Smooth muscle cell genome browser: Enabling the identification of novel serum response factor target genes

Moon Young Lee, Chanjae Park, Robyn M. Berent, Paul J. Park, Robert Fuchs, Hannah Syn, Albert Chin, Jared Townsend, Craig C. Benson, Doug Redelman, Tsaiwei Shen, Jong Kun Park, Joseph M. Miano, Kenton M. Sanders, Seungil Ro

Research output: Contribution to journalArticle

24 Scopus citations

Abstract

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

Original languageEnglish (US)
Article numbere0133751
JournalPloS one
Volume10
Issue number8
DOIs
StatePublished - Aug 4 2015

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Lee, M. Y., Park, C., Berent, R. M., Park, P. J., Fuchs, R., Syn, H., Chin, A., Townsend, J., Benson, C. C., Redelman, D., Shen, T., Park, J. K., Miano, J. M., Sanders, K. M., & Ro, S. (2015). Smooth muscle cell genome browser: Enabling the identification of novel serum response factor target genes. PloS one, 10(8), [e0133751]. https://doi.org/10.1371/journal.pone.0133751