About: Evolutionary selection against short nucleotide sequences in viruses and their related hosts

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An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Evolutionary selection against short nucleotide sequences in viruses and their related hosts
Creator	Siridechadilok, Bunpote Julander, Justin Tuller, Tamir Zafrir, Zohar Roopin, Modi Suphatrakul, Amporn Zarai, Yoram
source	Medline; PMC
abstract	Viruses are under constant evolutionary pressure to effectively interact with the host intracellular factors, while evading its immune system. Understanding how viruses co-evolve with their hosts is a fundamental topic in molecular evolution and may also aid in developing novel viral based applications such as vaccines, oncologic therapies, and anti-bacterial treatments. Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. These sequences cannot be explained by the coding regions’ amino acid content, codon, and dinucleotide frequencies. We specifically show that short homooligonucleotide and palindromic sequences tend to be under-represented in many viruses probably due to their effect on gene expression regulation and the interaction with the host immune system. In addition, we show that more sequences tend to be under-represented in dsDNA viruses than in other viral groups. Finally, we demonstrate, based on in vitro and in vivo experiments, how under-represented sequences can be used to attenuated Zika virus strains.
has issue date	2020-04-27(xsd:dateTime)
bibo:doi	10.1093/dnares/dsaa008
bibo:pmid	32339222
has license	cc-by-nc
sha1sum (hex)	15c6b1738b20b774b7400c66eec3d8f18d84d78b
schema:url	https://doi.org/10.1093/dnares/dsaa008
resource representing a document's title	Evolutionary selection against short nucleotide sequences in viruses and their related hosts
has PubMed Central identifier	PMC7320823
has PubMed identifier	32339222
schema:publication	DNA Res
resource representing a document's body	covid:15c6b1738b20b774b7400c66eec3d8f18d84d78b#body_text
is schema:about of	named entity 'codon' named entity 'addition' named entity 'host' named entity 'Viruses' named entity 'acid' named entity 'co-evolve' named entity 'vaccines' named entity 'Zika virus' named entity 'Understanding' named entity 'immune system' named entity 'These' named entity 'viral' named entity 'intracellular' named entity 'palindromic sequences' named entity 'amino acid' named entity 'Zika' named entity 'viruses' named entity 'virus' named entity 'molecular evolution' named entity 'viruses' named entity 'evolutionary pressure' named entity 'co-evolve' named entity 'viruses' named entity 'nucleotide sequences' named entity 'viruses' named entity 'World Health Organization' named entity 'gene expression' named entity 'ribosomal' named entity 'functional group' named entity 'wild-type' named entity 'small RNA' named entity 'nucleotides' named entity 'ZIKV' named entity 'coding region' named entity 'prokaryotic genomes' named entity 'mice' named entity 'genome' named entity 'nucleotide sequences' named entity 'virus genome' named entity 'reading frame' named entity 'protein' named entity 'effective population size' named entity 'amino-acid' named entity 'Mice' named entity 'genome' named entity 'interferon' named entity 'infection' named entity 'nucleotides' named entity 'nucleotides' named entity 'genome' named entity 'clone' named entity 'codon' named entity 'palindrome' named entity 'plasmid' named entity 'intracellular' named entity 'biological entity' named entity 'infectious agents' named entity 'mutation' named entity 'enzyme' named entity 'serum' named entity 'Gibson assembly' named entity 'cell culture' named entity 'coding regions' named entity 'P-values' named entity 'dsDNA' named entity 'mice' named entity 'ZIKV' named entity 'Zika' named entity 'DNA polymerase' named entity 'Vero cells' named entity 'weight gain' named entity 'palindrome' named entity 'randomly selected' named entity 'evolution' named entity 'ZIKV'

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