Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners

Abstract

Histone variants fine-tune transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether and how nucleosome variants encode unique mechanical properties to their cognate chromatin structures remains elusive. Here, using in silico and in vitro nanoindentation methods, extending to in vivo dissections, we report that histone variant nucleosomes are intrinsically more elastic than their canonical counterparts. Furthermore, binding proteins, which discriminate between histone variant nucleosomes, suppress this innate elasticity and also compact chromatin. Interestingly, when we overexpress the binding proteins in vivo, we also observe increased compaction of chromatin enriched for histone variant nucleosomes, correlating with diminished access. Taken together, these data suggest a plausible link between innate mechanical properties possessed by histone variant nucleosomes, the adaptability of chromatin states in vivo, and the epigenetic plasticity of the underlying locus.

Job Opening for Nucleosome Mechanic: Flexibility Required

“…One logical prediction of a macromolecule with greater intrinsic internal motions is that they are more elastic (lower Young's modulus) than their canonical counterpart. Indeed, this is what was observed [15]. Interestingly, MCA showed that the heterotypic CENP-A:H3.3 nucleosome, which has been observed in cancer cells [81,82], had a Young's modulus in between CENP-A and H3 nucleosomes [80].…”

“…Elasticity is formally defined by Hooke's law, which states that the strain in a material is proportional to the applied stress within the elastic limit, which is quantified by Young's modulus. Elastic properties of macromolecules are encoded by their quaternary and higher order structures, as either structurally disordered networks of flexible fibers, or structurally ordered macromolecules [14,15]. Chromatin fibers are in the regime of elastomers found elsewhere in nature, yet little is understood about how equivalent mechanical properties might contribute to its function.…”

Job Opening for Nucleosome Mechanic: Flexibility Required

“…Interestingly, MCA showed that the heterotypic CENP-A:H3.3 nucleosome, which has been observed in cancer cells (81,82), had a Young's modulus in between CENP-A and H3 nucleosomes (80). Furthermore, the CENP-A binding protein CENP-C suppressed the internal motions, resulting in a higher Young's modulus (15). In addition to histone variants, the linker histone H1 family (83) impact the chromatin fiber dynamics, most notably by inducing chromatin condensation (84).…”

“…Examples of the extrusion idea, whether by mechanical features, or phase transitions, exist in the literature (15,80,(95)(96)(97). First, a recent cryoEM study of tri-nucleosomes showed that a single CENP-A nucleosome flanked by two H3 nucleosomes created an untwisted structure, demonstrating the power of a single nucleosome to alter the "stitch" of the fiber (95).…”

“…A second example comes from a recent study (from our lab), which dissected nucleosomal elasticity for the first time using both computational approaches and nanoindentation AFM studies, we reported that CENP-A nucleosomes are twice as elastic as canonical H3 nucleosomes, but that kinetochore protein binding suppressed the elastic state. Indeed, in vivo, a domain of more elastic CENP-A nucleosomes, in a bed of otherwise rigidified kinetochore bound CENP-A was postulated to extrude small stretches of elastic chromatin fiber, upon which the local recruitment of transcription machinery depended (15,80). A third example is that of fission yeast heterochromatin protein Swi6, which binds to H3K9me3 nucleosomes and subsequently compacts and transcriptionally represses the chromatin fiber ( Figure 3B).…”