Fig. 4

ALKBH3 is recruited to locations with single-stranded DNA. a ALKBH3 profiles at the two groups of ALKBH3 bound promoters. Group I is characterized by a strong binding upstream of the transcription start site. Group II shows a weaker binding downstream of the TSS and a ‘shoulder’ upstream of the TSS. b Profiles of ALKBH3 and RNA polymerase II at of all promoters (excluding group I promoters) divided in quintiles according their gene expression. ALKBH3 and RNA polymerase II profiles show an almost linear correlation, supporting interdependency. c Group I promoters are characterized by a strong occupancy of the TFIIH helicase XPB/ERCC3 (data from HT1080 cells). The profile of XPB at group I promoters culminates upstream of the transcription start site, similar to ALKBH3. The heatmaps show the comparison of ALKBH3 (identical to Fig. 1b) and XPB at all ALKBH3 bound promoters (−1,500/+1,500 bp). d Overview of putative ALKBH3 targets in PC3 cells and the respective ALKBH3 enrichment and cellular frequency. The left panel shows a speculative formation of an atypical transcription initiation bubble at group I promoters, potentially explaining the strong recruitment of ALKBH3. See also Additional file 1: Figure S4