title: Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes.
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.
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America; Department of Physiology, Wonkwang Digestive Disease Research Institute and Institute of Wonkwang Medical Science, School of Medicine, Wonkwang University, Iksan, Jeollabuk-do, Korea.
authors.forename: Moon Young
authors.initials: MY
authors.lastname: Lee
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Chanjae
authors.initials: C
authors.lastname: Park
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Robyn M
authors.initials: RM
authors.lastname: Berent
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Park
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Robert
authors.initials: R
authors.lastname: Fuchs
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Hannah
authors.initials: H
authors.lastname: Syn
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Albert
authors.initials: A
authors.lastname: Chin
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Jared
authors.initials: J
authors.lastname: Townsend
authors.affiliation: Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America.
authors.forename: Craig C
authors.initials: CC
authors.lastname: Benson
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Doug
authors.initials: D
authors.lastname: Redelman
authors.affiliation: LC Sciences, 2575 West Bellfort Street Suite 270, Houston, Texas, United States of America.
authors.forename: Tsai-Wei
authors.initials: TW
authors.lastname: Shen
authors.affiliation: Division of Biological Science, Wonkwang University, Iksan, Jeollabuk-do, South Korea.
authors.forename: Jong Kun
authors.initials: JK
authors.lastname: Park
authors.affiliation: Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America.
authors.forename: Joseph M
authors.initials: JM
authors.lastname: Miano
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Kenton M
authors.initials: KM
authors.lastname: Sanders
authors.affiliation: Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America.
authors.forename: Seungil
authors.initials: S
authors.lastname: Ro
mesh_terms: D000818:Animals; D001665:Binding Sites; D002352:Carrier Proteins / Q000235:genetics; D003106:Colon / Q000166:cytology; D003198:Computer Simulation; D015723:Gene Library; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins; D042421:Histone Code; D006657:Histones / Q000378:metabolism; D007473:Ion Channels / Q000235:genetics; D007583:Jejunum / Q000166:cytology; D051379:Mice; D018345:Mice, Knockout; D008822:Mice, Transgenic; D009124:Muscle Proteins / Q000235:genetics*; D032389:Myocytes, Smooth Muscle / Q000378:metabolism*; D009928:Organ Specificity; D040901:Proteomics; D012333:RNA, Messenger / Q000235:genetics*; D027602:Serum Response Element / Q000235:genetics*; D026362:Serum Response Factor / Q000172:deficiency / Q000378:metabolism*; D059467:Transcriptome; D064878:Web Browser
chemical_list: D002352:Carrier Proteins; D006657:Histones; D007473:Ion Channels; D009124:Muscle Proteins; D012333:RNA, Messenger; D026362:Serum Response Factor; D049452:Green Fluorescent Proteins