High throughput characterization of the m6A demethylase FTO by CLIP and RNAseq

We performed the CLIP-seq analysis of RNAs bound by 3xFLAG-tagged FTO protein stably expressed in human HEK293 cells. In parallel, we profiled the transcriptome of the same cells by RNA-seq, which was used for CLIPseq bioinformatics analysis as an input. The CRISPR-Cas9 was used to knock-out FTO expression in HEK293 to compare the mRNA expression changes and exon usage between FTO KO and WT cell lines. All experiments were performed in three replicates. Overall design: CLIP-seq analysis of RNAs bound by 3xFLAG-tagged FTO protein and RNA-seq of wildtype and FTO KO HEK293 cells.