Structural basis of nucleosome dynamics modulation by histone variants H2A.B and H2A.Z.2.2.

Nucleosomes are dynamic entities with wide-ranging compositional variations. Human histone variants H2A.B and H2A.Z.2.2 play critical roles in multiple biological processes by forming unstable nucleosomes and open chromatin structures, but how H2A.B and H2A.Z.2.2 confer these dynamic features to nucleosomes remains unclear. Here, we report cryo-EM structures of nucleosome core particles containing human H2A.B (H2A.B-NCP) at atomic resolution, identifying large-scale structural rearrangements in the histone octamer in H2A.B-NCP. H2A.B-NCP compacts approximately 103 bp of DNA wrapping around the core histones in approximately 1.2 left-handed superhelical turns, in sharp contrast to canonical nucleosome encompassing approximately 1.7 turns of DNA. Micrococcal nuclease digestion assay reveals that nineteen H2A.B-specific residues, including a ROF ("regulating-octamer-folding") sequence of six consecutive residues, are responsible for loosening of H2A.B-NCPs. Unlike H2A.B-NCP, the H2A.Z.2.2-containing nucleosome (Z.2.2-NCP) adopts a less-extended structure and compacts around 125 bp of DNA. Further investigation uncovers a crucial role for the H2A.Z.2.2-specific ROF in both H2A.Z.2.2-NCP opening and SWR1-dependent histone replacement. Taken together, these first high-resolution structure of unstable nucleosomes induced by histone H2A variants elucidate specific functions of H2A.B and H2A.Z.2.2 in enhancing chromatin dynamics.

Structural basis of nucleosomal H4K20 methylation by methyltransferase SET8.

Histone H4 lysine 20 monomethylation (H4K20me1) plays a crucial role in multiple processes including DNA damage repair, DNA replication, and cell cycle control. Histone methyltransferase SET8 (previously named PR-Set7/KMT5A) mediates the chromatin deposition of H4K20me1, but how SET8 recognizes and modifies H4 in the context of the nucleosome is not fully understood. Here, we developed a simple chemical modification approach for H4K20 substitution by using the lysine analog S-ethyl-L-cysteine (Ecx). Substitution of H4K20 with H4Ecx20 improves the stability of the SET8-nucleosome complex, allowing us to determine the cryo-EM structure at 3.2 Å resolution. Structural analyses show that SET8 directly interacts with the H4 tail and the H2A-H2B acidic patch to ensure nucleosome binding. SET8 residues R339, K341, K351 make contact with nucleosomal DNA at the super helical location 2 (SHL2). Substitution of SET8 DNA-binding residues with alanines decreases the SET8-nucleosome interaction and impairs the methyltransferase activity. Disrupting the binding between SET8 R192 and H2A-H2B acidic patch decreases the cellular level of H4K20me1. Together, these results reveal a near-atomic resolution structure of SET8-bound nucleosome and provide insights into the SET8-mediated H4K20 recognition and modification. The lysine-to-Ecx substitution approach can be applied to the study of other methyltransferases.

Effect of DNMT inhibitor on bovine parthenogenetic embryo development.

DNA methylation catalyzed by DNA methyltransferase (DNMT) family plays an important role during mammal preimplanted embryo development. However, the effects of RG108, a DNMT inhibitor (DNMTi), on DNMT in the development of bovine preimplanted embryos are not fully elucidated. In this study, we investigated the role of RG108 on the development, dynamics of gene-specific DNA methylation and transcription of bovine parthenogenetic preimplantation embryos. We found that Dnmt1 and Dnmt3b showed highly transcription in parthenogenetic 2-cell embryos, and then the transcription levels decreased during the following development stages, whereas Dnmt3a was always maintained at a lower transcription level during bovine parthenogenetic preimplantation embryo development. Treatment with RG108 blocked the development of bovine parthenogenetic preimplantation embryos and induced hypomethylation in the embryos. RG108 decreased the methylation level of the Nanog gene promoter region, which caused activation of the Nanog gene in 8-cell embryos and increased the transcription level. RG108 also induced the hypomethylation of the repeat elements (satellite I and α-satellite), which may cause genome instability, increasing the number of apoptotic cells in the blastocysts and also the transcription level of the apoptotic gene Bax. These results indicate that RG108, a DNMT inhibitor (DNMTi), inhibits the development of bovine parthenogenetic preimplantation embryos, suggesting that the DNMT is necessary for bovine parthenogenetic preimplanatation embryo development.

