Fig. 1

Characterization of scaRNA2 as an ATR-binding lncRNA and its influence on the transcriptome. A Schematic view of RIP and sequencing analysis in HCT116 cell lysate with an ATR-specific antibody. B The top 30 ATR-binding lncRNAs are shown in the column graph based on the expression level from RIP-seq. C ATR-binding lncRNAs were confirmed with a RIP-qPCR assay in HCT116 cells with an ATR-specific antibody. A representative image of immunoblotted ATR from RIP experiments is shown. D Representative images of RNA FISH staining with a specific probe for scaRNA2 in HCT116 cells. U6 was used as a positive marker for nuclear lncRNAs. Scale bar: 20 μm. E Relative scaRNA2 expression was determined with nuclear and cytoplasmic RNA extracted from HCT116 cells. F Representative images of ATR fragments immunoblotted with Flag antibody in RIP experiments. ATR-F: full-length; ATR-N: ATR N-terminal; ATR-M: ATR middle region; ATR-C: ATR C-terminal. G The relative expression of scaRNA2 measured with an RT-PCR assay in the ATR RIP complex. ***P < 0.001 compared with the IgG group. H Representative images of immunoblotted ATR from the RNA pulldown complex using biotin-labelled sense and antisense scaRNA2. I The structure of scaRNA2 predicted using RNAfold software. J Representative images of ATR from RNA pulldown experiments with scaRNA2 full-length (SCA-FL), scaRNA2 fragment 1 (SCA-F1), scaRNA2 fragment 2 (SCA-F2), and the respective antisense sequences. K GO analysis of the key signalling pathways affected by scaRNA2