@article {1458,
	title = {Transcription regulation of a yeast gene from a downstream location.},
	journal = {J Mol Biol},
	volume = {425},
	year = {2013},
	month = {2013 Feb 8},
	pages = {457-65},
	abstract = {<p>Mechanisms for coregulation of transcription of tandem genes in yeast remain largely speculative. This study focused on inositol-mediated regulation of the tandem gene pair SNA3-INO1. While the pattern of regulation of these two genes was similar, results showed that intermediate levels of inositol repressed INO1 and induced SNA3. Results also showed that inositol-mediated regulation of the SNA3 gene was not a function of its promoter but occurred from factors within the SNA3-INO1 intergenic region. The basic helix-loop-helix proteins, Ino2p and Ino4p, mediated this regulation through the upstream activation sequence (UAS)(INO) (E-box) sequences in the intergenic region. These results provide a model for studying coregulation of yeast tandem genes. This is especially significant given that many tandem gene pairs in yeast are coregulated even though context-specific UAS sequences are known only for one gene in the pair.</p>
},
	keywords = {Gene Expression Regulation, Fungal, Inositol, Membrane Proteins, Myo-Inositol-1-Phosphate Synthase, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic},
	issn = {1089-8638},
	doi = {10.1016/j.jmb.2012.11.018},
	author = {Shetty, Ameet and Swaminathan, Aishwarya and Lopes, John M}
}
@article {32,
	title = {Transcription regulation of the Saccharomyces cerevisiae PHO5 gene by the Ino2p and Ino4p basic helix-loop-helix proteins.},
	journal = {Mol Microbiol},
	volume = {83},
	year = {2012},
	month = {2012 Jan},
	pages = {395-407},
	abstract = {<p>The Saccharomyces cerevisiae PHO5 gene product accounts for a majority of the acid phosphatase activity. Its expression is induced by the basic helix-loop-helix (bHLH) protein, Pho4p, in response to phosphate depletion. Pho4p binds predominantly to two UAS elements (UASp1 at -356 and UASp2 at -247) in the PHO5 promoter. Previous studies from our lab have shown cross-regulation of different biological processes by bHLH proteins. This study tested the ability of all yeast bHLH proteins to regulate PHO5 expression and identified inositol-mediated regulation via the Ino2p/Ino4p bHLH proteins. Ino2p/Ino4p are known regulators of phospholipid biosynthetic genes. Genetic epistasis experiments showed that regulation by inositol required a third UAS site (UASp3 at -194). ChIP assays showed that Ino2p:Ino4p bind the PHO5 promoter and that this binding is dependent on Pho4p binding. These results demonstrate that phospholipid biosynthesis is co-ordinated with phosphate utilization via the bHLH proteins.</p>
},
	keywords = {Acid Phosphatase, Basic Helix-Loop-Helix Transcription Factors, Chromatin Immunoprecipitation, DNA, Fungal, Enhancer Elements, Genetic, Gene Expression Regulation, Fungal, Inositol, Models, Biological, Phospholipids, Promoter Regions, Genetic, Protein Binding, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors, Transcription, Genetic},
	issn = {1365-2958},
	doi = {10.1111/j.1365-2958.2011.07941.x},
	author = {He, Ying and Swaminathan, Aishwarya and Lopes, John M}
}
@article {34,
	title = {Transcription regulation of the Saccharomyces cerevisiae PIS1 gene by inositol and the pleiotropic regulator, Ume6p.},
	journal = {Mol Microbiol},
	volume = {70},
	year = {2008},
	month = {2008 Dec},
	pages = {1529-39},
	abstract = {In Saccharomyces cerevisiae, transcription of most of the phospholipid biosynthetic genes (e.g. INO1, CHO1, CHO2 and OPI3) is repressed by growth in the presence of inositol and choline and derepressed in their absence. This regulation requires the Ino2p and Ino4p activators and the Opi1p repressor. The PIS1 structural gene is required for the synthesis of the essential lipid phosphatidylinositol. Previous reports show that PIS1 expression is uncoupled from inositol/choline regulation, but is regulated by carbon source, hypoxia and zinc. However, in this study we found that the expression of PIS1 is induced twofold by inositol. This regulation did not require Ino2p and Ino4p, although Ino4p was required for full expression. Ino4p is a basic helix-loop-helix protein that requires a binding partner. Curiously, none of the other basic helix-loop-helix proteins affected PIS1 expression. Inositol induction did require another general regulator of phospholipid biosynthesis, Ume6p. Ume6p was found to be a positive regulator of PIS1 gene expression. Ume6p, and several associated factors, were required for inositol-mediated induction and chromatin immunoprecipitation analysis showed that Ume6p directly regulates PIS1 expression. Thus, we demonstrate novel regulation of the PIS1 gene by Ume6p.},
	keywords = {Chromatin Immunoprecipitation, DNA-Binding Proteins, Gene Expression Regulation, Fungal, Histone Deacetylases, Inositol, Repressor Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic, Transferases (Other Substituted Phosphate Groups)},
	issn = {1365-2958},
	doi = {10.1111/j.1365-2958.2008.06506.x},
	author = {Jani, Niketa M and Lopes, John M}
}
@article {36,
	title = {Transcriptional regulation of yeast phospholipid biosynthetic genes.},
	journal = {Biochim Biophys Acta},
	volume = {1771},
	year = {2007},
	month = {2007 Mar},
	pages = {310-21},
	abstract = {The last several years have been witness to significant developments in understanding transcriptional regulation of the yeast phospholipid structural genes. The response of most phospholipid structural genes to inositol is now understood on a mechanistic level. The roles of specific activators and repressors are also well established. The knowledge of specific regulatory factors that bind the promoters of phospholipid structural genes serves as a foundation for understanding the role of chromatin modification complexes. Collectively, these findings present a complex picture for transcriptional regulation of the phospholipid biosynthetic genes. The INO1 gene is an ideal example of the complexity of transcriptional control and continues to serve as a model for studying transcription in general. Furthermore, transcription of the regulatory genes is also subject to complex and essential regulation. In addition, databases resulting from a plethora of genome-wide studies have identified regulatory signals that control one of the essential phospholipid biosynthetic genes, PIS1. These databases also provide significant clues for other regulatory signals that may affect phospholipid biosynthesis. Here, we have tried to present a complete summary of the transcription factors and mechanisms that regulate the phospholipid biosynthetic genes.},
	keywords = {CDP-Diacylglycerol-Inositol 3-Phosphatidyltransferase, Fungal Proteins, Gene Expression Regulation, Enzymologic, Gene Expression Regulation, Fungal, Intramolecular Lyases, Myo-Inositol-1-Phosphate Synthase, Phospholipids, Saccharomyces cerevisiae Proteins, Transcription Factors, Transcription, Genetic, Yeasts},
	issn = {0006-3002},
	doi = {10.1016/j.bbalip.2006.05.017},
	author = {Chen, Meng and Hancock, Leandria C and Lopes, John M}
}
