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. 2016 Nov 9;20(5):666-673.
doi: 10.1016/j.chom.2016.10.002. Epub 2016 Oct 20.

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

Gianluigi Lichinchi  1 , Boxuan Simen Zhao  2 , Yinga Wu  1 , Zhike Lu  2 , Yue Qin  3 , Chuan He  2 , Tariq M Rana  4
Affiliations

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

Gianluigi Lichinchi et al. Cell Host Microbe. .

Abstract

Infection with the flavivirus Zika (ZIKV) causes neurological, immunological, and developmental defects through incompletely understood mechanisms. We report that ZIKV infection affects viral and human RNAs by altering the topology and function of N6-adenosine methylation (m6A), a modification affecting RNA structure and function. m6A nucleosides are abundant in ZIKV RNA, with twelve m6A peaks identified across full-length ZIKV RNA. m6A in ZIKV RNA is controlled by host methyltransferases METTL3 and METTL14 and demethylases ALKBH5 and FTO, and knockdown of methyltransferases increases, while silencing demethylases decreases, ZIKV production. YTHDF family proteins, which regulate the stability of m6A-modified RNA, bind to ZIKV RNA, and their silencing increases ZIKV replication. Profiling of the m6A methylome of host mRNAs reveals that ZIKV infection alters m6A location in mRNAs, methylation motifs, and target genes modified by methyltransferases. Our results identify a mechanism by which ZIKV interacts with and alters host cell functions.

Keywords: 2′-O methylation; Zika virus; m(6)A methylation; methyltransferases.

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Conflict of interest statement

The authors declare that they have no conflicts of interest.

Figures

Figure 1
Figure 1. ZIKV RNA Contains m6A and 2′-O-Me Modifications, and Methylation is Regulated by Host METTL3, METTL14, and ALKBH5
(A) LC-MS/MS quantification of m6A and 2′-O-Me modifications on all four bases of ZIKV genomic RNA (RNA, 50 ng/sample). Data are expressed as the ratio of modified to unmodified bases (m6A/A, Am/A, Gm/G, Um/U, and Cm/C). N = 3. (B) m6A-seq of ZIKV RNA showing the distribution of m6A reads mapped to the ZIKV genome (red line). The baseline signal from input samples is shown as a black line, and the m6A peaks are shown as blue rectangles along the x-axis. A schematic diagram of the ZIKV genome is shown below to indicate the location of the m6A-enriched sequences. Data are representative of n = 3 determinations. (C) Modulation of ZIKV RNA methylation by METTL3/METTL14 and ALKBH5. 293T cells were transfected with a non-targeting control shRNA (NTC) or shRNAs targeting METTL3, METTL14, ALKBH5 or FTO (knockdown, KD). RNA was isolated by Me-RIP and quantified by qRT-PCR. N = 3 (D) Localization of METTL3, METTL14, and ALKBH5 in the nucleus and cytoplasm of ZIKV-infected cells. Nuclear and cytoplasmic fractions of mock- or ZIKV-infected 293T cells were subjected to western blot analysis using antibodies against METTL3, METTL14, and ALKBH5 enzymes. Histone H3 and GAPDH were probed as controls for each fraction. Data are the mean ± SEM of the indicated number of replicates. Student’s t-test: * p < 0.05, ** p < 0.005, *** p < 0.0005. See also Figure S1.
Figure 2
Figure 2. m6A RNA Methylation Modulates the ZIKV Life Cycle
(A) Enhancement of ZIKV replication by METTL3/METTL14 silencing and reduction by ALKBH5/FTO silencing. 293T cells expressing a non-targeting control shRNA (NTC) or shRNAs targeting METTL3, METTL14, ALKBH5 or FTO shRNA (KD) were infected with ZIKV. Supernatants were harvested 6, 12 and 24 h later for quantification of ZIKV RNA by qRT-PCR. N = 3. (B) Viral titers (PFU/ml) at 24 h post-infection. Cells were treated as described in (A). N = 3 (C) Immunostaining of viral envelope protein in cells treated as described in (A). Scale bars, 100 μm. (D) Enhancement of ZIKV RNA expression by YTHDF1–3 silencing. 293T cells were transduced with shRNAs targeting YTHDF1–3 or control shRNA. Supernatants were harvested 24 h later for quantification of ZIKV RNA by qRT-PCR. N = 5. (E) Decrease in ZIKV RNA expression by overexpression of YTHDF 1, 2, and 3 proteins. 293T cells were transfected with FLAG-tagged YTHDF1–3 or control pcDNA vectors. Supernatants were harvested 24 h later for quantification of ZIKV RNA by qRT-PCR. N = 5. (F) Binding of YTHDF1–3 proteins to ZIKV RNA. 293T cells transfected as described for (E) were immunoprecipitated with an anti-FLAG antibody and immunoblotted for FLAG proteins (top). “IN” (input) lanes contained 5% of the lysate. ZIKV RNA in the FLAG-immunoprecipitates was quantified by qRT-PCR and normalized to percentage of total intracellular ZIKV RNA (bottom). N = 3 (G) Reduction and enhancement of YTHDF2–RNA binding by RNA methylation status. 293T cells were transfected with control or FLAG-YTHDF2 overexpression vector and co-transfected with the indicated shRNAs. Lysates were immunoprecipitated with an anti-FLAG antibody and immunoblotted for FLAG protein (top). Input lanes contained 5% of the lysate. ZIKV RNA in YTHDF2 immunoprecipitates was quantified by qRT-PCR and normalized to the level in cells expressing NTC shRNA (bottom). N = 3 All data are the mean ± SEM of the indicated number of replicates. Student’s t-test * p < 0.05, ** p < 0.005, *** p < 0.0005. See also Figure S2.
Figure 3
Figure 3. ZIKV Infection Influences RNA Methylation of Host Cell Transcripts
(A) Metagene analysis of normalized m6A peak distribution along a reference mRNA. (B) Distribution of m6A peaks in the 5′-UTR (blue), coding sequence (CDS, red), exon junction (pink), and 3′-UTR (green) of host cell RNA transcripts. 293T cells were mock- or ZIKV-infected, and m6A peaks in total cellular RNA were analyzed at 24 h after infection. Charts show the proportion of m6A peaks in the indicated regions in uninfected and ZIKV-infected cells (top) and the appearance of newly emerged m6A peaks or loss of existing m6A peaks after ZIKV infection (bottom). Representative of N = 2 determinations. (C) GSEA analysis of reactome analysis of pathways associated with newly emerged m6A modifications (top, blue) and loss of existing m6A modifications (bottom, red) at 24 h after ZIKV infection of 293T cells. The top 10 enriched categories for each condition are shown. (D) Motif analysis to identify consensus sequences for m6A methylation in uninfected and ZIKV-infected 293T cells. The top 5 motifs for each are shown.
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