Epigenome Regulation by Dynamic Nucleosome Unwrapping

Abstract

Gene regulation in eukaryotes requires the controlled access of sequence-specific transcription factors (TFs) to their sites in a chromatin landscape dominated by nucleosomes. Nucleosomes are refractory to TF binding, and often must be removed from regulatory regions. Recent genomic studies together with in vitro measurements suggest that the nucleosome barrier to TF binding is modulated by dynamic nucleosome unwrapping governed by ATP-dependent chromatin remodelers. Genome-wide occupancy and the regulation of subnucleosomal intermediates have gained recent attention with the application of high-resolution approaches for precision mapping of protein-DNA interactions. We summarize here recent findings on nucleosome substructures and TF binding dynamics, and highlight how unwrapped nucleosomal intermediates provide a novel signature of active chromatin.

Keywords: ATP-dependent remodeling; fragile nucleosome; nucleosome dynamics; structural epigenomics; transcription factors.

Figure 1:. Promoter nucleosome organization is regulated by many factors.

(A) Nucleosome organization relative to the TSS (shown by an arrow) of a representative transcriptionally active gene in budding yeast. Strongly positioned nucleosomes flank a NDR, and positioning decreases towards the gene-body (“fuzziness”). A dynamic MNase-sensitive nucleosome or a fragile nucleosome (FN, shown with broken margins) is often occupies the NDR when the gap between the strongly positioned −1 and +1 nucleosomes is larger than 150 bp. The top panel shows the readout from a representative genomic nucleosome profiling experiment (for example MNase-seq). Positioned nucleosomes are seen as discrete peaks (blue). The FN peak (cyan) is seen with partial MNase-digestion of chromatin, but is lost upon extensive digestion. (B) Transcriptionally active or “open” promoter architecture is the result of a tightly regulated interplay of DNA sequence, GRFs, and ATP-dependent nucleosome remodelers. In this configuration, TF-binding sites and the TATA-box are accessible, and the TSS (green arrow) is in a permissive position. (C) In the absence of RSC function, nucleosomes intrude into the NDR-space resulting in occlusion of TF-binding motifs, the TATA box, and the TSS (red arrow). Increased spacing (longer linker DNA) between nucleosomes is typical of these repressed or “closed” promoters.

Figure 2:. Promoter nucleosome substructures.

(A) Canonical nucleosomes have ~147 bp of DNA wrapped around the histone octamer with close to two helical turns of DNA, forming two distinct gyres. The dyad axis (an imaginary axis of symmetry) runs through the center of the nucleosomal DNA. (B) RSC engulfing a nucleosome asymmetrically distorts histone-DNA interactions along one DNA gyre, but the distorted DNA is protected from nuclease cleavage by RSC. (C) Partial unwrapping of DNA from either side (DNA entry and exit) results in increased sensitivity to nucleases (depicted as broken lines). (D) Loss of one of the two H2A-H2B dimers results in a hexasome with increased nuclease sensitivity of DNA close to the edge from where the dimer is lost. (E) Histone-DNA interactions can be lost from an entire gyre (one half of the nucleosome) asymmetrically.

Figure 3(key figure):. A model for catalyzed nucleosome-unwrapping facilitating TF-binding

A SWI/SNF remodeler first engulfs a promoter nucleosome behind the replication fork. The remodeler uses energy from ATP hydrolysis to partially unwrap the nucleosome so as to expose the TF-binding motif. TFs (such as the GRFs in yeast) binding to exposed sequence motifs within unwrapped nucleosomes trap the nucleosome in a partially unwrapped state, but the unstable nucleosome is eventually displaced. TFs binding to non-nucleosomal DNA have short dwell-time, and a new nucleosome is deposited, occluding the site for a displaced TF, thus constituting a dynamic cycle.