Isolation of four core histones from human sperm chromatin representing a minor subset of somatic histones

Using high performance liquid chromatography we have successfully purified four core histones from mature human sperm chromatin. The H2A variants present in sperm (H2A.X and limited H2A.Z) have been shown previously to be minor variants in somatic chromatin. The histones are highly modified as evidenced by extensive acetylation and an as yet uncharacterized multicharge modification of H2B. Based on our data, we conclude that histone proteins are a minor component of each mature spermatozoa. Given the unique nature of the histone variants present in sperm, we propose that this chromatin component has a specific function and may possibly facilitate the programming of genes which will be active in early development.     

Dynamic expression of combinatorial replication-dependent histone variant genes during mouse spermatogenesis

Nucleosomes are basic chromatin structural units that are formed by DNA sequences wrapping around histones. Global chromatin states in different cell types are specified by combinatorial effects of post-translational modifications of histones and the expression of histone variants. During mouse spermatogenesis, spermatogonial stem cells (SSCs) self-renew while undergo differentiation, events that occur in the company of constant re-modeling of chromatin structures. Previous studies have shown that testes contain highly expressed or specific histone variants to facilitate these epigenetic modifications. However, mechanisms of regulating the epigenetic changes and the specific histone compositions of spermatogenic cells are not fully understood. Using real time quantitative RT-PCR, we examined the dynamic expression of replication-dependent histone genes in post-natal mouse testes. It was found that distinct sets of histone genes are expressed in various spermatogenic cells at different stages during spermatogenesis. While gonocyte-enriched testes from mice at 2-dpp (days post partum) express pre-dominantly thirteen histone variant genes, SSC-stage testes at 9-dpp highly express a different set of eight histone genes. During differentiation stage when testes are occupied mostly by spermatocytes and spermatids, another twenty-two histone genes are expressed much higher than the rest, including previously known testis-specific hist1h1t, hist1h2ba and hist1h4c. In addition, histone genes that are pre-dominantly expressed in gonocytes and SSCs are also highly expressed in embryonic stem cells. Several of them were changed when embryoid bodies were formed from ES cells, suggesting their roles in regulating pluripotency of the cells. Further more, differentially expressed histone genes are specifically localized in either SSCs or spermatocytes and spermatids, as demonstrated by in situ hybridization using gene specific probes. Taken together, results presented here revealed that different combinations of histone variant genes are expressed in distinct spermatogenic cell types accompanying the progression of self-renewal and differentiation of SSCs, suggesting a systematic regulatory role histone variants play during spermatogenesis.     

Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering

Chromatin modifications, such as post-translational modification of histone proteins and incorporation of histone variants, play an important role in regulating gene expression. Joint analyses of multiple histone modification maps are starting to reveal combinatorial patterns of modifications that are associated with functional DNA elements, providing support to the 'histone code' hypothesis. However, due to the lack of analytical methods, only a small number of chromatin modification patterns have been discovered so far. Here, we introduce a scalable subspace clustering algorithm, coherent and shifted bicluster identification (CoSBI), to exhaustively identify the set of combinatorial modification patterns across a given epigenome. Performance comparisons demonstrate that CoSBI can generate biclusters with higher intra-cluster coherency and biological relevance. We apply our algorithm to a compendium of 39 genome-wide chromatin modification maps in human CD4(+) T cells. We identify 843 combinatorial patterns that recur at >0.1% of the genome. A total of 19 chromatin modifications are observed in the combinatorial patterns, 10 of which occur in more than half of the patterns. We also identify combinatorial modification signatures for eight classes of functional DNA elements. Application of CoSBI to epigenome maps of different cells and developmental stages will aid in understanding how chromatin structure helps regulate gene expression.     

Partitioning and plasticity of repressive histone methylation states in mammalian chromatin

Methylation of position-specific lysine residues in histone N termini is a central modification for regulating epigenetic transitions in chromatin. Each methylatable lysine residue can exist in a mono-, di-, or trimethylated state, thereby extending the indexing potential of this particular modification. Here, we examine all possible methylation states for histone H3 lysine 9 (H3-K9) and lysine 27 (H3-K27) in mammalian chromatin. Using highly specific antibodies together with quantitative mass spectrometry, we demonstrate that pericentric heterochromatin is selectively enriched for H3-K27 monomethylation and H3-K9 trimethylation. This heterochromatic methylation profile is dependent on the Suv39h histone methyltransferases (HMTases) but independent of the euchromatic G9a HMTase. In Suv39h double null cells, pericentric heterochromatin is converted to alternative methylation imprints and accumulates H3-K27 trimethylation and H3-K9 monomethylation. Our data underscore the selective presence of distinct histone lysine methylation states in partitioning chromosomal subdomains but also reveal a surprising plasticity in propagating methylation patterns in eukaryotic chromatin.     

