Viral Nucleases Induce an mRNA Degradation-Transcription Feedback Loop in Mammalian Cells

Abstract

Gamma-herpesviruses encode a cytoplasmic mRNA-targeting endonuclease, SOX, that cleaves most cellular mRNAs. Cleaved fragments are subsequently degraded by the cellular 5'-3' mRNA exonuclease Xrn1, thereby suppressing cellular gene expression and facilitating viral evasion of host defenses. We reveal that mammalian cells respond to this widespread cytoplasmic mRNA decay by altering RNA Polymerase II (RNAPII) transcription in the nucleus. Measuring RNAPII recruitment to promoters and nascent mRNA synthesis revealed that the majority of affected genes are transcriptionally repressed in SOX-expressing cells. The transcriptional feedback does not occur in response to the initial viral endonuclease-induced cleavage, but instead to degradation of the cleaved fragments by cellular exonucleases. In particular, Xrn1 catalytic activity is required for transcriptional repression. Notably, viral mRNA transcription escapes decay-induced repression, and this escape requires Xrn1. Collectively, these results indicate that mRNA decay rates impact transcription and that gamma-herpesviruses use this feedback mechanism to facilitate viral gene expression.

Graphical abstract

Figure 1

Enhanced mRNA Turnover in the Cytoplasm Suppresses RNAPII Transcription (A) NIH 3T3 cells were infected with WT or ΔHS MHV68 for 24 hr, whereupon 500 μM of 4sU was added for 30 min and labeled RNA was isolated by biotin-streptavidin pull-down. Levels of newly transcribed RNA were measured by RT-qPCR. All samples were normalized to 18S, and mock-infected levels were set to 1. (B) 4sU was added to NIH 3T3 cells for 30 min, followed by fractionation into nuclear and cytoplasmic fractions. Purified 4sU-labeled RNA was quantified by RT-qPCR for the indicated genes. (C) NIH 3T3 cells were infected with MHV68 for 24 hr and 4sU-labeled for 30 min. RNA was quantified as above using intron-specific primers. (D) HEK293T cells were transfected with the indicated plasmids for 24 hr, then labeled with 4sU for 30 min prior to RNA purification and quantification by RT-qPCR. (E) HEK293T cells were transfected as above for 24 hr, and cells were crosslinked prior to analysis of RNAPII occupancy at the indicated promoters by ChIP followed by qPCR. No antibody was added to the IgG sample. (F) iSLK cells latently infected with WT or P176S KSHV were reactivated for 48 hr with dox and sodium butyrate. 4sU was added for 30 min, and labeled RNA was isolated and quantified by RT-qPCR. Error bars represent the mean with SEM of ≥ 3 independently performed experiments. Student’s t test was used to determine statistical significance. ^∗p ≤ 0.05, ^∗∗p ≤ 0.005, ^∗∗∗p ≤ 0.0005.

Figure 2

Cellular Exonucleases Are Required for the mRNA Decay-Transcription Feedback Mechanism (A–E) HEK293T cells with dox-inducible Xrn1, Dis3L2, or Ccr4 shRNAs were mock or dox-treated for 4 days. (A) Xrn1 knockdown cells were transfected with the indicated plasmid for 24 hr. Level of RNAPII at the Gapdh promoter was measured by ChIP followed by qPCR. The level of protein knockdown was assessed by western blot with the indicated antibodies, with actin serving as a loading control. (B) Xrn1 was knocked down in cells lacking the viral nuclease, and RNAPII ChIP was performed at the Gapdh and Rplp0 promoters. (C) RNAPII ChIP at the Gapdh promoter was performed on cells with and without Dis3L2 knockdown. (D) Dis3L2 was knocked down in cells lacking the viral nuclease, and RNAPII ChIP was performed at the Gapdh and Rplp0 promoters. (E) RNAPII ChIP for Gapdh was performed on cells with Ccr4 knockdown, both alone and in combination with siRNA-mediated knockdown of Pan2. (F) Ccr4 was knocked down alone and in combination with Pan2 in cells lacking the viral nuclease, and RNAPII ChIP was performed at the Gapdh and Rplp0 promoters. Error bars represent the mean with SEM of ≥ 3 independently performed experiments. ^∗p ≤ 0.05, ^∗∗p ≤ 0.005, ^∗∗∗p ≤ 0.0005.

