Combinatorial readout of dual histone modifications by paired chromatin-associated modules

The study of histone modifications and their interaction with effector modules/proteins has attracted increasing attention in recent years. Accumulating evidence indicates that epigenetic regulation, which involves post-translational modification on histones and DNAs or the participation of RNAs, plays an important role in many cellular processes. Histone modifications can function individually but are also capable of functioning combinatorially as a pattern. Recently, much more attention has focused on interpreting combined histone patterns by their downstream effectors. Structure/function-based studies on paired module-mediated histone cross-talk have greatly enhanced our understanding of the plasticity of the "histone code" hypothesis.     

Posttranslational modifications of CENP-A: marks of distinction

Centromeres are specialized chromosome domain that serve as the site for kinetochore assembly and microtubule attachment during cell division, to ensure proper segregation of chromosomes. In higher eukaryotes, the identity of active centromeres is marked by the presence of CENP-A (centromeric protein-A), a histone H3 variant. CENP-A forms a centromere-specific nucleosome that acts as a foundation for centromere assembly and function. The posttranslational modification (PTM) of histone proteins is a major mechanism regulating the function of chromatin. While a few CENP-A site-specific modifications are shared with histone H3, the majority are specific to CENP-A-containing nucleosomes, indicating that modification of these residues contribute to centromere-specific function. CENP-A undergoes posttranslational modifications including phosphorylation, acetylation, methylation, and ubiquitylation. Work from many laboratories have uncovered the importance of these CENP-A modifications in its deposition at centromeres, protein stability, and recruitment of the CCAN (constitutive centromere-associated network). Here, we discuss the PTMs of CENP-A and their biological relevance.     

Bioinformatic tools for DNA methylation and histone modification: A survey

Epigenetic inheritance occurs due to different mechanisms such as chromatin and histone modifications, DNA methylation and processes mediated by non-coding RNAs. It leads to changes in gene expressions and the emergence of new traits in different organisms in many diseases such as cancer. Recent advances in experimental methods led to the identification of epigenetic target sites in various organisms. Computational approaches have enabled us to analyze mass data produced by these methods. Next-generation sequencing (NGS) methods have been broadly used to identify these target sites and their patterns. By using these patterns, the emergence of diseases could be prognosticated. In this study, target site prediction tools for two major epigenetic mechanisms comprising histone modification and DNA methylation are reviewed. Publicly accessible databases are reviewed as well. Some suggestions regarding the state-of-the-art methods and databases have been made, including examining patterns of epigenetic changes that are important in epigenotypes detection.     

Interpreting the language of histone and DNA modifications

A major mechanism regulating the accessibility and function of eukaryotic genomes are the covalent modifications to DNA and histone proteins that dependably package our genetic information inside the nucleus of every cell. Formally postulated over a decade ago, it is becoming increasingly clear that post-translational modifications (PTMs) on histones act singly and in combination to form a language or ‘code’ that is read by specialized proteins to facilitate downstream functions in chromatin. Underappreciated at the time was the level of complexity harbored both within histone PTMs and their combinations, as well as within the proteins that read and interpret the language. In addition to histone PTMs, newly-identified DNA modifications that can recruit specific effector proteins have raised further awareness that histone PTMs operate within a broader language of epigenetic modifications to orchestrate the dynamic functions associated with chromatin. Here, we highlight key recent advances in our understanding of the epigenetic language encompassing histone and DNA modifications and foreshadow challenges that lie ahead as we continue our quest to decipher the fundamental mechanisms of chromatin regulation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.     

Engineering chromatin states: Chemical and synthetic biology approaches to investigate histone modification function

Patterns of histone post-translational modifications (PTMs) and DNA modifications establish a landscape of chromatin states with regulatory impact on gene expression, cell differentiation and development. These diverse modifications are read out by effector protein complexes, which ultimately determine their functional outcome by modulating the activity state of underlying genes. From genome-wide studies employing high-throughput ChIP-Seq methods as well as proteomic mass spectrometry studies, a large number of PTMs are known and their coexistence patterns and associations with genomic regions have been mapped in a large number of different cell types. Conversely, the molecular interplay between chromatin effector proteins and modified chromatin regions as well as their resulting biological output is less well understood on a molecular level. Within the last decade a host of chemical approaches has been developed with the goal to produce synthetic chromatin with a defined arrangement of PTMs. These methods now permit systematic functional studies of individual histone and DNA modifications, and additionally provide a discovery platform to identify further interacting nuclear proteins. Complementary chemical- and synthetic-biology methods have emerged to directly observe and modulate the modification landscape in living cells and to readily probe the effect of altered PTM patterns on biological processes. Herein, we review current methodologies allowing chemical and synthetic biological engineering of distinct chromatin states in vitro and in vivo with the aim of obtaining a molecular understanding of histone and DNA modification function. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.     

