G-quadruplex forming sequences in the genome of all known human viruses: a comprehensive guide

Enrico Lavezzo; Michele Berselli; Ilaria Frasson; Rosalba Perrone; Giorgio Palù; Alessandra R. Brazzale; Sara N. Richter; Stefano Toppo

The analysis is performed at two distinct levels, globally for each viral genome and individually for each detected G4 pattern. First, we asked the following: is the number of putative G4s found in a viral genome simply due to chance, hence trivially reflecting genomic G/C content? Are putative G4s scattered on the genome or preferentially found in regulatory regions? To address these questions, we collected the whole viral genomes deposited in databanks, we clustered them in multiple sequence alignments, and searched for the presence of G4s looking for their conservation in variable/constant genomic regions. The results were compared with an in silico generated set of simulated genomes containing the same nucleotide composition of the corresponding real ones. Results show that many viruses have a highly significant content of putative G4s and their distribution is not random but rather peculiar to specific genomic regions (e.g. coding sequences, repeats, regulatory regions). Once attested that the presence of putative G4s is significant for some viruses, we further analyzed every single identified G4 in a virus species for its conservation across virus strains, as shown in Figure 1 reporting the data analysis workflow. The detailed information on the putative G4s present in each human virus is available in an easily accessible web site with interactive graphics for the straightforward interpretation and navigation of the data (http://www.medcomp.medicina.unipd.it/main_site/doku.php?id=g4virus). author/funder. All rights reserved. No reuse allowed without permission.