Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes

• DOI: 10.1371/journal.pone.0133751
• Publication Date: 2015-08-04T18:16:25Z
• Authors: Moon Young Lee; Chanjae Park; Robyn M. Berent; Paul J. Park; Robert Fuchs; Hannah Syn; Albert Chin; Jared Townsend; Craig C. Benson; Doug Redelman; Tsai-wei Shen; Jong Kun Park; Joseph M. Miano; Kenton M. Sanders; Seungil Ro
• Keywords: Genome browser

Genome-scale expression data on the absolute numbers of gene isoforms offers essential clues in cellular functions and biological processes. Smooth muscle cells (SMCs) perform a unique contractile function through specific genes controlled by serum response factor (SRF), transcription that binds to DNA sites known as CArG boxes. To identify SRF-regulated specifically expressed SMCs, we isolated SMC populations from mouse small intestine colon, obtained their transcriptomes, constructed an interactive genome CArGome browser. our knowledge, this is first online resource provides comprehensive library all genetic transcripts primary SMCs. The browser also serves genome-wide map SRF binding sites. analysis revealed novel SMC-specific transcriptional variants target genes, which provided new insights into gastrointestinal (GI) physiology. were discovered silico, confirmed proteomic Srf knockout mice. Our perspective alternative context SMCs valuable reference for future functional studies.