Open Access Highly Accessed Methodology article

Genome-wide identification of the regulatory targets of a transcription factor using biochemical characterization and computational genomic analysis

Emmitt R Jolly†, Chen-Shan Chin†, Ira Herskowitz and Hao Li*

Department of Biochemistry and Biophysics, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94143, USA

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BMC Bioinformatics 2005, 6:275 doi:10.1186/1471-2105-6-275

Published: 18 November 2005

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Supplemental Materials.

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Additional File 2:

Quantitative analysis of in vivo expression driven by MSE variants. Northern hybridization bands were analyzed on phosphoImager. SPO77 and GFP levels are quantitated relative to the loading control PFY1.

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The location of the MSE is critical for sporulation specific expression of RNA at the SPO77 locus. In a heterologous strain where SPO77 is replaced with GFP at one locus, the MSE was relocated to positions (a) -450 or (c) -50 and the endogenous MSE at -152 was mutated to a non-functional MSE. As a control, the MSE was inserted at positions (b) -450 and (d) -50 in a strain where the endogenous MSE is functional and unchanged.

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Additional File 4:

Clustering diagram of microarray expression[1] for those genes identified as NDT80 targets by the ChIP-on-Chip experiments[9] using p-value < 0.01.

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