Graphical Abstract Highlights d The yeast transcription factor Rap1 can invade compact chromatin d Rap1 directly opens chromatin structure by preventing nucleosome stacking d Stable Rap1 binding requires collaboration with RSC to shift promoter nucleosomes In Brief Mivelaz et al. use single-molecule fluorescence approaches and highly defined chromatin systems to show that the yeast transcription factor Rap1 can invade compact chromatin fibers and directly open chromatin structure. For stable binding, Rap1 then collaborates with RSC to displace nucleosomes from its binding sites, generating an active promoter state. SUMMARY Pioneer transcription factors (pTFs) bind to target sites within compact chromatin, initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood.Here, we reveal, using single-molecule fluorescence, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture, we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting inter-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to displace promoter nucleosomes, paving the way for long-lived bound states on newly exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression.

Due to the essential roles of glutamate, detection and response to a large range of extracellular concentrations of this excitatory amino acid are necessary for the fine-tuning of brain functions. Metabotropic glutamate receptors (mGluRs) are implicated in shaping the activity of many synapses in the central nervous system. Among the eight mGluR subtypes, there is increasing interest in studying the mGlu receptor which has recently been linked to various diseases, including psychiatric disorders. This receptor displays striking functional properties, with a high and, often, full basal activity, making its study elusive in heterologous systems. Here, we demonstrate that Cl ions exert strong positive allosteric modulation of glutamate on the mGlu receptor. We have also identified the molecular and structural determinants lying behind this allostery: a unique interactive "chloride-lock" network. Indeed, Cl ions dramatically stabilize the glutamate-induced active state of the extracellular domain of the mGlu receptor. Thus, the mGlu receptors' large basal activity does not correspond to a constitutive activity in absence of agonist. Instead, it results mostly from a Clmediated amplified response to low ambient glutamate concentrations, such as those measured in cell media. This strong interaction between glutamate and Cl ions allows the mGlu receptor to sense and efficiently react to sub-micromolar concentrations of glutamate, making it the most sensitive member of mGluR family.