A global alliance declaring war on cassava viruses in Africa

[Without Abstract

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

<div><p>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 <i>in silico</i>, were confirmed by proteomic analysis of SMC-specific <i>Srf</i> 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.</p></div

transcript GTF annotation of smooth muscle cells in colon

<p>trascript annotation of smooth muscle cells in colon</p

Analysis of CArG boxes and SRF binding sites on SMC transcriptome.

<p>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 <i>Srf</i> KO mice are indicated in bold green letters. (G) Proportion of SRF-regulated proteins identified in jejunal SM from SMC-specific <i>Srf</i> KO mice. Eight-six SRF-associated genes were compared with the SRF-regulated proteins identified in a proteomics study involving <i>Srf</i> 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 <i>Srf</i> KO SM.</p

transcript GTF annotation of ICC in jejunum smooth muscle

<p>transcript annotation of ICC in jejunum smooth muscle</p

transcript GTF annotation of PDGFRa+ cells in colon mucosa

<p>transcript annotation of PDGFRa+ cells in colon mucosa</p

Identification of SMCs in the intestinal smooth muscle with eGFP and MYH11 antibody.

<p>(A) A confocal microscopy z-stack image of whole-mount jejunum muscularis showing longitudinal and circular SMCs expressing eGFP. (B) Immunohistochemistry of SMCs using anti-MYH11(smMHC) antibody. (C) Merged images of eGFP and MYH11(smMHC). (D & E) Primary eGFP⁺ SMCs from jejunum and colon identified (circled) on flow cytometry.</p

Identification of SMC-specific genes by expression profiles and histone modifications.

<p>(A) Specificity of SMC-enriched genes. Cell specificity was determined by comparative analysis of gene expression profiles among SMCs, ICCs, and PDGFRα⁺ cells: SMCs^{expression level (FPKM)}/[ICC^{expression level (FPKM)} + PDGFRα⁺ cells^{expression level (FPKM)}] (B) Comparison of JSMC- and CSMC-enriched gene expression. (C) Genomic map views of histone modications (H3K4m3, H3K27a, and H3K27m3 in 8 week small intestine) on <i>Cnn1</i> (specifically expressed in JSMCs and CSMCs) and <i>Ubb</i> (ubiquitiously expressed). (D) Comparison of histone modifications on SMC-enriched genes. The signal value is the average of the mininum and maxium values of the ChIP-seq signal for each histone modification. (E) Comparison of histone modifications on ubiquitious genes. (F) Expression levels of SMC-enriched genes not altered by histone modifications.</p

transcript GTF annotation of PDGFRa+ cells in colon smooth muscle

<p>transcript annotation of PDGFRa+ cells in colon smooth muscle</p