Structural and biochemical analyses of monoubiquitinated human histones H2B and H4.

Shinichi Machida,Hitoshi Kurumizaka,Yuuki Nishiyama,Satoshi Sekine,Naoki Horikoshi

doi:10.1098/rsob.160090

Abstract

Monoubiquitination is a major histone post-translational modification. In humans, the histone H2B K120 and histone H4 K31 residues are monoubiquitinated and may form transcriptionally active chromatin. In this study, we reconstituted nucleosomes containing H2B monoubiquitinated at position 120 (H2Bub120) and/or H4 monoubiquitinated at position 31 (H4ub31). We found that the H2Bub120 and H4ub31 monoubiquitinations differently affect nucleosome stability: the H2Bub120 monoubiquitination enhances the H2A–H2B association with the nucleosome, while the H4ub31 monoubiquitination decreases the H3–H4 stability in the nucleosome, when compared with the unmodified nucleosome. The H2Bub120 and H4ub31 monoubiquitinations both antagonize the Mg2+-dependent compaction of a poly-nucleosome, suggesting that these monoubiquitinations maintain more relaxed conformations of chromatin. In the crystal structure, the H2Bub120 and H4ub31 monoubiquitinations do not change the structure of the nucleosome core particle and the ubiquitin molecules were flexibly disordered in the H2Bub120/H4ub31 nucleosome structure. These results revealed the differences and similarities of the H2Bub120 and H4ub31 monoubiquitinations at the mono- and poly-nucleosome levels and provide novel information to clarify the roles of monoubiquitination in chromatin.

Highlights

In eukaryotes, genomic DNA is folded into a higher-order structure called chromatin and is accommodated within the nucleus [1]
The H2B K120C and H4ub31 or (H4) K31C mutants, in which the H2B K120 and H4 K31 residues were replaced by cysteine, respectively, were purified as recombinant proteins, and the ubiquitin molecule was chemically conjugated by a disulfide bond to the H2B C120 and H4 C31 residues [32]
These results indicated that the H2Bub120 and H4 monoubiquitinated at position 31 (H4ub31) molecules were properly assembled into the nucleosomes

Summary

Introduction

Genomic DNA is folded into a higher-order structure called chromatin and is accommodated within the nucleus [1]. The 145– 147 base-pair DNA segments are left-handedly wrapped by about 1.7 turns around the histone octamer in the nucleosome [3,4,5]. The activities of genomic DNA, such as transcription, must be regulated in chromatin [6]. Numerous histone modifications and histone variants contribute to the structural and physical versatility of nucleosomes and affect the chromatin dynamics, and play a crucial role to accomplish the regulation of genomic DNA in chromatin [10,11,12,13,14,15,16,17,18,19,20,21]

Methods

Results

Conclusion