Figure 3

Xrn1 Catalytic Activity Is Required for Reduced RNAPII Transcription (A) Diagram showing the complementation assay procedure. HEK293T cells with dox-inducible Xrn1 were mock or dox-treated for 4 days, whereupon cells were transfected with plasmids expressing WT or the catalytically dead D208A Xrn1 mutant, as well as with muSOX or muSOX D219A. (B) Following the above procedure, ChIP and qPCR were performed to measure RNAPII recruitment to the human Gapdh promoter. (C) NIH 3T3 cells were infected with WT or ΔHS MHV68 for 24 hr. RNAPII recruitment to the Rpl37 and ActB promoters and internal genes was measured by ChIP followed by qPCR. (D) Ser2 ChIP was performed using the internal Rpl37 and ActB promoters. The level of Ser2-phosphorylated RNAPII was determined by dividing the Ser2 values over the total RNAPII within the same region of the gene. (E) Diagram showing procedure for calculating transcription elongation rates. DRB was added to infected cells for 3 hr, then removed, and cells were 4sU-labeled. Conditions tested include no DRB treatment (NT), DRB without washout (DRB), 8 min 4sU after DRB washout (8 min), and 12 min 4sU after DRB washout (12 min). (F) Relative kb/min calculated by normalizing RNA levels to NT and DRB and subtracting the amount of 4sU-labeled RNA at 10 kb (distal) at 12 min from the amount at 1 kb (proximal) at 8 min. Error bars represent the mean with SEM of ≥ 3 independently performed experiments. ^∗p ≤ 0.05, ^∗∗p ≤ 0.005, ^∗∗∗p ≤ 0.0005.

Figure 4

Cellular Transcriptional Changes Occur throughout the mRNA Transcriptome (A) Libraries were generated from purified 4sU-labled RNA isolated from NIH 3T3 cells infected with WT or ΔHS MHV68 for 24 hr, and sequenced on an Illumina platform. (B) All genes that aligned to the mouse genome (13,516 genes) were graphed with differential log2 expression values on the y axis and read counts on the x axis. The percentages of genes showing > 1.5-fold increased or decreased expression during infection relative to uninfected cells are indicated. (C) Venn diagram showing genes that scored as significantly changed during a WT or ΔHS infection, with the overlap region depicting the number of genes significantly reduced or increased in both infections. (D) Results from a GO-term analysis using DAVID bioinformatics software on the genes found to be increased upon both WT and ΔHS infection.

Figure 5

Viral mRNAs Escape Degradation-Induced Transcriptional Repression (A) 4sU-seq data were used to determine the differential expression of all viral genes between WT and ΔHS infection. Log2 expression changes of WT/ΔHS are shown on the x axis and ORFs are listed in genome order on the y axis. Values outside the shaded box indicate a significant fold change. (B) Validations of 4sU-seq data by RT-qPCR of purified 4sU-labeled RNA isolated from cells infected with the WT or ΔHS MHV68. Results are normalized to 18S and ΔHS values are set to 1. (C) ChIP for total RNAPII was performed on NIH 3T3 cells infected with WT or ΔHS MHV68, and the % input values of the viral M1 and ORF8 promoters were compared. (D) iSLK cells latently infected with WT or P176S KSHV were reactivated for 48 hr with dox and sodium butyrate, then labeled with 4sU for 30 min prior to RNA isolation. RNA levels were compared by RT-qPCR for the indicated viral genes. Error bars represent the mean with SEM of ≥ 3 independently performed experiments.

Figure 6

Xrn1 Positively Influences Viral Transcription during Widespread mRNA Decay (A) NIH 3T3 cells were infected with WT or ΔHS MHV68 for 25 hr, whereupon actinomycin D (ActD) was added to halt transcription, and RNA was harvested at 0, 2, 4, 6, and 8 hr post-addition. RT-qPCR was used to measure the abundance of the viral M1 and vtRNA1 transcripts, and values were normalized to 18S. (B and C) Complementation assays were performed as described in Figure 3A, except that following 4 days of dox treatment, cells were infected with WT or ΔHS MHV68 for 24 hr. For complementation, exogenous Xrn1 was transfected into the cells prior to MHV68 infection. RT-qPCR was performed for M1 or vtRNA1 on steady-state levels, all samples were normalized to 18S, and ΔHS levels were set to 1 for each condition. (D) RNAPII ChIP was performed on infected HEK293T cells with or without Xrn1 knockdown. Viral genes M1 and ORF54 were analyzed. (E) 293T cells containing dox-inducible shRNAs against Ccr4 were mock or dox treated for 4 days, whereupon levels of the viral M1 mRNA were measured by RT-qPCR. Error bars represent the mean with SEM of ≥ 3 independently performed experiments. ^∗p ≤ 0.05, ^∗∗p ≤ 0.005, ^∗∗∗p ≤ 0.0005.