Gene control with a “twist”: Exploring the dynamic chromatin landscape

Abstract

The dynamic organization of the eukaryotic genome into chromatin is integral to genome regulation. Chromatin structure and dynamics, modulated by histone post-translational modifications (PTMs) as well as architectural proteins, dictate DNA access for transcription factors and the gene expression machinery. While of key importance, the detailed mechanisms of DNA access regulation by chromatin dynamics are however still poorly understood.

We dissect chromatin signaling on the single-molecules scale, combining chemical biology approaches and mechanistic biophysics. We recently developed a single-molecule FRET (smFRET) approach to directly observe the dynamic architecture of chemically defined chromatin fibers. We find that local chromatin organization is based on tetranucleosome units, which undergo structural fluctuations on the micro- to millisecond timescale. These dynamics are regulated by histone PTMs and linked to function. Indeed, internal chromatin dynamics are exploited by transcription factors (TF) to invade chromatin structure. Employing single-molecule fluorescence imaging we could observe how a yeast pioneer TF, Rap1, binds its target promoter in compact chromatin. Importantly, we show that Rap1 binding opens chromatin fiber structure by inhibiting nucleosome-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to shift promoter nucleosomes, paving the way to form long-lived bound states on now exposed DNA.

In summary, our results provide a mechanistic view of how a pioneer TF gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression.