Agrawal and Ganley, 2018)

Summary

Structures in Control of Replication and Transcription of rRNA Genes

Reviewed by: Zhong-Hui Zhang, South China Normal University, China Hao Wang, South China Agricultural University, China. We understand as epigenetic factors (affecting gene expression without a change in DNA sequence), namely DNA methylation, histone posttranslational modifications, histone variants, RNA interference, nucleosome remodeling and assembly, and chromosome position effect. All these were shown to affect activity and stability of rDNA. Sites with a high propensity to form G4 were described in yeast, animal, and plant rDNAs, in addition to G4 at telomeres, some gene promoters, and transposons, suggesting the evolutionary ancient origin of G4 as a regulatory module. We present examples of rDNA promoter regions with extremely high potential to form G4 in two model plants, Arabidopsis thaliana and Physcomitrella patens.

INTRODUCTION

CONCLUSION