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. Author manuscript; available in PMC: 2017 Jul 14.
Published in final edited form as: Nat Struct Mol Biol. 2014 Jun 15;21(7):585–590. doi: 10.1038/nsmb.2842

Figure 4.

Figure 4

cMyc-binding sites of lncRNAs affect their sensitivity to Dcr loss. (a) cMyc-binding-site enrichment in Dcr-dependent lncRNA genes. Top inset, schematic of bioinformatics strategy. TF, transcription factor; DB, database. Bottom inset, cMyc downregulation in Dcr-KO mESCs. RPKM, reads per kilobase per million. (b) cMyc ChIP-seq binding data, plotted alongside the expression change of lncRNAs in Dcr KO. (c) Cumulative distribution functions (cdfs) of log2 fold change (LFC) for lncRNA genes (dark red) and protein-coding genes (blue) between cMycflox/flox (denoted f/f) and cMyc−/− mESCs. lncRNA genes with cMyc-binding sites are shown in red, and lncRNA genes without cMyc-binding sites are shown in gray. lncRNAs (especially those encoded by lncRNA genes with cMyc-binding sites) are significantly downregulated in cMyc−/− mESCs relative to protein-coding genes (P < 2.2 × 10−16 by two-sided Wilcoxon rank-sum test, n = 2,229 known lncRNA transcripts). (d) NanoString measurement of expression of 102 lncRNAs in three lines of Dcr-KO mESCs (K01–K03, normalized to WT, as in Fig. 2b) and cMyc rescue in Dcr KO (normalized to the control plasmid). The blue and yellow colors in the heat map indicate down- and upregulated lncRNAs respectively (n = 2 cultures). (e) Changes in intensity of H3K4me3 (left) and H3K36me3 (right) at lncRNA genes with (red) or without (gray) cMyc-binding sites between WT and Dcr-KO mESCs.