Structure of Chromatin
David S. Latchman in Gene Control, 2020
Eukaryotic gene regulation requires both long-term processes which regulate chromatin structure and more short-term processes which actually result in the activation of gene transcription. The structure formed by DNA and its associated proteins is known as chromatin. An understanding of how long-term gene regulation is achieved therefore requires knowledge of the structure of chromatin. Several multiprotein chromatin remodeling complexes exist in eukaryotic cells and these are classified into several families, the best characterized of which are the SWI/SNF family and the ISWI family. The factors that control the interconversion of the 10 nm and 30 nm fibers are of critical importance therefore in terms of both chromatin structure and gene control. Specific functional domains of chromatin thus exist in which chromatin structure is altered in a particular situation to allow transcription to occur. Euchromatin contains most of the DNA in the cell and is packaged in the looped form of the 30 nm fiber.
Gene regulation without and with chromatin
Ralf Blossey in Chromatin, 2017
Gene regulation without chromatin essentially means gene regulation in bacteria which lacks the nucleosomal level of compaction and regulation. Instead of looking at bacteria, this chapter describes the regulation of genes in an even simpler organism, which is a phage: the famous lambda-phage which infects E. coli bacteria. In some sense nucleosomes—although structurally much more complex—can also serve as "transcription factors"—either by being in the way of other regulators, or giving access to regulatory sequences and the gene by being absent from such sequences. Given the presence of nucleosomes in chromatin, it cannot be sufficient in eukaryote organisms. The model is built with the intention to test the hypothesis that dinucleotide probability functions are sufficient to predict the nucleosome binding preferences—their free energy landscape. In order to pass from prokaryote to eukaryote it is thus important to know where the nucleosomes are.
Structure of Chromatin
David S. Latchman in Gene Control, 2018
This chapter discusses the structure of chromatin. The link between locus-control region (LCR) and chromatin structure has been supported by detailed studies of the β-globin gene cluster at different stages of erythroid development. It has been shown that in early erythroid development the cluster forms a looped structure in which the active γ-globin genes are brought into close proximity with the LCR. The existence of elements such as LCRs which can alter the chromatin structure of large regions of the chromosome leads to the question of how the action of such elements is confined to the appropriate gene or genes. Some mechanism must exist to prevent the effect of LCRs from spreading to other genes in adjacent regions of the chromosome and producing an inappropriate pattern of gene expression. LCRs and insulators share the ability of preventing the structure of a particular DNA region from being inappropriately influenced by that of adjacent regions.
Regulation of cellular chromatin state
Published in Organogenesis, 2010
Surabhi Srivastava, Rakesh K. Mishra, Jyotsna Dhawan
The identity and functionality of eukaryotic cells is defined not just by their genomic sequence which remains constant between cell types, but by their gene expression profiles governed by epigenetic mechanisms. Epigenetic controls maintain and change the chromatin state throughout development, as exemplified by the setting up of cellular memory for the regulation and maintenance of homeotic genes in proliferating progenitors during embryonic development. Higher order chromatin structure in reversibly arrested adult stem cells also involves epigenetic regulation and in this review we highlight common trends governing chromatin states, focusing on quiescence and differentiation during myogenesis. Together, these diverse developmental modules reveal the dynamic nature of chromatin regulation providing fresh insights into the role of epigenetic mechanisms in potentiating development and differentiation.
Binding of circulating SLE autoantibodies to oxygen free radical damaged chromatin
Published in Autoimmunity, 2005
Farah Mansoor, Asif Ali, Rashid Ali
Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease characterized by various immunologic disorders, including production of autoantibodies, formation of immune complexes, decreased serum complement levels, and lymphocytopenia. One of the hallmarks of this disease is the loss of tolerance to nuclear antigens. The dominant presence of antibodies against the exposed conformational epitopes on chromatin strongly suggests that the pathogenic immune response in lupus is driven by chromatin. In the present study, the binding of SLE autoantibodies with native chromatin and oxygen free radical damaged chromatin was studied. As assessed by direct binding and inhibition ELISA, circulating SLE autoantibodies exhibited a high degree of specificity towards the reactive oxygen species (ROS)-modified chromatin in comparison to native chromatin and this binding specificity was reiterated visually by gel retardation assay. The data suggested possible role of modified chromatin in the induction of SLE autoantibodies and higher recognition of oxidatively damaged chromatin by antibodies in sera of SLE patients. It is indicated that free radical modified chromatin or nucleosomes might be the antigen for the production of circulating autoantibodies in SLE.
Unravelling the biology of chromatin in health and cancer using proteomic approaches
Published in Expert Review of Proteomics, 2017
Cassandra G. Eubanks, Gerald Dayebgadoh, Xingyu Liu, Michael P. Washburn
Introduction: Chromatin remodeling complexes play important roles in the control of genome regulation in both normal and diseased states, and are therefore critical components for the regulation of epigenetic states in cells. Given the role epigenetics plays in cancer, for example, chromatin remodeling complexes are routinely targeted for therapeutic intervention. Areas covered: Protein mass spectrometry and proteomics are powerful technologies used to study and understand chromatin remodeling. While impressive progress has been made in this area, there remain significant challenges in the application of proteomic technologies to the study of chromatin remodeling. As parts of large multi-subunit complexes that can be heavily modified with dynamic post-translational modifications, challenges in the study of chromatin remodeling complexes include defining the content, determining the regulation, and studying the dynamics of the complexes under different cellular states. Expert commentary: Impwortant considerations in the study of chromatin remodeling complexes include the complexity of sample preparation, the choice of proteomic methods for the analysis of samples, and data analysis challenges. Continued research in these three areas promise to yield even greater insights into the biology of chromatin remodeling and epigenetics and the dynamics of these systems in human health and cancer.
Related Knowledge Centers
- DNA
- Heterochromatin
- Histones
- Nucleoproteins
- Rna
- Chromosome Structures
- NON Chromosomal Proteins