Chromatin3D: Chromatin Dynamics in Development and Disease
...... a Marie Sklodowska Curie Actions Innovative Training Network
Most, if not all, DNA-dependent transactions must function within the context of chromatin. To do so, chromatin fibres must reversibly alternate between compact and relaxed structural states. The latter ensures that the underlying DNA sequences are properly exposed to protein complexes involved in transcription and replication, recombination or repair. Defects in DNA-templated processes are thought to be causal to a number of detrimental pathologies, including cancer.
The basic unit of chromatin is the nucleosome, which is composed of two copies of the histones H2A, H2B, H3 and H4 wrapped with 146 bp of DNA. Based on the decondensed beads-on-a-string configuration of repeating nucleosome units, complex interactions between the main units can result in the progressive condensation of the structure. Chromatin’s ability for condensation is regulated in part by post-translational modifications of the N-terminal tails of histones, including acetylation, phosphorylation, methylation and ubiquitination. Modifications of the histone tails can influence both internucleosomal and chromatin fibres interactions. They can also facilitate the recruitment of chromatin associated proteins and chromatin remodelling complexes. Thus the chromatin structure is characterized by the degree of chromatin condensation, the location within the nuclear architecture and the type of histone modifications.
Higher order organization of chromatin results in chromosomes, the main organizing factors in the nucleus that occupy discrete territories. Most nuclear processes occur or at least being initiated onto the chromosomes which makes them the main organizing factors in the nucleus. Several proteins that are involved in the replication of DNA, gene transcription and the processing of RNA are found enriched in discrete focal structures. An emerging question is how these structures assemble and are maintained in the absence of membranes and moreover what are the kinetics of stable binding and/or rapid exchange of their components. This dynamic assembly and modification of chromatin that ultimately leads to shaping the genome and regulating the kinetics of physiological processes lacks mechanistic insights at present. Most technologies that have been developed in the last decade for the study of macromolecular complexes and chromatin dynamics are based on either static views or the average behaviour of molecular ensembles leading to the loss of meaningful information. We should also consider that the modifications of individual chromatin components are not as important as the resulting chromatin structure they establish. It is then imperative to develop technologies to accurately measure chromatin compaction, chromatin structure and chromosome associations in cells and even better in individual cells. Such technologies include several modifications of the Chromosome Conformation Capture technology, which is widely applied in several participating laboratories of this network. Such approaches will help us deduce the chromosome domain structure and the involvement of distinct chromatin modification patterns. One step further is the understanding on how these domains influence chromatin fibre association with subnuclear entities and how these associations alter during developmental processes and cell differentiation. Moreover, abnormal expression patterns or genomic alterations in chromatin regulators can lead to the alteration of the overall three-dimensional structure of the genome leading to the induction and maintenance of various malignancies such as cancer, aging or autoimmune diseases.