Two new articles on ArXiv: Facilitated diffusion

teaserArXivWe are happy to announce the submission of two new articles to arXiv prior to publication in peer-reviewed open access journals:

 arXiv:1303.6793: The effects of transcription factor competition on gene regulation

 arXiv:1303.6869: The influence of transcription factor competition on the relationship between occupancy and affinity

If facilitated diffusion, stochastic simulation or transcriptional regulation are your thing, please have a look, send us comments and suggestions, tweet it, write about it on your blog (but let us know so we can engage in a fruitful scientific discussion) etc.

In brief, in arXiv:1303.6793 (Zabet & Adryan) we discuss the influence of TF abundance on the arrival time of TFs on their target sites as well as the time they stay bound to the DNA. There is an “emerging property” in cases where many molecules compete in some sort of molecular traffic jam on the DNA. This noise component may be a contributor to transcriptional noise, which we found pretty interesting.

The second article, arXiv:1303.6869 (Zabet, Foy & Adryan) deals with the discrepancy between “predicted occupancy” of a TF to a binding site on the basis of, say, a PWM, in contrast to a “measured occupancy” when we simulate the system with our GRiP framework. Again, we can show that absolute TF abundances play an important role in gene expression, and also provide a compelling case where selecting “the highest peaks” from a ChIP experiment may not necessarily identify the most affine binding sites.

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