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Full-Text Articles in Genetics and Genomics
Using Competition Assays To Quantitatively Model Cooperative Binding By Transcription Factors And Other Ligands., Jacob Peacock, James B Jaynes
Using Competition Assays To Quantitatively Model Cooperative Binding By Transcription Factors And Other Ligands., Jacob Peacock, James B Jaynes
Department of Biochemistry and Molecular Biology Faculty Papers
BACKGROUND: The affinities of DNA binding proteins for target sites can be used to model the regulation of gene expression. These proteins can bind to DNA cooperatively, strongly impacting their affinity and specificity. However, current methods for measuring cooperativity do not provide the means to accurately predict binding behavior over a wide range of concentrations.
METHODS: We use standard computational and mathematical methods, and develop novel methods as described in Results.
RESULTS: We explore some complexities of cooperative binding, and develop an improved method for relating in vitro measurements to in vivo function, based on ternary complex formation. We derive …
Drawing Lines In The Sand: Even Skipped Et Al. And Parasegment Boundaries., James B. Jaynes, Miki Fujioka
Drawing Lines In The Sand: Even Skipped Et Al. And Parasegment Boundaries., James B. Jaynes, Miki Fujioka
Department of Biochemistry and Molecular Biology Faculty Papers
The pair-rule segmentation gene even skipped (eve) is required to activate engrailed stripes and to organize odd-numbered parasegments (PSs). The protein product Eve has been shown to be an active repressor of transcription, and recent models for Eve function suggest that activation of engrailed is indirect, but these models have not been fully tested. Here we identify the forkhead domain transcription factor Sloppy-paired as the key intermediate in the initial activation of engrailed by Eve in odd-numbered parasegments. We also analyze the roles of the transcription factors Runt and Odd-skipped in this process. Detailed analysis of engrailed and pair-rule gene …