Nucleosome DNA unwrapping does not affect prototype foamy virus integration efficiency or site selection.

Randi M Mackler,Nathan D Jones,Richard Fishel,Anne M Gardner,Cecil J Howard,Kristine E Yoder,Miguel A Lopez,Michael Nevels

doi:10.1371/journal.pone.0212764

Abstract

Eukaryotic DNA binding proteins must access genomic DNA that is packaged into chromatin in vivo. During a productive infection, retroviral integrases (IN) must similarly interact with chromatin to integrate the viral cDNA genome. Here we examine the role of nucleosome DNA unwrapping in the retroviral integrase search for a target site. These studies utilized PFV intasomes that are comprised of a tetramer of PFV IN with two oligomers mimicking the viral cDNA ends. Modified recombinant human histones were used to generate nucleosomes with increased unwrapping rates at different DNA regions. These modifications included the acetylmimetic H3(K56Q) and the chemically engineered H4(K77ac, K79ac). While transcription factors and DNA damage sensors may search nucleosome bound DNA during transient unwrapping, PFV intasome mediated integration appears to be unaffected by increased nucleosome unwrapping. These studies suggest PFV intasomes do not utilize nucleosome unwrapping to search nucleosome targets.

Highlights

Eukaryotic biology is dependent on proteins interacting with DNA in the context of chromatin
prototype foamy virus (PFV) intasomes covalently join the viral DNA ends (vDNA) ends to a target DNA in two kinetically distinct strand transfer reactions separated by 4 bp of target DNA, termed concerted integration (Fig 3)
We have used recombinant human histones with specific posttranslational modifications (PTMs) that increase nucleosome positioning sequence (NPS) unwrapping to dissect the mechanism of PFV intasome target search

Summary

Introduction

Eukaryotic biology is dependent on proteins interacting with DNA in the context of chromatin. Human immunodeficiency virus 1 (HIV-1) and murine leukemia virus (MLV) integration were found to favor DNA wrapped in nucleosomes in vitro and in vivo [9,10,11,12]. Since those initial studies, host proteins that serve as integration cofactors have been identified, including LEDGF/p75 for HIV-1 and BET proteins for MLV [2, 7, 13, 14]. Host cofactors of integration had not been described at the time

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Conclusion