Fig. 2: m6A-Seq analysis of CHIKV RNA reveals a single putative m6A peak.
From: N6-methyladenosine modification is not a general trait of viral RNA genomes
a Most significantly enriched motif identified in conserved m6A peaks across cellular poly(A) + RNA in CHIKV-infected cells. HOMER software was used for motif analysis. b Genome browser tracks showing mapped CHIKV reads (strain LR2006-OPY1) for input and m6A-IP samples. The reads are scaled to the same read depth against the viral genome using counts per million normalization. Both biological replicates for each condition (input and m6A-IP) are displayed within each track. The common m6A peak identified by m6aViewer and MACS2 is indicated. The fold change of m6A-IP/input, averaged from two replicates is shown above the called m6A peak. HEK293T cells were infected for 12 h at an MOI of 4. The 11 qPCR amplicons generated by the 11 primer sets (CHIKV_1 to CHIKV_11) are indicated. The qPCR amplicon spanning the CHIKV m6A peak is also shown. c Genome browser tracks showing mapped reads for input and m6A-IP samples across the SLC39A14 transcript. The reads are scaled against the merged genome using counts per million (CPM) normalization. The SLC39A14 qPCR amplicons used as negative and positive controls in m6A-IP-qRT-PCRs are also indicated. d Violin and box plot of the log2 fold-change (log2FC) distribution of all 23,539 m6aViewer-called cellular peaks in CHIKV-infected HEK293T cells, conserved between two independent replicates. The SLC39A14 and CHIKV peaks are indicated by red dots. The boxplot shows the median (middle line), 25–75th percentile values and 1.5x interquartile range, while the overlaid violin plot shows the full data distribution. e m6A-IP-qRT-PCRs performed to validate the putative m6A peak identified via m6A-Seq. HEK293T cells were infected for 12 h at an MOI of 4. Total RNA was fragmented to 100–200 nt. The bar chart shows mean values from 3 m6A-IPs from 3 independent infections with the error bars showing SD. The CHIKV_10 and CHIKV_11 primer sets were used as negative controls amplifying regions without m6A enrichment, according to our m6A-Seq data. n.s. not significant (p > 0.05, using the two-tailed t-test). Source data are provided with this paper.
