Barrier-to-Autointegration Factor 1 Protects against a Basal cGAS-STING Response

Abstract

Although the pathogen recognition receptor pathways that activate cell-intrinsic antiviral responses are well delineated, less is known about how the host regulates this response to prevent sustained signaling and possible immune-mediated damage. Using a genome-wide CRISPR-Cas9 screening approach to identify host factors that modulate interferon-stimulated gene (ISG) expression, we identified the DNA binding protein Barrier-to-autointegration factor 1 (Banf1), a previously described inhibitor of retrovirus integration, as a modulator of basal cell-intrinsic immunity. Ablation of Banf1 by gene editing resulted in chromatin activation near host defense genes with associated increased expression of ISGs, including Oas2, Rsad2 (viperin), Ifit1, and ISG15. The phenotype in Banf1-deficient cells occurred through a cGAS-, STING-, and IRF3-dependent signaling axis, was associated with reduced infection of RNA and DNA viruses, and was reversed in Banf1 complemented cells. Confocal microscopy and biochemical studies revealed that a loss of Banf1 expression resulted in higher level of cytosolic double-stranded DNA at baseline. Our study identifies an undescribed role for Banf1 in regulating the levels of cytoplasmic DNA and cGAS-dependent ISG homeostasis and suggests possible therapeutic directions for promoting or inhibiting cell-intrinsic innate immune responses. IMPORTANCE Although the interferon (IFN) signaling pathway is a key host mechanism to restrict infection of a diverse range of viral pathogens, its unrestrained activity either at baseline or in the context of an immune response can result in host cell damage and injury. Here, we used a genome-wide CRISPR-Cas9 screen and identified the DNA binding protein Barrier-to-autointegration factor 1 (Banf1) as a modulator of basal cell-intrinsic immunity. A loss of Banf1 expression resulted in higher level of cytosolic double-stranded DNA at baseline, which triggered IFN-stimulated gene expression via a cGAS-STING-IRF3 axis that did not require type I IFN or STAT1 signaling. Our experiments define a regulatory network in which Banf1 limits basal inflammation by preventing self DNA accumulation in the cytosol.

Nuclear cGAS: guard or prisoner?

“…Linker histones are not the only proteins restricting accessibility of cGAS to nuclear DNA, as the barrier‐to‐autointegration factor 1 (BAF1) can also dynamically outcompete cGAS for DNA binding upon acute loss of nuclear envelope integrity (Guey et al , 2020; Ma et al , 2020) (Fig 5D). BAF1 is a small (10 kDa) chromatin‐bound protein essential for mitosis, nuclear assembly, and the DNA damage response (Haraguchi et al , 2001; Margalit et al , 2005; Haraguchi et al , 2008; Jamin & Wiebe, 2015).…”

Di-phosphorylated BAF shows altered structural dynamics and binding to DNA, but interacts with its nuclear envelope partners

“…It was first identified as a host protein that captures viral DNA ( 1 , 9–11 ). It binds genomic self-DNA upon loss of nuclear membrane integrity, thus outcompeting cGAS and preventing aberrant immune response ( 12 , 13 ). However, BAF was also described as playing several essential roles during the cell cycle of metazoan cells.…”

Transfected plasmid DNA is incorporated into the nucleus via nuclear envelope reformation at telophase

“…Although BAF is expected to function as a defense against viral infection 23,57,58 , it unexpectedly assists in the integration of the human immunodeficiency virus (HIV) genome into the host genome 15,16 . In addition, a recent report showed that BAF protects against the cGAS-STING response to prevent innate immune activation 59,60 . Collectively, these data suggest that BAF can suppress the innate immune response and act to safely carry the cytosolic DNA to the next cell cycle stages by wrapping it in the NE-like membrane.…”