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. Author manuscript; available in PMC: 2017 Feb 4.
Published in final edited form as: Mol Cell. 2016 Jan 28;61(3):393–404. doi: 10.1016/j.molcel.2015.12.024

Figure 5. GAL10 forms lncRNA-dependent gene loops.

Figure 5

(A) Schematic of GAL10 showing restriction sites (vertical lines) and primers for Chromosome Conformation Capture (3C) (arrows). P1 and T1 correspond to the GAL1/10 promoter and GAL10 terminator, respectively, whereas F and R are internal control primers. (B-C) 3C of GAL10 in wild type, lncRNAΔ, dbp2Δ and dbp2Δ lncRNAΔ cells during a glucose to galactose shift. Samples were quantified across three biological replicates relative to the control PCR with error bars representing SEM. (B) Ethidium bromide-stained agarose gel showing representative PCR products. (C) Quantification of looping at 0, 90 and 180 min post-induction. (D-E) Chromatin immunoprecipitation (ChIP) of 3XFLAG-tagged Cyc8 in wild type, lncRNAΔ, dbp2Δ and dbp2Δ lncRNAΔ strains grown under transcriptionally repressive (+glucose) conditions. ChIP-qPCR was performed as described (Cloutier et al., 2013). Results are presented as the mean percent of input with SEM. * = p < 0.05 with respect to the lncRNAΔ strain. (F) Western blot of Cyc8-3XFLAG. Whole cell lysate was extracted and resolved by SDS-PAGE. Cyc8, G6PDH and Pgk1 were detected using antibodies specific to FLAG, G6PDH and Pgk1, respectively, from the indicted strains.