Messenger RNA associates with gypsy insulator complexes.

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Messenger RNA associates with gypsy insulator complexes. Messenger RNA associates with gypsy insulator complexes. (A) Purification scheme for gypsy insulator‐associated RNA. Embryo nuclear extracts were passed sequentially over α‐Su(Hw) and α‐CP190 immunoaffinity columns. Purified RNA was 5′ end labelled and purified by electrophoresis. 35‐ and 55‐nt bands were excised from NE and IP lanes, directionally cloned and sequenced. (B) Scatterplot of annotated genes corresponding to transcripts identified in total unbound and Su(Hw)/CP190 RIP. Mean scaled tag count across replicates of total unbound input (x‐axis) and Su(Hw)/CP190 RIP (y‐axis) for each gene is calculated as the mean number of tags across replicates mapping to the entire gene body, scaled by library size. Transcripts corresponding to su(Hw) and Cp190 (padj<0.02, red) are indicated. All other transcripts (black) correspond to padj=1. Note that genes displaying similar average fold‐enrichment to su(Hw) and Cp190 show high variance across biological replicates, resulting in lack of statistical significance. The su(Hw), Cp190 and RpL32 transcripts are circled. (C) Reads mapping to the su(Hw) or neighbouring RpII15 locus from total unbound (2.4 M read alignments) or Su(Hw)/CP190 RIP (1.3 M read alignments) libraries. The height of each Watson (blue) and Crick (red) read is scaled to respective library size. Thin bars interrupting reads span splice junctions. (D) Reads mapping to the Cp190 locus as in (C). CP190, Centrosomal protein 190; IP, immunopurified; NE, nuclear extract; RIP, RNA immunoprecipitation; Su(Hw), Suppressor of Hairy wing. Leah H Matzat et al. EMBO Rep. 2013;14:916-922 © as stated in the article, figure or figure legend