Viral cis-regulatory elements as sensors of cellular states and environmental cues

Abstract

To withstand a hostile cellular environment and replicate, viruses must sense, interpret, and respond to many internal and external cues. Retroviruses and DNA viruses can intercept these cues impinging on host transcription factors via cis-regulatory elements (CREs) in viral genomes, allowing them to sense and coordinate context-specific responses to varied signals. Here, we explore the characteristics of viral CREs, the classes of signals and host transcription factors that regulate them, and how this informs outcomes of viral replication, immune evasion, and latency. We propose that viral CREs constitute central hubs for signal integration from multiple pathways and that sequence variation between viral isolates can rapidly rewire sensing mechanisms, contributing to the variability observed in patient outcomes.

Keywords: cell signaling; cis-regulatory element; transcription factor; viral latency; viral replication; virus.

Figure 1:. Viral replication cycle and transcriptional control

Schematic of a representative replication cycle for retroviruses and dsDNA viruses. Following initial infection, retroviruses and most dsDNA viruses localize to the nucleus. Here, these viruses may transition to latency through episome formation (e.g. herpesviruses) or via integration into the host genome (e.g. retroviruses and non-enveloped dsDNA viruses). Internal or external cues can promote reactivation from latency or direct entry to the lytic cycle, marked by activation of viral transcription followed by assembly and release of new virions.

Figure 2:. Pathways sensed by viral CREs

Viral CREs sense immune activation, stress, metabolic states, as well as cell proliferation and differentiation by recruiting host TFs downstream of these pathways.

Figure 3:. Viral CREs as signal integration hubs

(A) Consequences of TF and vTR recruitment to viral CREs, including remodeling of local chromatin structure, modification of histone marks or DNA methylation, and alteration of RNA Pol II recruitment, pause-release, and elongation. (B) Mechanisms for signal integration including cooperative or antagonistic recruitment of TFs to viral CREs, co-recruitment of cofactor by different TFs, and functional synergism or antagonism between cofactors.

Figure 4:. Evolution of viral CREs

(A) Schematic of TF binding variation between CREs from different isolates due to single nucleotide or indel variants. (B) Scatter plot showing the average number of TF binding sites (TFBS) versus the standard deviation across isolates for TFs that bind a viral CRE. (C) Viral dendrogram where isolates are colored based on the number TF2 binding sites in a CRE. The heatmap shows the fraction of isolates in each subclade that contains a binding site for TF2 at each position in the CRE.

Figure I:. Methods to identify and characterize viral CREs

(A) Viral CREs are often predicted based on their location upstream of protein coding sequences, using 5’RACE or CAGE to identify transcription start sites, and using CRE bashing reporter assay experiments. (B) Binding of TFs to viral CREs can be determined using yeast one-hybrid assays, ChIP or ChIP-seq, DNase footprinting in the presence of a TF or nuclear extract, and using electrophoretic mobility shift assay (EMSA). The regulatory effect of these TFs is often measured in reporter or functional assays overexpressing or knocking down the TF or mutating TF binding sites.