基于ChIP-seq的差异组蛋白修饰区域的筛选

组蛋白修饰是在基因组水平上起到重要调控作用的表观遗传修饰,随着ChIP-Seq的广泛使用,高通量数据的积累,为从全基因组研究组蛋白修饰模式奠定了基础。但目前缺乏在多样本间筛选疾病相关的调控区域的方法,因而本文开发了一种多细胞系的差异筛选算法来识别差异组蛋白修饰区域。本文通过窗口移动法来估计组蛋白修饰水平,并根据信息熵理论定量各个细胞系之间的差异。基于随机背景来确定差异显著性阈值。利用此算法来筛选人类全基因组9个细胞系间H3K4me3差异的区域,结果显示这些区域显著富集在基因启动子上和其他重要的染色质状态上,且与先前人们发现的活性启动子染色质状态显著重叠。通过文献挖掘进一步证实了与白血病相关的基因组标记。这些结果表明基于熵的策略可有效地挖掘多细胞系间以及与疾病相关的差异组蛋白修饰。     

The role of histones in chromatin remodelling during mammalian spermiogenesis.

One of the most dramatic chromatin remodelling processes takes place during mammalian spermatogenesis. Indeed, during the postmeiotic maturation of male haploid germ cells, or spermiogenesis, histones are replaced by small basic proteins, which in mammals are transition proteins and protamines. However, nothing is known of the mechanisms controlling the process of histone replacement. Two hints from the literature could help to shed light on the underlying molecular events: one is the massive synthesis of histone variants, including testis-specific members, and the second is a stage specific post-translational modification of histones. A new testis-specific 'histone code' can therefore be generated combining both histone variants and histone post-translational modifications. This review will detail these two phenomena and discuss possible functional significance of the global chromatin alterations occurring prior to histone replacement during spermiogenesis.     

Histones and Plant Hormones: New Evidence for an Interesting Interplay

As any living organism, plants have to respond to a wide variety of biotic and abiotic signals. One of the most important challenges for the plant cell is the response to plant hormones, compounds that regulate almost all aspects of plant development. This process involves the appropriate alteration of chromatin structure and function which can be facilitated by a number of different mechanisms, including histone covalent modifications, incorporation of distinct histone variants, chromatin remodeling and epigenetic regulation of gene expression. On the other hand, distinct chromatin states may in turn influence plant hormone biosynthesis and signaling. This article aims to review the evidence accumulated the last years concerning the effect of the major plant hormones - auxin, gibberellins, cytokinins, ethylene, abscisic acid, brassinosteroids and jasmonic acid - signaling on histone variants and modification pattern and to discuss the interplay between histones and hormones at plant chromatin.     

Remodelling chromatin to shape development of plants

Establishment and dynamic regulation of a higher order chromatin structure is an essential component of development. Chromatin remodelling complexes such as the SWI2/SNF2 family of ATP-dependent chromatin remodellers can alter chromatin architecture by changing nucleosome positioning or substituting histones with histone variants. These remodellers often act in concert with chromatin modifiers such as the polycomb group proteins which confer repressive states through modification of histone tails. These mechanisms are highly conserved across the eukaryotic kingdom although in plants, owing to the maintenance of dedifferentiated cell states that allow for post-embyronic changes in development, strict control of chromatin remodelling is even more paramount. Recent and ongoing studies in the model plant Arabidopsis thaliana have found that while the major families of the SWI2/SNF2 ATPase chromatin remodellers are represented, a number of redundancies and divergent functions have emerged that show a break from the roles of their metazoan counterparts. This review focusses on the SNF2 and CHD families of ATP-dependent remodellers and their roles in plant development.     

Histone Variants in Development and Diseases

Eukaryotic genomic DNA is highly packaged into chromatin by histones to fit inside the nucleus. Other than the bulk packaging role of canonical histones with an expression peak at S phase and replication-coupled deposition, different histone variants have evolved distinct regulatory mechanisms for their expression, deposition and functional implications. The diversity of histone variants results in structural plasticity of chromatin and highlights functionally distinct chromosomal domain, which plays critical roles in development from a fertilized egg into a complex organism, as well as in aging and diseases. However, the mechanisms of this fundamental process are poorly understood so far. It is of particular interest to investigate how the variants are incorporated into chromatin and mark specific chromatin states to regulate gene expression, and how they are involved in development and diseases. In this review, we focus on recent progress in studies of epigenetic regulation of three extensively investigated variants including H2A.Z, macroH2A and H3.3, and their functional implications in development and diseases.     

Phosphorylation of histone variant regions in chromatin: unlocking the linker?

Histone variants illuminate the behavior of chromatin through their unique structures and patterns of postsynthetic modification. This review examines the literature on heteromorphous histone structures in chromatin, structures that are primary targets for histone kinases and phosphatases in vivo. Special attention is paid to certain well-studied experimental systems: mammalian culture cells, chicken erythrocytes, sea urchin sperm, wheat sprouts, Tetrahymena, and budding yeast. A common theme emerges from these studies. Specialized, highly basic structures in histone variants promote chromatin condensation in a variety of developmental situations. Before, and sometimes after condensed chromatin is formed, the chromatin is rendered soluble by phosphorylation of the heteromorphous regions, preventing their interaction with linker DNA. A simple structural model accounting for histone variation and phosphorylation is presented.