Hexasomal particles: consequence or also consequential?

Abstract

It is long known that an RNA polymerase transcribing through a nucleosome can generate subnucleosomal particles called hexasomes. These particles lack an H2A-H2B dimer, breaking the symmetry of a nucleosome and revealing new interfaces. Whether hexasomes are simply a consequence of RNA polymerase action or they also have a regulatory impact remains an open question. Recent biochemical and structural studies of RNA polymerases and chromatin remodelers with hexasomes motivated us to revisit this question. Here, we build on previous models to discuss how formation of hexasomes can allow sophisticated regulation of transcription and also significantly impact chromatin folding. We anticipate that further cellular and biochemical analysis of these subnucleosomal particles will uncover additional regulatory roles.

Figure 1

Comparison of nucleosome and hexasome structures. (a) Nucleosome structure (PDB: 1KX5) consisting of ~147 bp of DNA wrapped around an octamer core containing one H3–H4 tetramer (gray) and two H2A–H2B dimers (blue or cyan). The flanking DNA is shown in gold. (b) Hexasome structure (PDB: 6ZHY) consisting of ~112 bp of DNA wrapped around a hexamer core containing an H3–H4 tetramer and one H2A–H2B dimer. The DNA wrapped around a nucleosome can be divided into waypoints at superhelical locations (SHLs) separated by 10 base-pairs across the histone octamer surface, which are mirrored on the opposite face. The dyad is defined by SHL0. Note that here we show the promoter-proximal dimer (blue) as that closest to the end of the DNA away from the flanking DNA. The flanking (gold) and unwrapped (orange) DNA has been modeled in.

Figure 2

Models for the interplay between hexasomes and RNAPII transcription. (a) A hexasome missing either the promoter-proximal or promoter-distal dimer results in stalling of RNAPII or facilitates passage of RNAPII, respectively [10]. TSS refers to transcription start site. Notably, RNAPII transcribes faster through a hexasome missing the promoter-distal dimer compared with a nucleosome. (b) When RNAPII and elongation factors (RNAPII EC), encounter a nucleosome, DNA is unwrapped from the promoter-proximal dimer, which may destabilize the dimer and lead to its loss and formation of a hexasome that would lead to RNAPII stalling. Model based on Ref. [12]. (c) When RNAPII EC and a histone chaperone FACT encounter a nucleosome, DNA is unwrapped from the promoter-proximal dimer but FACT stabilizes and prevents loss of the dimer. Downstream-distal DNA is simultaneously unwrapped, which destabilizes the promoter-distal dimer, leading to its loss. A FACT subunit may interact with the dissociated free dimer. Multiple kinetically partitioned pathways can be imagined at this stage, that include the hexasome orientation remaining the same, FACT flipping the orientation of the hexamer, and FACT redepositing the dimer to regenerate a nucleosome. Each pathway has a different consequence for the next RNAPII EC. Model based on Refs. [–11,13]. For all panels, H3–H4 tetramer is in gray and H2A–H2B dimers are in blue or cyan.

Figure 3

Model for chromatin remodelers acting on hexasomes in the wake of transcription. The context for the model is a promoter as found in S. cerevisiae. The promoter contains a nucleosome-depleted region (NDR) that contains the TSS. Well-positioned nucleosomes flank the NDR. Nucleosomes within the gene body are shown numbered with ‘+’ signs and the nucleosome upstream of the NDR is shown numbered with a ‘−’ sign. (a) RNAPII EC at the TSS. (b) As RNAPII EC moves through the gene body, hexasomes may form with either the promoter-proximal or promoter-distal dimer missing. All (sub)nucleosomes are shifted toward the promoter in the process (black arrows). Chromatin remodelers can slide the hexasomes in a directional manner depending on which dimer is lost [–37]. How these remodelers coordinate to reposition these particles correctly remains an open question. (c) Binding of Reb1 and other factors has been shown to change the directionality of sliding by Chd1 [35]. Binding of additional factors may also play a role in regulating the process modeled in (B).