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

Lee MY, Park C, Berent RM, Park PJ, Fuchs R, Syn H, Chin A, Townsend J, Benson CC, Redelman D, Shen TW, Park JK, Miano JM, Sanders KM, Ro S - PLoS ONE (2015)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Analysis of CArG boxes and SRF binding sites on SMC transcriptome.A total of 1,540 SRF binding sites (peak height >1.5) obtained from SRF ChIP-seq of C2C12 myoblasts were analyzed for association with CArG boxes, CpG islands, and genes. (A) Proportion of SRF binding sites associated with CArG boxes. (B) Proportion of SRF binding sites associated with CArG boxes conserved between mice and humans. (C) Proportion of SRF binding sites associated with CpG islands. (D) Proportion of SRF binding sites associated with genes. (E) Locations of SRF binding sites on genes expressed in SMCs. (F) A representative list of SMC genes that were highly expressed and associated with SRF binding sites. Eighty-six genes containing SRF binding sites (peak hight >1.5) and highly expressed (>100 FPKM) in SMCs are shown. The SMC genes of the 34 proteins regulated by SRF in SMC-specific Srf KO mice are indicated in bold green letters. (G) Proportion of SRF-regulated proteins identified in jejunal SM from SMC-specific Srf KO mice. Eight-six SRF-associated genes were compared with the SRF-regulated proteins identified in a proteomics study involving Srf KO mice: 34 proteins were down-regulated (SRF-regulated; blue), 40 proteins were not detected (red), and 12 proteins did not change expression levels (others; green) in the Srf KO SM.
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pone.0133751.g004: Analysis of CArG boxes and SRF binding sites on SMC transcriptome.A total of 1,540 SRF binding sites (peak height >1.5) obtained from SRF ChIP-seq of C2C12 myoblasts were analyzed for association with CArG boxes, CpG islands, and genes. (A) Proportion of SRF binding sites associated with CArG boxes. (B) Proportion of SRF binding sites associated with CArG boxes conserved between mice and humans. (C) Proportion of SRF binding sites associated with CpG islands. (D) Proportion of SRF binding sites associated with genes. (E) Locations of SRF binding sites on genes expressed in SMCs. (F) A representative list of SMC genes that were highly expressed and associated with SRF binding sites. Eighty-six genes containing SRF binding sites (peak hight >1.5) and highly expressed (>100 FPKM) in SMCs are shown. The SMC genes of the 34 proteins regulated by SRF in SMC-specific Srf KO mice are indicated in bold green letters. (G) Proportion of SRF-regulated proteins identified in jejunal SM from SMC-specific Srf KO mice. Eight-six SRF-associated genes were compared with the SRF-regulated proteins identified in a proteomics study involving Srf KO mice: 34 proteins were down-regulated (SRF-regulated; blue), 40 proteins were not detected (red), and 12 proteins did not change expression levels (others; green) in the Srf KO SM.

Mentions: Since alternative SMC transcripts appeared to be closely associated with binding of SRF to different CArG boxes, we performed an analysis of all SRF binding sites in the mouse genome. A total of 6,759 SRF binding sites were identified in the myocyte genome, and 1,540 of these binding sites were selected for further analysis based on the strength of the SRF signal (peak height > 1.5 signal value). A complete list of SRF binding sites associated with CArG boxes, CpG islands, and JSMC transcripts is shown in S6 Table. Fifty-seven percent (877) of SRF binding sites were associated with CArG boxes, and 32% (413) of the SRF binding sites were conserved between humans and mice (Fig 4A and 4B). Approximately 43% (560) of all SRF binding sites were found within the CpG islands of transcriptional start sites (Fig 4C). Most SRF binding sites were found within the promoter regions and were followed by exon 1 or intron 1 (Fig 4E), and a total of 1,116 genes (86%) were associated with SRF binding sites (Fig 4D), of which most were abundantly expressed in SMCs. There were 86 genes that were closely associated with SRF binding sites and highly expressed in SMCs (Fig 4F). Of the SRF-associated genes, several new genes were identified in additional to known contractile genes such as Acta2, Tagln, and Des (Fig 4F).