Sodium butyrate-induced histone hyperacetylation up-regulating WT1 expression in porcine kidney fibroblasts.

OBJECTIVES: Wilms' tumor 1 gene (WT1) is essential for the development of kidney and histone acetylation and is involved in its expression regulation in mice. However, whether WT1 expression is associated with histone acetylation in porcine kidney cells is unclear. Here, the effect of histone deacetylase inhibitor sodium butyrate (NaBu)-induced hyperacetylation on WT1 expression in porcine kidney fibroblasts (PKF) was examined. RESULTS: Treatments of NaBu (1, 3, 6 mM) for 24 h increased PKF viability, and 24, 48 h-treatments of 1 mM NaBu enhanced PKF proliferation. WT1 mRNA levels were significantly elevated in NaBu-treated (1, 3 mM for 24, 48 h, respectively) PKF samples. Consistently, strengthened expression of WT1 protein and histone acetylation level were detected in NaBu-treated PKF cells. CONCLUSION: Together, NaBu-induced hyperacetylation up-regulates WT1 expression in PKF, suggesting the involvement of histone acetylation in the transcriptional modulation of WT1 in porcine kidney cells.

Molecular basis for the selective recognition and ubiquitination of centromeric histone H3 by yeast E3 ligase Psh1.

Centromeres are chromosomal loci marked by histone variant CenH3 (centromeric histone H3) and essential for genomic stability and cell division. The budding yeast E3 ubiquitin ligase Psh1 selectively recognizes the yeast CenH3 (Cse4) for ubiquitination and controls the cellular level of Cse4 for proteolysis, but the underlying mechanism remains largely unknown. Here, we show that Psh1 uses a Cse4-binding domain (CBD, residues 1-211) to interact with Cse4-H4 instead of H3-H4, yielding a dissociation constant (Kd) of 27 nM. Psh1 recognizes Cse4-specific residues in the L1 loop and α2 helix to ensure Cse4 binding and ubiquitination. We map the Psh1-binding region of Cse4-H4 and identify a wide range of Cse4-specific residues required for the Psh1-mediated Cse4 recognition and ubiquitination. Further analyses reveal that histone chaperone Scm3 can impair Cse4 ubiquitination by abrogating Psh1-Cse4 binding. Together, our study reveals a novel Cse4-binding mode distinct from those of known CenH3 chaperones and elucidates the mechanism by which Scm3 competes with Psh1 for Cse4 binding.

Recognition of the inherently unstable H2A nucleosome by Swc2 is a major determinant for unidirectional H2A.Z exchange.

The multisubunit chromatin remodeler SWR1/SRCAP/p400 replaces the nucleosomal H2A-H2B dimer with the free-form H2A.Z-H2B dimer, but the mechanism governing the unidirectional H2A-to-H2A.Z exchange remains elusive. Here, we perform single-molecule force spectroscopy to dissect the disassembly/reassembly processes of the H2A nucleosome and H2A.Z nucleosome. We find that the N-terminal 1-135 residues of yeast SWR1 complex protein 2 (previously termed Swc2-Z) facilitate the disassembly of nucleosomes containing H2A but not H2A.Z. The Swc2-mediated nucleosome disassembly/reassembly requires the inherently unstable H2A nucleosome, whose instability is conferred by three H2A α2-helical residues, Gly47, Pro49, and Ile63, as they selectively weaken the structural rigidity of the H2A-H2B dimer. It also requires Swc2-ZN (residues 1-37) that directly anchors to the H2A nucleosome and functions in the SWR1-catalyzed H2A.Z replacement in vitro and yeast H2A.Z deposition in vivo. Our findings provide mechanistic insights into how the SWR1 complex discriminates between the H2A nucleosome and H2A.Z nucleosome, establishing a simple paradigm for the governance of unidirectional H2A.Z exchange.