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. 2019 Aug;25(8):897–904. doi: 10.1261/rna.069484.118

FIGURE 3.

FIGURE 3.

Presence of a tissue-specific alternative TSS leads to a brain-specific rescue of lnc-sox4a expression. (A) The lnc-sox4a locus in zebrafish (chr19:29,161,676-29,270,573). Shown are the corresponding CAGE (Nepal et al. 2013; Haberle et al. 2014), H3K4me3 ChIP-Seq (Ulitsky et al. 2011), and RNA-seq tracks from WT zebrafish. (B) The lnc-sox4aΔTSS mutant allele showing deletion of the sequence around the TSS (dotted, blue line). Indicated are positions of the 5′ RACE primers, qPCR primers, and alternative TSS. (C) lnc-sox4a expression in 72 h postfertilization (hpf) WT and homozygous lnc-sox4aΔTSS embryos detected by qRT-PCR. (D) lnc-sox4a expression across adult WT and homozygous lnc-sox4aΔTSS zebrafish tissues detected by qRT-PCR. eef1α1l1 was used as a reference gene in all qRT-PCR experiments. Each dot represents an individual biological replicate. Data are presented as mean ± S.E.M.; (*) P < 0.05, (**) P < 0.01, n.s., not significant, unpaired t-tests.