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

Lee MY, Park C, Berent RM, Park PJ, Fuchs R, Syn H, Chin A, Townsend J, Benson CC, Redelman D, Shen TW, Park JK, Miano JM, Sanders KM, Ro S - PLoS ONE (2015)

Analysis of CArG boxes and SRF binding sites on SMC transcriptome.A total of 1,540 SRF binding sites (peak height >1.5) obtained from SRF ChIP-seq of C2C12 myoblasts were analyzed for association with CArG boxes, CpG islands, and genes. (A) Proportion of SRF binding sites associated with CArG boxes. (B) Proportion of SRF binding sites associated with CArG boxes conserved between mice and humans. (C) Proportion of SRF binding sites associated with CpG islands. (D) Proportion of SRF binding sites associated with genes. (E) Locations of SRF binding sites on genes expressed in SMCs. (F) A representative list of SMC genes that were highly expressed and associated with SRF binding sites. Eighty-six genes containing SRF binding sites (peak hight >1.5) and highly expressed (>100 FPKM) in SMCs are shown. The SMC genes of the 34 proteins regulated by SRF in SMC-specific Srf KO mice are indicated in bold green letters. (G) Proportion of SRF-regulated proteins identified in jejunal SM from SMC-specific Srf KO mice. Eight-six SRF-associated genes were compared with the SRF-regulated proteins identified in a proteomics study involving Srf KO mice: 34 proteins were down-regulated (SRF-regulated; blue), 40 proteins were not detected (red), and 12 proteins did not change expression levels (others; green) in the Srf KO SM.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4524680&req=5

pone.0133751.g004: Analysis of CArG boxes and SRF binding sites on SMC transcriptome.A total of 1,540 SRF binding sites (peak height >1.5) obtained from SRF ChIP-seq of C2C12 myoblasts were analyzed for association with CArG boxes, CpG islands, and genes. (A) Proportion of SRF binding sites associated with CArG boxes. (B) Proportion of SRF binding sites associated with CArG boxes conserved between mice and humans. (C) Proportion of SRF binding sites associated with CpG islands. (D) Proportion of SRF binding sites associated with genes. (E) Locations of SRF binding sites on genes expressed in SMCs. (F) A representative list of SMC genes that were highly expressed and associated with SRF binding sites. Eighty-six genes containing SRF binding sites (peak hight >1.5) and highly expressed (>100 FPKM) in SMCs are shown. The SMC genes of the 34 proteins regulated by SRF in SMC-specific Srf KO mice are indicated in bold green letters. (G) Proportion of SRF-regulated proteins identified in jejunal SM from SMC-specific Srf KO mice. Eight-six SRF-associated genes were compared with the SRF-regulated proteins identified in a proteomics study involving Srf KO mice: 34 proteins were down-regulated (SRF-regulated; blue), 40 proteins were not detected (red), and 12 proteins did not change expression levels (others; green) in the Srf KO SM.
Mentions: Since alternative SMC transcripts appeared to be closely associated with binding of SRF to different CArG boxes, we performed an analysis of all SRF binding sites in the mouse genome. A total of 6,759 SRF binding sites were identified in the myocyte genome, and 1,540 of these binding sites were selected for further analysis based on the strength of the SRF signal (peak height > 1.5 signal value). A complete list of SRF binding sites associated with CArG boxes, CpG islands, and JSMC transcripts is shown in S6 Table. Fifty-seven percent (877) of SRF binding sites were associated with CArG boxes, and 32% (413) of the SRF binding sites were conserved between humans and mice (Fig 4A and 4B). Approximately 43% (560) of all SRF binding sites were found within the CpG islands of transcriptional start sites (Fig 4C). Most SRF binding sites were found within the promoter regions and were followed by exon 1 or intron 1 (Fig 4E), and a total of 1,116 genes (86%) were associated with SRF binding sites (Fig 4D), of which most were abundantly expressed in SMCs. There were 86 genes that were closely associated with SRF binding sites and highly expressed in SMCs (Fig 4F). Of the SRF-associated genes, several new genes were identified in additional to known contractile genes such as Acta2, Tagln, and Des (Fig 4F).

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.