HITS-CLIP analysis of ALKBH8 revealed non-tRNA types of RNA. (A) Top-scoring bound RNAs according to CPM (Supplemental Table S2). Targets that were recapitulated by RIP-seq analysis are colored gray. Genes are listed in numerical and alphabetical order. (B) Representation of ALKBH8 binding to selected genomic regions of RNA. (C) RT-PCR analysis of selected RNAs coprecipitated with ALKBH8. GFP is the control HEK293T cell line that expresses FLAG-GFP. ALKBH8 is the HEK293T stable cell line that expresses FLAG-ALKBH8. The coprecipitated RNA was reverse transcribed, the targets were amplified using gene-specific primers, and the amplicons were resolved on agarose gel. The faster migrating bands in the 7SK panel correspond to the primer-dimer signal. The slower migrating PCR product in the SNORD34 panel is an unspecific PCR product.
