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. 2015 Feb 15;29(4):362–378. doi: 10.1101/gad.253534.114

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© 2015 Hainer et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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Figure 5. — esBAF silences ncRNA expression by increasing nucleosome occupancy adjacent to NDRs. (A) Diagram of the DHS-chr2 locus with qPCR amplicons depicted. (B) Histone H3 ChIP-qPCR over the −1 nucleosome in wild-type (WT) or nucleosome SB homozygote (SB/SB) lines upon either EGFP knockdown (KD) or Smarca4 knockdown. H3 levels are expressed as a fraction of the input. Shown are the mean ± SD values of three biological replicates. (C) Randomly primed RT-qPCR of DHS transcripts in EGFP knockdown or Smarca4 knockdown cells. Expression levels were normalized to GAPDH and are shown relative to wild-type EGFP knockdown. Shown are the mean ± SD values of three biological replicates. (D) Diagram of the Ttc25 locus with qPCR amplicons depicted. (E) Histone H3 ChIP-qPCR over the −1 nucleosome in wild-type, SB heterozygote (+/SB), or SB/SB lines upon either EGFP knockdown or Smarca4 knockdown. Data are depicted as in B. (F) Randomly primed RT-qPCR of antisense transcripts in EGFP knockdown (E) or Smarca4 knockdown (S) cells, as in C. Statistical significance of alterations in expression or occupancy is indicated. (*) P < 0.05; (**) P < 0.01; (ns) not significant.