Widespread remodeling of the m ⁶ A RNA-modification landscape by a viral regulator of RNA processing and export

Abstract

N6-methyladenosine (m6A) is the most abundant internal messenger RNA (mRNA) modification, contributing to the processing, stability, and function of methylated RNAs. Methylation occurs in the nucleus during pre-mRNA synthesis and requires a core methyltransferase complex consisting of METTL3, METTL14, and WTAP. During herpes simplex virus (HSV-1) infection, cellular gene expression is profoundly suppressed, allowing the virus to monopolize the host transcription and translation apparatus and antagonize antiviral responses. The extent to which HSV-1 uses or manipulates the m6A pathway is not known. Here, we show that, in primary fibroblasts, HSV-1 orchestrates a striking redistribution of the nuclear m6A machinery that progresses through the infection cycle. METTL3 and METTL14 are dispersed into the cytoplasm, whereas WTAP remains nuclear. Other regulatory subunits of the methyltransferase complex, along with the nuclear m6A-modified RNA binding protein YTHDC1 and nuclear demethylase ALKBH5, are similarly redistributed. These changes require ICP27, a viral regulator of host mRNA processing that mediates the nucleocytoplasmic export of viral late mRNAs. Viral gene expression is initially reduced by small interfering RNA (siRNA)-mediated inactivation of the m6A methyltransferase but becomes less impacted as the infection advances. Redistribution of the nuclear m6A machinery is accompanied by a wide-scale reduction in the installation of m6A and other RNA modifications on both host and viral mRNAs. These results reveal a far-reaching mechanism by which HSV-1 subverts host gene expression to favor viral replication.

An eIF3d-dependent switch regulates HCMV replication by remodeling the infected cell translation landscape to mimic chronic ER stress

“…Total DNA was isolated from HCMV-infected NHDFs using an Allprep DNA Kit according to the manufacturer’s instructions. Virus DNA was subsequently quantified by qPCR as described ( Srinivas et al, 2021 ). Briefly, relative amounts of HCMV DNA were determined by qPCR using UL44 forward and Reverse primers.…”

Nanopore-Based Detection of Viral RNA Modifications

“…Beyond human coronaviruses, the use of nanopore DRS in detecting viral RNA modifications has thus far been limited, with just two studies published to date ( 54 , 116 ). The first examined the role of m 6 A in the life cycle of adenovirus serotype 5.…”

“…Further analysis of the DRS data sets generated in the absence of METTL3 showed a significant reduction in the splicing efficiency of late viral RNAs. The second study examined the role of m 6 A in the life cycle of herpes simplex virus 1 (HSV-1) ( 116 ). Remarkably, HSV-1 induces relocalization of multiple host proteins associated with RNA modifications from the nucleus to the cytoplasm and, with this, a loss of RNA modifications, including m 6 A, from both host and viral mRNAs in a manner mediated by the viral ICP27 protein.…”

Minding the message: tactics controlling RNA decay, modification, and translation in virus-infected cells

“…How specific virus m 6 A acceptor sites impact the spectrum of discrete alternatively spliced isoforms remains unanswered. The m 6 A pathway becomes progressively less important for HSV-1 gene expression over time, as the virus ICP27 protein redistributes nuclear methyltransferase components into the cytoplasm, reducing RNA modification on host and virus mRNAs ( Srinivas et al 2021 ). This could represent another way HSV-1 limits host RNA processing, as most late virus RNAs do not contain introns.…”