Fig. 3: seRNA-1 and seRNA-2 regulate target gene expression.

a Genomic snapshots of mouse seRNA-1 and seRNA-2 genes showing Pol II and histone marks ChIP-seq profiles, Poly A+ RNA-seq and GRO-seq in MB and MT cells. The red bar highlights the SE region and the red box indicates the seRNA locus. GRO-seq signals are displayed in “+” (red) and “−” (light green) strands separately. b Top: schematic illustration of genomic structure of mouse seRNA-1 relative to the neighboring genes Mb and Apol6. Bottom: Left: Product of RACE cloning (5′ and 3′) of seRNA-1; Right: Detection of seRNA-1 molecules (red) in MT by single molecule RNA FISH. Scale bar, 5 μm. c Top: schematic illustration of genomic structure of mouse seRNA-2 relative to the neighboring genes Atp1a1 and Igsf3. Bottom: Left: Product of RACE (5′ and 3′) cloning of seRNA-2; Right: FISH detection of seRNA-2 in MT. Scale bar, 5 μm. Quantification of FISH signals in b, c corresponding to seRNA transcripts in MB and MT cells. Cells with at least one spot in the nucleus were regarded as “transcribing”. DNA (blue) was stained with DAPI. A representative image was shown. d qRT-PCR analysis of RNAs purified from nuclear and cytosolic fractions of C2C12 cells. e qRT-PCR detection of seRNA-1 and seRNA-2 in the differentiating SCs isolated from muscles of Tg: Pax7-nGFP mice. f Left: qRT-PCR detection of seRNA-1 and neighboring genes from 48-h-differentiated C2C12 cells transfected with either control or seRNA-1 siRNA (si-se1#1 or si-se1#2). Right: qRT-PCR measurement of expression kinetics of seRNA-1 and the Mb and Apol6 during C2C12 differentiation. g The above experiments were performed for seRNA-2 and its neighboring Atp1a1 and Igsf3 genes. Data represent the average of three independent experiments ± s.d. Statistical analysis was performed by one-way ANOVA with Tukey’s post-hoc test (e), or two-tailed unpaired Student’s t-test (f, g) n.s., not significant, *P < 0.05, **P < 0.01 and ***P < 0.001. Source data are provided as a Source Data file.