(600a) Assessing the Role of Chromatin in Decoding NF-?b Signals

Background

The transcription factor, NF-KB, is an important regulator of immune cells' responses to inflammatory stimuli including cytokines released from immune cells as well as pathogen-associated molecular factors [1]. Single-cell measurements of NF-KB nuclear translocation and mRNA expression of downstream genes have revealed the role of dynamics in controlling distinct cytokine expression patterns [2,3]. However, our labs recently discovered that the interactions between NF-KB and chromatin produce another layer of regulation which also impacts how dynamic signals are decoded [4]. In fact, for some phenotype relevant signals, this layer of regulation will control the variability in expression patterns. For example, in our system of latent HIV LTR promoters (which has KB binding sites), the nature of transcriptional bursting is associated with different chromatin states and drives divergent NF-KB-dependent viral activation profiles. These observations prompted us to ask the question, Is there a general network motif (logical connection) that can explain NF-KB dependent gene expression variability?

Work in brief

We started with a mechanistic model of RelA (NF-KB subunit) dynamics that describes its cytoplasmic sequestration and stimulus-induced nuclear translocation. In the nucleus, we model RelA binding to different KB sites on the chromatin with different affinities, including competitive inhibition from protein complexes containing certain other NF-KB subunits. This model was then calibrated to measurements of nuclear RelA and transcriptional dynamics in Jurkat T lymphocyte clones. Finally, based on the distributions of uncertain parameters and their biological underpinnings, we introduced network connections to recapitulate the key experimental observations that were not captured with a simpler model. These network connections model the integration of information from NF-KB binding dynamics and the chromatin environment.

Conclusions and future directions

Our modeling results show which parameter constraints can dictate how the chromatin environment near a target promoter puts a check on information transmission from an input of NF-KB activation to an output of RNA polymerase-mediated transcription. Because it is anchored in quantitative experimental data, the logical underpinnings from this work will enable us to quantitatively explain divergent HIV reactivation phenotypes as well as divergent transcriptional responses among endogenous NF-KB targets.

References:

[1] Hoffmann, A. and Baltimore, D. (2006) Immunol Rev, 210, pp 171-186

[2] Lane, K., Van Valen, D., et al. (2017) Cell Sys, 4(4), pp 458-469

[3] Kobayashi, T. and Kageyama, R. (2009) Sci Sig, 2(81), pe 47

[4] Wong, V. et al. (2018) Cell Rep 22(3), pp 585-599