GSE134754
Mapping the targeting transcripts and binding sites of ALKBH5 by individual-nucleotide resolution UV crosslinking and immunoprecipitation-based sequencing (iCLIP-seq)
To investigate whether the ALKBH5-mediated metabolic changes via demethylation of its target mRNA(s) is important in regulating viral response,  we mapped the targeting transcripts and binding sites of ALKBH5 in the virus infected cells and uninfected cells by using iCLIP-seq. Biological replicates of iCLIP-seq confirmed that OGDH is the direct targeting transcript of ALKBH5 and the binding capacity of ALKBH5 to OGDH mRNA was decreased upon viral infection. By combining the ALKBH5-iCLIP-seq results with m6A-seq data, we identified that there are overlapped ALKBH5-iCLIP peaks and m6A-seq peaks on OGDH mRNA. Furthermore,  other mRNAs, such as GOT2 mRNA, were also the ALKBH5's targeting transcripts and m6A demethylation substrates. GOT2 is an important metabolic enzyme well known to be involved in host response to viral infection. These data demonstrated that ALKBH5-mediated metabolic rewiring via demethylation of target OGDH mRNA and other transcripts is important in regulating cellular viral replication. Overall design: Mapping the targeting transcripts and binding sites of ALKBH5 in macrophages infected with or without VSV by iCLIP-seq, two biological replicates.