Tunable Optogenetic Signal Decoding through Epigenome Editors

Authors: 
Lee, J. B. - Presenter, North Carolina State University
Caywood, L., NC State University
Keung, A. J., North Carolina State University
Levering, N., North Carolina State University
Lo, J. Y., North Carolina State University
In eukaryotic cells, access of transcription machinery to genomic binding sites is controlled by chromatin structure, which can be modified by various epigenome editors (EEs). EEs are used for various applications including high-throughput screens for cell phenotypes and drug targets, cell differentiation, and mechanistic studies of epigenetic regulation. EEs have mostly been used bimodally to activate or repress gene expression; however, by utilizing dynamic signaling, they could be used to execute a larger landscape of gene outputs in terms of expression level and information transmission.
Inspired by natural systems that use transcription factor dynamics to encode different gene expression programs, we developed an optogenetic system to dynamically recruit a representative EE, VP16, to a fluorescent reporter in Saccharomyces cerevisiae. The input signal was modulated via frequency, intensity, and pulse width of light pulses. This system resulted in tunable expression levels that spanned two orders of magnitude. Additionally, we quantified the reliability of this system at transmitting information using the maximal mutual information (MI). We found that frequency modulation was the most reliable mode of modulation; however, it was limited to three error-free states (1.6 bits). To determine how chromatin state affects MI and expression levels, we modulated the chromatin state by constitutively recruiting a library of over 100 orthogonal EEs. A handful of the EEs increased the MI, and many decreased the MI. Furthermore, we found some of the EEs are able to alter the input-output transfer function. For example, many of the EEs exhibited band-pass filtering. We conclude that dynamic recruitment of EEs can increase the tunability of expression levels but are limited in the amount of information that can be reliably transmitted. However, altering the chromatin state can increase the information capacity and also provide complex signal processing behavior.