Fig. 3. Identification of m⁶Am-modified cellular genes altered by HIV infection.

a m⁶Am-Exo-MeRIP peaks in the 5′UTR are decreased in PCIF1 KO cells. Metagene analysis of m⁶Am-Exo-MeRIP peaks near the transcription start site (TSS) of all expressed genes in control or PCIF1 KO Jurkat cells. b m⁶Am-Exo-MeRIP peaks in the 5′UTR are reduced in HIV-infected cells. Metagene analysis of m⁶Am-Exo-MeRIP peaks in Jurkat cell mock-infected or infected with HIV_LAI at an MOI of 4. c m⁶Am peaks are altered by HIV infection. m⁶A-MeRIP peaks were aligned to the human genome. And peaks that are located in the 5′UTR and decreased in PCIF1 KO cells were considered as high-confidence m⁶Am peaks. Of them, peaks that are decreased by HIV infection were shown as potential m⁶Am peaks changed by HIV. All the peaks from a–c were conserved peaks called from two independent samples. d HIV-changed m⁶Am genes are enriched in the category of transcriptional factors. Molecular function GO analysis was performed in the 854 m⁶Am genes changed by HIV using GSEA (http://www.gsea-msigdb.org/gsea/msigdb/annotate.jsp). e Venny plot shown the 18 HIV altered m6Am targeted transcription factors. The 854 HIV-changed m6Am genes were overlapped the 93 transcription regulatory genes and the HIV interaction database (listed in Supplementary Table 4, https://www.ncbi.nlm.nih.gov/genome/viruses/retroviruses/hiv-1/interactions/). f m⁶Am-Exo-MeRIP peak of ETS1 gene in the 5′UTR is decreased in PCIF1 KO cells and HIV-infected cells. Genome tracks of the ETS1 gene were plotted with called m⁶A peaks. The m⁶Am peaks were enlarged in the right panel. One representative of two experiments is shown. g Kinetics of ETS1 mRNA during HIV infection. ETS1 mRNA expression was quantified in MT4 cells infected with HIV_LAI at MOI 0.4 for 1, 2, or 3 days. n = 3 independent experiments. Two-sided t-test. Mean ± SD. *p = 0.039.