Protein copy number distributions for a self-regulating gene in the presence of decoy binding sites

PLoS One. 2015 Mar 26;10(3):e0120555. doi: 10.1371/journal.pone.0120555. eCollection 2015.

Abstract

A single transcription factor may interact with a multitude of targets on the genome, some of which are at gene promoters, others being part of DNA repeat elements. Being sequestered at binding sites, protein molecules can be prevented from partaking in other pathways, specifically, from regulating the expression of the very gene that encodes them. Acting as decoys at the expense of the autoregulatory loop, the binding sites can have a profound impact on protein abundance--on its mean as well as on its cell-to-cell variability. In order to quantify this impact, we study in this paper a mathematical model for pulsatile expression of a transcription factor that autoregulates its expression and interacts with decoys. We determine the exact stationary distribution for protein abundance at the single-cell level, showing that in the case of non-cooperative positive autoregulation, the distribution can be bimodal, possessing a basal expression mode and a distinct, up-regulated, mode. Bimodal protein distributions are more feasible if the rate of degradation is the same irrespective of whether protein is bound or not. Contrastingly, the presence of decoy binding sites which protect the protein from degradation reduces the availability of the bimodal scenario.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Binding Sites*
  • Gene Expression Regulation*
  • Models, Biological*
  • Transcription Factors / metabolism*
  • Transcriptional Activation*

Substances

  • Transcription Factors

Grants and funding

PB is supported by the Slovak Research and Development Agency (contract no. APVV-0134-10) and also by the VEGA grant agency (contract no. 1/0319/15). AS is supported by the National Science Foundation Grant DMS-1312926, University of Delaware Research Foundation (UDRF), and Oak Ridge Associated Universities (ORAU).