Figure 3.

Dynamic density change, distribution, and modification motif of m6A mRNA during infection. (A) Enrichment analysis of IP reads around start and stop codons in duckling liver infected with virulent CH and attenuated CH60 strains. During infection, the m6A peak read density in livers infected with the attenuated CH60 strain is much higher than that in livers infected with the virulent CH strain. Each time point after infection is indicated by a different colour. (B–C) This m6A modification in attenuated CH60-infected livers is dominantly distributed near the start codon position and near the 5’UTR. (C) The m6A distribution of input and IP samples among all samples is analyzed. Inputs and IPs of CH60- or CH-infected livers are displayed in different colours. The m6A density distribution at different infection times is displayed. (D) Gene region analysis indicated that the 5’UTR and antisense region are highly modified by m6A (lower panel). Three biological replicates of both m6A IP samples and Input samples were used to calculate m6A IP/Input ratio. The P values were determined using Student’s unpaired t test. *P < 0.05, **P < 0.01. (E) The number of peaks and genes with m6A modification detected in both DHAV CH60- and CH strain-infected livers. The m6A modification is highly enriched in the exonic region. (F) Distribution of m6A modification in different gene regions. The entire span of a gene, including the 5’UTR, coding sequence (CDS), 3’UTR, and certain noncoding exons, can be modified by m6A. (G) The top five enriched m6A motifs are listed and detected by HOMER. As shown, GAAGAAG was the top m6A-modified motif in both the CH60- and CH strain-infected groups.