Extracts were sequentially passed over anti-su(Hw) and anti-Cp190 columns. Associated RNA was isolated by oligo-dT selection for polyadenylated transcripts and characterized by next generation sequencing.

Using dl as a negative control, it was shown that a chromatin-associated protein does not typically copurify with its own coding transcript in this protocol.

Polyadenylated su(Hw), Cp190, CG43338, brm, CG10555, dbr, ems, Msh6 and mute transcripts were enriched in insulator complexes containing su(Hw) and Cp190 protein. Only two of these nine transcripts overlap a su(Hw) protein ChIP peak.

Source was embryonic nuclear extract of wild-type fly line; bait produced from endogenous gene; prey produced from endogenous gene.