Extended Data Fig. 7. Promoters of lncRNAs and mRNAs have enhancer-like functions.

(a) Allele-specific GRO-seq signal for clones with the indicated modifications at the Bendr locus. Only reads specifically mapping to one of the two alleles are shown. Y-axis scale represents normalized read count and is the same for all tracks. (b) Allele-specific p(A)+ RNA expression for genetic modifications at the linc1405, Snhg17, Gpr19, and Slc30a9 loci. Bars: Average RNA expression on modified compared to unmodified (wild-type) alleles. Error bars: 95% CI for the mean (n ≥ 2 alleles, see Table S1). Gray arrows indicates distance from the targeted locus promoter to the affected neighboring gene. We note that, based on their location, the Snhg17 and Gpr19 pAS insertions likely allow more substantial splicing and transcription; for these loci, it is clear that the majority of the transcript is dispensable but it is possible that transcription close to the promoter may be involved in the cis regulatory function. (c) Presence (gray) or absence (white) of various chromatin marks and transcription factors in mESCs in a 1.5-kb window centered on the TSS of each targeted gene. (d) Distance from each knocked-out gene to its neighboring target gene (x-axis) versus the magnitude of the effect on the expression of the neighboring gene (% compared to wild-type, y-axis). Blue genes represent those discussed in main text; gray genes are discussed in Note S5. (e) Proximity-based contacts between the linc1405 and Eomes loci (the pair of loci separated by the greatest linear distance). The y-axis shows enrichment in a sequencing-based proximity assay in which we used antisense oligos to capture linc1405 DNA and any interacting, crosslinked proximal DNA (see Methods). TAD annotations are derived from Hi-C experiments in mESCs (see Methods). Blue arrow: focal contact between the linc1405 and Eomes loci.