“Direct” and “Indirect” Effects of Histone Modifications: Modulation of Sterical Bulk as a Novel Source of Functionality

Abstract

The chromatin‐regulatory principles of histone post‐translational modifications (PTMs) are discussed with a focus on the potential alterations in chromatin functional state due to steric and mechanical constraints imposed by bulky histone modifications such as ubiquitin and SUMO. In the classical view, PTMs operate as recruitment platforms for histone “readers,” and as determinants of chromatin array compaction. Alterations of histone charges by “small” chemical modifications (e.g., acetylation, phosphorylation) could regulate nucleosome spontaneous dynamics without globally affecting nucleosome structure. These fluctuations in nucleosome wrapping can be exploited by chromatin‐processing machinery. In contrast, ubiquitin and SUMO are comparable in size to histones, and it seems logical that these PTMs could conflict with canonical nucleosome organization. An experimentally testable hypothesis that by adding sterical bulk these PTMs can robustly alter nucleosome primary structure is proposed. The model presented here stresses the diversity of mechanisms by which histone PTMs regulate chromatin dynamics, primary structure and, hence, functionality.

The Effects of Histone H2B Ubiquitylations on the Nucleosome Structure and Internucleosomal Interactions

“…Histone H2B ubiquitylations are implicated in facilitated transcription and hexasome formation. ,, Our results suggest that the direct effects are likely from H2BK34ub inducing favorable changes in the nucleosome structure , and that indirect effects are expected from H2BK120 mainly recruiting histone methyltransferase Dot1L. ,,, The results with H2BK34ub add support to the hypothesis that bulky polypeptide PTMs can directly program stably altered dynamic chromatin structures that differ from canonical nucleosomes. , Interestingly, we also observe strengthened long- and short-range internucleosomal interactions with H2BK34ub that will facilitate chromatin compaction and help maintain the structural integrity of chromatin. On the basis of these results, we suggest that the ubiquitin molecules in H2BK34ub nucleosomes protrude between the DNA gyres and relax the DNA–(H2A–H2B) contact region, thereby destabilizing the nucleosome.…”

“…The decreased FRET efficiency is still very high compared to a stable mid-range FRET (∼0.5) observed from a DNA-unwrapped state in the DNA–(H2A–H2B) region as we previously reported during transcription elongation. , Therefore, we conclude that the FRET decrease is likely due to the widening of the gap between the DNA gyres in the H2BK34ub nucleosome. This is in line with the cryo-EM structures of nucleosomes reconstituted with H2BK34ub, suggesting that the ubiquitin moieties may protrude between the DNA gyres. , This protrusion would destabilize DNA–histone contacts in the DNA–(H2A–H2B) region and make the nucleosome conformationally more dynamic than unmodified nucleosomes, facilitating genome transactions in the nucleosome. ,, Expedited hexasome generation from H2BK34ub nucleosomes by histone chaperone Nap1 supports this mechanism. − ,, A similar effect was observed with H2BK120ub albeit to a much lesser extent, ,, possibly because the ubiquitin is far from the DNA–histone contact region and likely sits on the lateral surface of the histone core …”

Histone Modifications, Internucleosome Dynamics, and DNA Stresses: How They Cooperate to “Functionalize” Nucleosomes

“…These results suggest a hypothesis ( Krajewski, 2019 ; Krajewski WA., 2020 ) that in contrast to “small” histone PTMs, attachment to nucleosomes at certain positions of ubiquitin (and, supposedly, other bulky PTMs) could potentially represent an in vivo mechanism to functionalize canonic nucleosomes by strikingly increasing their dynamics and triggering the conversion of a nucleosome to a more functionally active hexasome particle.…”

“…This feature would be consistent with a series of recent findings showing that K34-ubiquitylation of histone H2B (and H2BK120ub to a lesser degree) can significantly enhance nucleosome dynamics, decrease nucleosome stability, and promote eviction of one histone H2A-H2B dimer ( Krajewski et al, 2018 ; Krajewski W. A., 2020 ), especially in the presence of histone chaperons. This effect is likely due to the steric hindrances by “bulky” ubiquitin moieties, which destabilize the nucleosome ( Krajewski, 2019 ; Krajewski WA., 2020 ). The resulting hexasome particle was stable, suggesting that dissociation of one ubiquitylated histone dimer is sufficient to relieve the steric stresses incurred by massive ubiquitin moieties ( Krajewski et al, 2018 ; Krajewski W. A., 2020 ).…”

“…A different situation could be if a nucleosome structure is already intrinsically destabilized by deposited bulky histone modification. We propose that DNA topology, favoring or disfavoring nucleosome wrapping, may contribute to the structural effects of histone ubiquitylation ( Krajewski, 2019 ; Krajewski WA., 2020 ) ( Figure 2C ). In our experiments, “physiological” negative and positive supercoiling in long DNA templates had opposing (stimulating or inhibitory, respectively) effects on the hexasome generation upon assembly of H2BK34ub nucleosomes ( Krajewski et al, 2018 ) but had no effect on unmodified nucleosomes.…”