Our paper “Homotypic clusters of transcription factor binding sites: A model system for understanding the physical mechanics of gene expression.” has been out for more than half a year, but I had not remembered putting up a brief post about it – probably because it was more of a review rather than the result of hard original graft. However, friends in the field have already picked up on our thoughts and the work has been cited by the Gordan and Hahnenhalli labs. So here it goes:
Homotypic clusters of transcription factor binding sites are common in regulatory contexts where a dosage-dependent transcriptional response is desired. The number, orientation and spacing of binding sites determines how the element will respond. While this is a known, experimentally often observed phenomenon, this paper provides the physical reasoning why homotypic clusters show their distinctive behaviour.
If you’re interested, go check it out at the Computational and Structural Biotechnology Journal.