Abstract:Eukaryotic cells contain a wide range of chromatin remodeling factors that mostly exist in the form of multi-subunit protein complexes. To initiate or maintain a specific cellular process, different chromatin remodeling complexes localize to particular nucleosome at certain times, resulting in the alteration of chromatin structure and gene transcription activity. Among all the chromatin remodeling factors, some structural and functional similarities could be found. However, most chromatin remodeling factors also have their own specific domains that allow them to exert diverse regulating effects. According to the different functional domains they contain, chromatin remodeling factors can be divided into four subfamilies: SWI/SNF, ISWI, CHD and INO80. This review will focus on the recent advances in chromatin remodeling research concerning the classification, structure, and biological function of chromatin remodeling factors in the cell, as well as lay the foundation for further illustration of chromatin remodeling processes in organism development and disease occurrence.

Abstract:Chromatin assembly in eukaryote is a well-organized process in which DNA and histone are hierarchically packaged into the nucleosome and chromatin. The assembly and disassembly of chromatin decode the genetic information stored within the chromatin. Histone variant and histone chaperone are major players in regulating the chromatin assembly and virtually involve in all DNA-based processes. In this review, we discuss the recent findings that provide insights into the assembly mechanism of histone variant H2A.Z and CENP-A, and highlight the important roleshistone chaperones play in this process.

Abstract:In eukaryotic cells, genomic DNA is hierarchically packed into chromatin by histones in the nucleus. Despite of over 30 years' study, the fundamental structure of 30 nm chromatin fiber remains controversial. In this review, we focus on recent progress in revealing the structure of 30 nm chromatin fiber, and emphasize on the most recent left-handed double helix structure of 30 nm chromatin fiber. In addition, we discuss the epigenetic regulation of the 30 nm chromatin structure. Finally, we discuss the possible challenge in elucidating the structure of 30 nm chromatin fiber and its regulation.

Abstract:Non-histone methylations on lysine or arginine residues have been proved to be a common fashion of post-translational modification on proteins. The diversity of methylation on different proteins or different modifying modes, such as adding one, two, or three methyl groups, dynamically affects extensive biological outcomes, including gene expression, protein activities, protein stabilities, DNA replication, genome stability, RNA processing and so on. In the manuscript, we summarized the features of protein methylation and recent progress in non-histone methylation modifiers, identified methylation sites, as well as their corresponding biological functions. Particularly, crosstalk between methylation and other types of post-translational modifications and advances in defining non-histone methylation approaches will be highlighted.

Abstract:The filamentous fungus Neurospora crassa is a global model for genetic research. The analyses of its 5S RNA genes' composition and distribution across the genome revealed the genomic defense system RIP (repeat-induced point mutation). And by analyzing its mutated 5S RNA pseudogenes, one important epigenetic modification, DNA methylation, was identified. Subsequent research made Neurospora crassa as one of the most extensive model organisms for investigation the mechanism of DNA methylation among the eukaryotes. During its vegetative growth stage, the homologous genes silencing (quelling) caused by transgene was demonstrated to be regulated by RNA interference which was exhibited to play a key role in meiotic silencing. The features of Neurospora crassa including its streamlined genome and the same DNA methylation and histone modifications as the higher eukaryotes will make it an important model organism to further research the epigenetic regulation of gene expression and genome stability.

Abstract:Transposable element (TE) is a fragment of DNA sequences that can move and integrate into new sites to proliferate itself in the host genome. Based on this proliferation, TEs have been considered as "junk" or "selfish DNA". Most research has focused on investigating mechanisms of TE amplificationor silencing whereas the regulatory function of TEs has not been completely unraveled. Previous studies have suggested a positive correlation between genome size and TE content, which provides a basis for the interpretation of the C-value paradox. Emerging studies on the regulatory functions of TEs in the host genome have updated the concept of TEs as junk DNA. In plants, especially in crops, these studies have demonstrated that TEs can reshape the transcription of adjacent genes in cis or trans, consistent with the first characterization of TEs as "controlling elements". TEs can also create epialleles, which confer stress-inducible gene expression that can increase the sessile plant's environmental fitness. In this review, we summarize recent progress on functional studies of TEs andtheir significance for crop breeding in the future.

Abstract:5-Methylcytosine is one major epigenetic modification which plays critical roles during development, cell differentiation and organogenesis. Recently, remarkable progress has been achieved in understanding the programming and inheritance of DNA methylation during early embryogenesis and gametogenesis in vertebrates. Studies have revealed that sperm DNA methylome can be stably inherited by early embryos in zebrafish. However, both paternal and maternal methylomes undergo dramatic demethylation and reprogramming during mammalian embryogenesis and germ cell development. Most germ-line imprinting control regions escape from demethylation during mammalian embryogenesis, but these regions are demethylated during primordial germ cell development.

Abstract:Pluripotent stem cells are capable of differentiation into different cell types, and therefore have great potential in clinical applications. The achievement of transcription-factor-induced pluripotent stem cells ( iPS cell) avoids ethical issues and offers an invaluable source of patient-specific pluripotent stem cells for disease modeling, drug screening, toxicology tests, personalized medicine selection, cell therapy and regenerative medicine. As a milestone, iPS technology initiates a new era of pluripotent stem cells. However, even untill now many problems especially the key molecular mechanism of epigenetic reprogramming during this process, are little understood. Uncovering the molecular mechanism of this unique platform would shed light on improving the reprogramming efficiency and iPSC quality, ultimately advancing their therapeutic applications. In this paper we will briefly introduce the significant progress in this field and attach importance to combining high-throughput sequencing technique and systematic biology in future research.

Abstract:The architecture and structural details of chromatin assembler, chromatin modifier, and chromatin remodeler, and their complexes with nucleosome and chromatin, are critical for revealing the molecular mechanisms for the establishment, maintenance and regulation of epigenetic information. The fast-developing cryo-electron microscopy (cryo-EM) provides an indispensible tool for the structure determiantion of the huge, multi-subunits, and flexible epigenetic regulation related macromolecular assemblies. In this review, we summarized the recent progresses on EM structural studies of macromolecules and complexes relating to epigenetic regulation.