Histone modifications during mammalian oocyte maturation: Dynamics,regulation and functions

Histone modifications are associated with many fundamental biological processes in cells. An emerging notion from recent studies is that meiosis stage-dependent histone modifications are crucial for the oocyte development in mammals. In this paper, we review the changes and regulation as well as functions of histone modifications during meiotic maturation of mammalian oocyte, with particular emphasis on histone acetylation, phosphorylation and methylation. In general, dynamic and differential modification patterns have been revealed during oocyte maturation, indicative of functional requirement. Disruption of histone modifications leads to defective chromosome condensation and segregation, delayed maturation progression and even oocyte aging. Although several histone-modifying enzymes have been identified in mammalian oocytes, more works are necessary to determine how they direct histone modifications globally and individually in oocytes. Studies on chromatin modification during oocyte development will have implications for our understanding of the mechanisms controlling nuclear architecture and genomic stability in female germ line.     

组蛋白翻译后修饰技术研究进展

翻译后修饰调控着真核生物大部分蛋白质的活性,这些修饰的解读对研究生物功能是必不可少的。组蛋白翻译后修饰是蛋白质翻译后修饰中研究的较好一类小分子碱性蛋白,易被各种生物大分子修饰,尤其易发生在N-末端的尾部。不同组合式修饰构成了"组蛋白密码",在细胞的发育、生长、分化和动态平衡中,组蛋白密码影响着染色体的结构状态,进而调控基因的表达状态。组蛋白翻译后修饰的研究可作为一种模式来解析蛋白质复杂的修饰状态及研究其分子功能。翻译后修饰分析技术的发展对组蛋白密码的解析是至关重要的。重点讨论组蛋白修饰分析技术的发展和应用。     

The analysis of histone modifications

The biological function of many proteins is often regulated through posttranslational modifications (PTMs). Frequently different modifications influence each other and lead to an intricate network of interdependent modification patterns that affect protein-protein interactions, enzymatic activities and sub-cellular localizations. One of the best-studied class of proteins that is affected by PTMs and combinations thereof are the histone molecules. Histones are very abundant, small basic proteins that package DNA in the eukaryotic nucleus to form chromatin. The four core-histones are densely modified within their first 20-40 N-terminal amino acids, which are highly evolutionary conserved despite playing no structural role. The modifications are thought to constitute a histone code that is used by the cell to encrypt various chromatin conformations and gene expression states. The analysis of modified histones can be used as a model to dissect complex modification patterns and to investigate their molecular functions. Here we review techniques that have been used to decipher complex histone modification patterns and discuss the implication of these findings for chromatin structure and function.     

A chemical field guide to histone nonenzymatic modifications

Histone nonenzymatic covalent modifications (NECMs) have recently emerged as an understudied class of posttranslational modifications that regulate chromatin structure and function. These NECMs alter the surface topology of histone proteins, their interactions with DNA and chromatin regulators, as well as compete for modification sites with enzymatic posttranslational modifications. NECM formation depends on the chemical compatibility between a reactive molecule and its target site, in addition to their relative stoichiometries. Here we survey the chemical reactions and conditions that govern the addition of NECMs onto histones as a manual to guide the identification of new physiologically relevant chemical adducts. Characterizing NECMs on chromatin is critical to attain a comprehensive understanding of this new chapter of the so-called “histone code”.     

Development of rabbit monoclonal and polyclonal antibodies for detection of site-specific histone modifications and their application in analyzing overall modification levels

In addition to DNA sequence information,site-specific histone modifications are another important determinant ofgene expression in a eukaryotic organism.We selected four modification sites in common histones that are known tosignificantly impact chromatin function and generated monoclonal or polyclonal antibodies that recognize each of thosesite-specific modifications.We used these antibodies to demonstrate that the site-specific histone modification levelsremain relatively constant in different organs of the same organism.We also compared the levels of selected histonemodifications among several representative organisms and found that site-specific modifications are highly variable amongdifferent organisms,providing new insight into the evolutionary divergence of specific histone modifications.