G4 Structures in Control of Replication and Transcription of rRNA Genes

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.

Mosaic Arrangement of the 5S rDNA in the Aquatic Plant Landoltia punctata (Lemnaceae)

“…We then used the pqsfinder algorithm ( Labudová et al, 2020 ) to determine the potential for forming regulatory G-quadruplex structures (G4), which consist of four guanine-rich regions held together via unconventional base pairing ( Lipps and Rhodes, 2009 ; Havlová and Fajkus, 2020 ). We discovered that the TG dinucleotide is a part of the 3' end of the sequence TGGGA on the reverse strand within the −37 to −8 sequence predicted to form a G4 structure, just upstream of the 5S rDNA gene ( Figure 4B ).…”

The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units

“…The 5′-ETS (region IV), a 1,255-bp region in Pistia , contains clusters of 17-bp repeats downstream of the TIS and a gradually increasing GC content toward the beginning of the 18S rDNA, averaging 75.1% within the 600-bp region adjacent to the 18S rDNA gene. This GC-enriched region may form G4 structures ( Figure 2 ), possibly contributing to the regulation of transcription and replication of rDNA ( Havlová and Fajkus, 2020 ). BLAST analysis of the Pistia 5′-ETS sequence upstream of the 18S gene, an IGS region of high similarity between species of the same family ( Cordesse et al, 1993 ; Borisjuk et al, 1997 ; Volkov et al, 2017 ), did not reveal any homologs in GenBank.…”

Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses

“…The high nonviral reads from RNA-Seq is well documented in other studies [ 5 , 55 , 56 ]. Notably, the variations of nonviral targets within the RNA-Seq data for instance within our three hosts (field pea, faba beans and lentil) from 29% to 90.65% could be associated with the genetic variation of rRNA present in each plant species [ 57 ]. Admittedly, as mentioned above, RNA-Seq is versatile for entire virome profiling than targeted approaches but its costs still remain prohibitive for routine diagnostic adoption.…”