Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion

The bacterial transcription factor LacI loops DNA by binding to two separate locations on the DNA si-multaneously. Despite being one of the best-studied model systems for transcriptional regulation, the number and conformations of loop structures ac-cessible to LacI remain unclear, though the impor-tance of multiple coexisting loops has been impli-cated in interactions between LacI and other cel-lular regulators of gene expression. To probe this issue, we have developed a new analysis method for tethered particle motion, a versatile and com-monly used in vitro single-molecule technique. Our method, vbTPM, performs variational Bayesian infer-ence in hidden Markov models. It learns the numbe