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

Abstract

Eukaryotic gene compaction takes place at multiple levels to package DNA to chromatin and chromosomes. Two of the most fundamental levels of DNA packaging are at the nucleosome and dinucleosome stacks. The nucleosome is the basic gene-packing unit and is composed of DNA wrapped around a histone core. Nucleosomes stack with one another for further compaction of DNA. The first stacking step leads to dinucleosome formation, which is driven by internucleosomal interactions between various parts of two nucleosomes. Histone proteins are rich targets for post-translational modifications, some of which affect the structure of the nucleosome and the interactions between nucleosomes. These effects are often implicated in the regulation of various genomic transactions. In particular, histone H2B ubiquitylation has been associated with facilitated transcription and hexasome formation. Here, we employed semi-synthetically ubiquitylated histone H2B and single-molecule FRET to investigate the effects of H2B ubiquitylations at lysine 34 (H2BK34) and lysine 120 (H2BK120) on the structure of the nucleosome and the interactions between two nucleosomes. Our results suggest that H2BK34 ubiquitylation widens the DNA gyre gap in the nucleosome and stabilizes long-and short-range internucleosomal interactions while H2BK120 ubiquitylation does not affect the nucleosome structure or internucleosomal interactions. These results suggest potential roles for H2B ubiquitylations in facilitated transcription and hexasome formation while maintaining the structural integrity of chromatin.

The Effects of Histone H2B ubiquitylations and H3K79me3on Transcription Elongation

“…These results suggest that the effects of H2BK34ub on transcription kinetics can be the major mechanisms of facilitated transcription by H2B ubiquitylations. The effects are likely due to localized perturbations of the nucleosome structure near the DNA-(H2B-H2B) contact region, which has been validated by our recent structural study based on smFRET 56 . We suspect that the weaker effects of H2BK120ub is due to its non-ideal location to affect DNA-histone interactions.…”

Effects of Histone H2B Ubiquitylations and H3K79me3 on Transcription Elongation

“… Since then, it has been shown that H2BK34ub nucleosomes have the ubiquitin moieties protrude between the two gyres of the nucleosomal DNA, weakening the structural integrity of the nucleosome and distorting DNA toward the entry region of the nucleosome. , These results suggest that the effects of H2BK34ub on transcription kinetics can be the major mechanisms of facilitated transcription by H2B ubiquitylations. The effects are likely due to localized perturbations of the nucleosome structure near the DNA–(H2B-H2B) contact region, which has been validated by our recent structural study based on smFRET . We suspect that the weaker effects of H2BK120ub are due to its nonideal location to affect DNA–histone interactions.…”

Beyond Sequence: Internucleosomal Interactions Dominate Array Assembly

“…However, affinity of nucleosomes to positioning sequences can prevent the assembly of nucleosome clusters. It has also been discussed 47 that the relaxed DNA− (H2A−H2B) region may contribute to long-range internucleosomal interactions between DNA and histone tails. Therefore, the decrease in the binding between DNA and histone octamers on the nonspecific substrate compared to that on the 601 sequence benefits the long-range internucleosomal interactions and, ultimately, the compaction of the oligonucleosomes.…”