SMC transcriptome, SRF binding sites, and CArG boxes built on the UCSC genome browser.

(A) A genomic map view of CArG boxes and SRF binding sites on Acta2, a gene expressed in SMCs. All predicted CArG boxes were mapped on the genome. Conserved CArG boxes beween mice and humans are indicated by red circles. Four transcriptional variants with alternative initiation sites were expressed in colonic and jejunal SMCs (set by view options; large red horizontal arrows). The transcriptional variants were aligned with H3K27ac sites (small intestine), RNA polymerase II and SRF binding sites (C2C12 myoblasts), which were publically available in the UCSC database. The two SRF binding sites contained three CArG boxes (red circles), which were located in the promoter and intron 1 regions, and conserved beween mice and humans (set by view options). Note that the SRF binding sites aligned with that of RNA polymerase II and the H3K27ac sites from SRF ChIP data. Directionality of each mRNA on the browser is indicated by the arrows on a line (e.g., >>>, sense strand; <<<, antisense strand). (B) Expression levels (FPKM) of Acta2 in SMCs and whole tissue. (C) Expression levels (FPKM) of Acta2 transcriptional variants in SMCs. The variant (V) ID represents the last three digits of the TCONS number. (D) PCR validation of Acta2 exons with different transcriptional initiation sites in isolated SMCs and muscularis of jejunum and colon. NTC is non-template control. Primer sets were designed from variant exons in the regions of interest (see S11 Table for primer sequences).