Figure 3.

Validation of New RNA/DNA Hybrid Interactome Candidates

(A) Workflow of RNA/DNA hybrid IP with RNase H digestion.

(B and C) HeLa genomic DNA input was either treated (+) or not (−) with RNase H before enrichment for RNA/DNA hybrids with the S9.6 antibody. Genomic RNA/DNA hybrids were incubated with nuclear extracts depleted for RNA/DNA hybrids with RNase A, followed by S9.6 IP. RNA/DNA hybrid slot blot (B) and western blot of RNA/DNA hybrid IP, probed with indicated antibodies (C).

(D–I) Genomic DNA from HeLa cells transfected with control (siCtrl) or indicated siRNAs was treated with RNase H. siTop1 (D), siDHX9 #1 (E), siWHSC1 (F), siSAFB2 (G), siDNA-PK (H), siPARP1 (I) were used. Top: RNA/DNA hybrid slot blot. Bottom: quantification of S9.6 signal. Values are normalized to the siCtrl and represent the means ± SEMs, n ≥ 3.

See also Figure S3.