H2A.Z is a highly conserved histone variant in all species. The chromatin deposition of H2A.Z is specifically catalyzed by the yeast chromatin remodeling complex SWR1 and its mammalian counterpart SRCAP. However, the mechanism by which H2A.Z is preferentially recognized by non-histone proteins remains elusive. Here we identified Anp32e, a novel higher eukaryote-specific histone chaperone for H2A.Z. Anp32e preferentially associates with H2A.Z-H2B dimers rather than H2A-H2B dimers in vitro and in vivo and dissociates non-nucleosomal aggregates formed by DNA and H2A-H2B. We determined the crystal structure of the Anp32e chaperone domain (186-232) in complex with the H2A.Z-H2B dimer. In this structure, the region containing Anp32e residues 214-224, which is absent in other Anp32 family proteins, specifically interacts with the extended H2A.Z αC helix, which exhibits an unexpected conformational change. Genome-wide profiling of Anp32e revealed a remarkable co-occupancy between Anp32e and H2A.Z. Cells overexpressing Anp32e displayed a strong global H2A.Z loss at the +1 nucleosomes, whereas cells depleted of Anp32e displayed a moderate global H2A.Z increase at the +1 nucleosomes. This suggests that Anp32e may help to resolve the non-nucleosomal H2A.Z aggregates and also facilitate the removal of H2A.Z at the +1 nucleosomes, and the latter may help RNA polymerase II to pass the first nucleosomal barrier.

The tandem Tudor-like domain-containing protein Spindlin1 has been reported to be a meiotic spindle-associated protein. Here we report that Spindlin1 is not associated with the spindle in mouse embryonic fibroblast cells during mitotic divisions. In interphase cells, Spindlin1 specifically localizes to the nucleoli. Moreover, Spindlin1 is a histone methylation effector protein that specifically recognizes H3K4 methylation. Finally, Spindlin1 localizes to the active ribosomal DNA (rDNA) repeats, and Spindlin1 facilitates the expression of rRNA genes.

Histone lysine methylation has been implicated in epigenetic regulation of transcription. Using stable-isotope labelling and quantitative mass spectrometry, we analysed the dynamics of histone lysine methylation. Here we report that histone methylation levels are transiently reduced during S phase and are gradually re-established during subsequent cell cycle stages. However, despite the recovery of overall methylation levels before the next S phase, the methylation levels of parental and newly incorporated histones differ significantly. In addition, histone methylation levels are maintained at steady states by both restriction of methyltransferase activity and the active turnover of methyl groups in cells undergoing an extended G1/S phase arrest. Finally, we propose a 'buffer model' that unifies the imprecise inheritance of histone methylation and the faithful maintenance of underlying gene silencing.

Recognition of methylated histone tail lysine residues by tudor domains plays important roles in epigenetic control of gene expression and DNA damage response. Previous studies revealed the binding of methyllysine in a cage of aromatic residues, but the molecular mechanism by which the sequence specificity for surrounding histone tail residues is achieved remains poorly understood. In the crystal structure of a trimethylated histone H3 lysine 4 (H3K4) peptide bound to the tudor-like domains of Spindlin1 presented here, an atypical mode of methyllysine recognition by an aromatic pocket of Spindlin1 is observed. Furthermore, the histone sequence is recognized in a distinct manner involving the amino terminus and a pair of arginine residues of histone H3, and disruption of the binding impaired stimulation of pre-RNA expression by Spindlin1. Our analysis demonstrates considerable diversities of methyllysine recognition and sequence-specific binding of histone tails by tudor domains, and the revelation furthers the understanding of tudor domain proteins in deciphering epigenetic marks on histone tails.H istone lysine methylation imparts epigenetic information in chromatin biology, and the transduction of epigenetic signal is mediated by a diverse group of proteins containing methyllysine recognition domains (1). Some of the best known methyllysine recognition modules include chromo, tudor, MBT (Malignant Brain Tumor), and PHD (Plant Homeodomain) domains (2-4). A recent addition of this family of histone methyllysine "readers" is the BAH domain ORC1 (5). These methyllysine "readers" can recognize histone lysine methylation in a site-specific and methylation state-specific manner. A common feature of methyllysine recognitions involves a cage of aromatic residues, whereas the ways for discriminating the surrounding amino acid sequence of histones appear to be divergent among different methyllysine "readers." In this study, we focus on the recognition of trimethylated lysine-4 of histone H3 (H3K4me3) by the tandem tudor-like domains of Spindlin1.Mammalian Spindlin1 is a nucleolar protein that localizes to the active ribosomal DNA (rDNA) repeats locus, where it is normally enriched with histone H3K4 and H3K36 methylations, and facilitates rRNA expression (6, 7). Spindlin1 contains three tandem tudor-like domains (8), and we previously demonstrated that the tudor-like domains bind to H3K4me3 in vitro (7). Furthermore, Spindlin1 mutants with impaired H3K4me3 binding showed reduced stimulation of rRNA expression (7). Hence, these observations directly link the ability of H3K4me3 binding with the transcription function of Spindlin1. However, several important aspects of the molecular mechanism of H3K4me3 recognition by Spindlin1 remain outstanding; foremost ones include how Spindlin1 achieves its H3K4me3 specificity and what features distinguish the H3K4me3-binding tudor-like domain from others in Spindlin1. Previous structural studies of tudor domains have yielded some understandings of how they recognize methylated histone ...

Placenta formation during pregnancy requires chorioallantoic branching morphogenesis that involves establishing an amplifying feedback loop between Frizzled5 and Gcm1 to regulate branching initiation and trophoblast differentiation.