@article {33,
	title = {Multiple bHLH proteins regulate CIT2 expression in Saccharomyces cerevisiae.},
	journal = {Yeast},
	volume = {27},
	year = {2010},
	month = {2010 Jun},
	pages = {345-59},
	abstract = {<p>The basic helix-loop-helix (bHLH) proteins comprise a eukaryotic transcription factor family involved in multiple biological processes. They have the ability to form multiple dimer combinations and most of them also bind a 6 bp site (E-box) with limited specificity. These properties make them ideal for combinatorial regulation of gene expression. The Saccharomyces cerevisiae CIT2 gene, which encodes citrate synthase, was previously known to be induced by the bHLH proteins Rtg1p and Rtg3p in response to mitochondrial damage. Rtg1p-Rtg3p dimers bind two R-boxes (modified E-boxes) in the CIT2 promoter. The current study tested the ability of all nine S. cerevisiae bHLH proteins to regulate the CIT2 gene. The results showed that expression of CIT2-lacZ reporter was induced in a rho(0) strain by the presence of inositol via the Ino2p and Ino4p bHLH proteins, which are known regulators of phospholipid synthesis. Promoter mutations revealed that inositol induction required a distal E-box in the CIT2 promoter. Interestingly, deleting the INO2, INO4 genes or the cognate E-box revealed phosphate induction of CIT2 expression. This layer of expression required the two R-boxes and the Pho4p bHLH protein, which is known to be required for phosphate-specific regulation. Lastly, the data show that the Hms1p and Sgc1p bHLH proteins also play important roles in repression of CIT2-lacZ expression. Collectively, these results support the model that yeast bHLH proteins coordinate different biological pathways.</p>
},
	keywords = {Basic Helix-Loop-Helix Leucine Zipper Transcription Factors, Basic Helix-Loop-Helix Transcription Factors, Citrate (si)-Synthase, Gene Expression Regulation, Enzymologic, Gene Expression Regulation, Fungal, Inositol, Regulatory Sequences, Nucleic Acid, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Species Specificity},
	issn = {1097-0061},
	doi = {10.1002/yea.1757},
	author = {Chen, Linan and Lopes, John M}
}
@article {35,
	title = {Multiple basic helix-loop-helix proteins regulate expression of the ENO1 gene of Saccharomyces cerevisiae.},
	journal = {Eukaryot Cell},
	volume = {6},
	year = {2007},
	month = {2007 May},
	pages = {786-96},
	abstract = {The basic helix-loop-helix (bHLH) eukaryotic transcription factors have the ability to form multiple dimer combinations. This property, together with limited DNA-binding specificity for the E box (CANNTG), makes them ideally suited for combinatorial control of gene expression. We tested the ability of all nine Saccharomyces cerevisiae bHLH proteins to regulate the enolase-encoding gene ENO1. ENO1 was known to be activated by the bHLH protein Sgc1p. Here we show that expression of an ENO1-lacZ reporter was also regulated by the other eight bHLH proteins, namely, Ino2p, Ino4p, Cbf1p, Rtg1p, Rtg3p, Pho4p, Hms1p, and Ygr290wp. ENO1-lacZ expression was also repressed by growth in inositol-choline-containing medium. Epistatic analysis and chromatin immunoprecipitation experiments showed that regulation by Sgc1p, Ino2p, Ino4p, and Cbf1p and repression by inositol-choline required three distal E boxes, E1, E2, and E3. The pattern of bHLH binding to the three E boxes and experiments with two dominant-negative mutant alleles of INO4 and INO2 support the model that bHLH dimer selection affects ENO1-lacZ expression. These results support the general model that bHLH proteins can coordinate different biological pathways via multiple mechanisms.},
	keywords = {Basic Helix-Loop-Helix Transcription Factors, beta-Galactosidase, Chromatin Immunoprecipitation, E-Box Elements, Epistasis, Genetic, Evolution, Molecular, Gene Expression Regulation, Fungal, Genes, Dominant, Models, Biological, Mutation, Phosphopyruvate Hydratase, Promoter Regions, Genetic, Recombinant Fusion Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins},
	issn = {1535-9778},
	doi = {10.1128/EC.00383-06},
	author = {Chen, Meng and Lopes, John M}
}
