Chromatin fiber allostery and the epigenetic code

Nucleosomes as allosteric scaffolds for genetic regulation

Nucleosomes are stable yet highly dynamic complexes exhibiting diverse types of motions, such as sliding, DNA unwrapping, and disassembly, encoding a landscape with a large number of metastable states. In this review, describing recent studies on these nucleosome structure changes, we propose that the nucleosome can be viewed as an ideal allosteric scaffold: regulated by effector molecules such as transcription factors and chromatin remodelers, the nucleosome controls the downstream gene activity. Binding of transcription factors to the nucleosome can enhance DNA unwrapping or slide the DNA, altering either the binding or the unbinding of other transcription factors to nearby sites. ATP-dependent chromatin remodelers induce a series of DNA deformations, which allosterically propagate throughout the nucleosome to induce DNA sliding or histone exchange.

Biomechanical modeling of invasive breast carcinoma under a dynamic change in cell phenotype: collective migration of large groups of cells

According to recent studies, cancer is an evolving complex ecosystem. It means that tumor cells are well differentiated and involved in heterotypic interactions with their microenvironment competing for available resources to proliferate and survive. In this paper, we propose a chemo-mechanical model for the growth of specific subtypes of an invasive breast carcinoma. The model suggests that a carcinoma is a heterogeneous entity comprising cells of different phenotypes, which perform different functions in a tumor. Every cell is represented by an elastic polygon changing its form and size under pressure from the tissue. The mechanical model is based on the elastic potential energy of the tissue including the effects of contractile forces within the cell perimeter and the elastic resistance to stretching or compressing the cell with respect to the reference area. A tissue can evolve via mechanisms of cell division and intercalation. The phenotype of each cell is determined by its environment and can dynamically change via an epithelial-mesenchymal transition and vice versa. The phenotype defines the cell adhesion to the adjacent tissue and the ability to divide. In this part, we focus on the forms of collective migration of large groups of cells. Numerical simulations show the different architectural subtypes of invasive carcinoma. For each communication, we examine the dynamics of the cell population and evaluate the complexity of the pattern in terms of the synergistic paradigm. The patterns are compared with the morphological structures previously identified in clinical studies.

Allosterism and signal transfer in DNA

We analysed the basic mechanisms of signal transmission in DNA and the origins of the allostery exhibited by systems such as the ternary complex BAMHI-DNA-GRDBD. We found that perturbation information generated by a primary protein binding event travels as a wave to distant regions of DNA following a hopping mechanism. However, such a structural perturbation is transient and does not lead to permanent changes in the DNA geometry and interaction properties at the secondary binding site. The BAMHI-DNA-GRDBD allosteric mechanism does not occur through any traditional models: direct (protein-protein), indirect (reorganization of the secondary site) readout or solvent-release. On the contrary, it is generated by a subtle and less common entropy-mediated mechanism, which might have an important role to explain other DNA-mediated cooperative effects.

Histone lysine methylation and congenital heart disease: From bench to bedside (Review)

Histone post-translational modifications (PTM) as one of the key epigenetic regulatory mechanisms that plays critical role in various biological processes, including regulating chromatin structure dynamics and gene expression. Histone lysine methyltransferase contributes to the establishment and maintenance of differential histone methylation status, which can recognize histone methylated sites and build an association between these modifications and their downstream processes. Recently, it was found that abnormalities in the histone lysine methylation level or pattern may lead to the occurrence of many types of cardiovascular diseases, such as congenital heart disease (CHD). In order to provide new theoretical basis and targets for the treatment of CHD from the view of developmental biology and genetics, this review discusses and elaborates on the association between histone lysine methylation modifications and CHD.