Fundamental features of chromatin structure

Which mechanisms regulate nuclear plasticity? Part of the answer to that question lies in understanding how genes are expressed and regulated in the context of chromatin structure. It is now clear that the genes are regulated in discrete and controlled stages, from packaging into chromatin to their localization within the nucleus. Whereas the genetic information provides the framework for the manufacture of all proteins necessary to create a living cell, chromatin structure controls how, where, and when the genetic information should be used. In this minireview, I summarize the main characteristics of chromatin structure and highlight some of the modifications usually associated with the regulation of gene expression.     

Regulation of chromatin structure during thymic T cell development

Development is the process whereby a multipotent cell gives rise, through series of divisions, to progeny with successively restricted potentials. During T cell development, the process begins with a multipotent hematopoietic stem cell (HSC) in the bone marrow, moves to the thymus where early T cells or thymocytes pass through signal‐initiated developmental checkpoints, and ends in the periphery where mature T cells reside. At each step along this developmental pathway, T lymphocyte progenitors must be able to turn genes on and off, creating a specialized program of gene expression, to allow further development. How is gene expression coordinated? This review will summarize what has been learned about the function of chromatin structure in generating a “blueprint” of gene expression during T cell development. This will include discussion of mechanisms of chromatin remodeling, histone modification, and heritable gene silencing. In many cases, these processes are carried out by multi‐protein complexes whose components are largely ubiquitously expressed. The spatial and temporal specificity of these complexes is contributed by sequence specific DNA binding factors, some of which are cell type restricted in their expression. This review will summarize research underway to identify these key genetic “targeters.” Taken together, the research reviewed here provides a glimpse into the importance of regulation of chromatin structure in T cell development and the “players” involved. © 2005 Wiley‐Liss, Inc.     

Plant chromatin: development and gene control

It is increasingly clear that chromatin is not just a device for packing DNA within the nucleus but also a dynamic material that changes as cellular environments alter. The precise control of chromatin modification in response to developmental and environmental cues determines the correct spatial and temporal expression of genes. Here, we review exciting discoveries that reveal chromatin participation in many facets of plant development. These include: chromatin modification from embryonic and meristematic development to flowering and seed formation, the involvement of DNA methylation and chromatin in controlling invasive DNA and in maintenance of epigenetic states, and the function of chromatin modifying and remodeling complexes such as SWI/SNF and histone acetylases and deacetylases in gene control. Given the role chromatin structure plays in every facet of plant development, chromatin research will undoubtedly be integral in both basic and applied plant biology.     

Chromatin techniques for plant cells

A large number of recent studies have demonstrated that many important aspects of plant development are regulated by heritable changes in gene expression that do not involve changes in DNA sequence. Rather, these regulatory mechanisms involve modifications of chromatin structure that affect the accessibility of target genes to regulatory factors that can control their expression. The central component of chromatin is the nucleosome, containing the highly conserved histone proteins that are known to be subject to a wide range of post-translational modifications, which act as recognition codes for the binding of chromatin-associated factors. In addition to these histone modifications, DNA methylation can also have a dramatic influence on gene expression. To accommodate the burgeoning interest of the plant science community in the epigenetic control of plant development, a series of methods used routinely in our laboratories have been compiled that can facilitate the characterization of putative chromatin-binding factors at the biochemical, molecular and cellular levels.     

The plant alkaloid chelerythrine binds to chromatin,alters H3K9Ac and modulates global gene expression

Chelerythrine (CHL), a plant alkaloid, possesses antimicrobial, anti-inflammatory, and antitumor properties. Although CHL influences several key signal transduction pathways, its ability to interact directly with nucleoprotein complex chromatin, in eukaryotic cells has so far not been looked into. Here we have demonstrated its association with hierarchically assembled chromatin components, viz. long chromatin, chromatosome, nucleosome, chromosomal DNA, and histone H3 and the consequent effect on chromatin structure. CHL was found to repress acetylation at H3K9. It is more target-specific in terms of gene expression alteration and less cytotoxic compared to its structural analog sanguinarine.     

植物三维染色质构型研究进展

染色质在细胞核内的缠绕、折叠及其在细胞核内的空间排布是真核生物染色质构型的主要特征。在经典DNA探针荧光原位杂交显微观察的基础上,基于新一代测序技术的Hi-C及ChIA-PET染色质构型捕获技术已经被广泛应用于动物及植物细胞核染色质构型的研究中,并以新的角度定义了包括:染色体(质)域(chromosome territory)、A/B染色质区室(compartment A/B)、拓扑偶联结构域(topological associated domains,TADs)、染色质环(chromatin loops)等在内的多个更为精细的染色质构型。利用以上两种主流技术,越来越多的植物物种染色质构型特征被鉴定、分析和比较。本文系统分析和总结了近年来以植物细胞为模型的细胞核染色构型领域取得的重要成果,包括各级染色质构型特征的组成、建立机制和主要影响因素等。在此基础上,分析了目前研究植物染色质构型技术的瓶颈和突破性的技术进展,并对后续研究主要关注的问题和研究内容进行了展望,以期为相关领域的研究提供更多的理论参考和依据。     

Plant chromatin -- epigenetics linked to ATP-dependent remodeling and architectural proteins

Studies in organisms belonging to different eukaryotic kingdoms have revealed that the structural state of chromatin is controlled by interactions of DNA, small RNAs and specific proteins, linked to a self-reinforcing complex network of biochemical activities involving histone and DNA modifications and ATP-dependent nucleosome remodeling. However, these findings must now be reinterpreted in light of the recent discovery of the highly dynamic character of interphase chromosomes exemplified by the constant flux of enzymatic and structural proteins through both eu- and heterochromatin and by short- and long-range chromosome movements in the nucleus. The available data on chromosome organization in Arabidopsis thaliana and links between proteins influencing chromatin structure and DNA and histone modifications documented in this model plant provide strong supportive evidence for the dynamic nature of chromosomes.     

30nm染色质纤维结构与表观遗传调控

真核生物的DNA以染色质形式通过逐级折叠压缩形成高级结构存在于细胞核中。染色质高级结构直接参与了真核基因的转录调控和其它与DNA相关的生物学事件,因此研究染色质高级结构对了解表观遗传学分子机制有着至关重要的作用。近些年,研究者们针对30 nm染色质高级结构提出了两个模型:螺线管模型和Zig-Zag模型。2014年,我们利用体外染色质组装体系重建了30 nm染色质纤维,运用高精度冷冻电镜技术得到了分辨率为11?的30 nm染色质纤维的精细结构,提出了30 nm染色质高级结构的左手双螺旋Zig-Zag模型。本文综述了30 nm染色质纤维结构研究方面的相关进展,并对30 nm染色质高级结构的表观遗传调控机理以及单分子成像和操纵技术在研究30 nm染色质高级结构中潜在的应用作出讨论和展望。