Cell identity and gene regulation

Cell identity, differentiation potential during organismic development and aberrations leading to malignant phenotypes and developmental abnormalities are all a function of distinct protein compositions. Those result from gene expression programmes that are established, executed and regulated by large protein complexes, dynamic ‘molecular machines’ that govern nucleic acid metabolism with high fidelity. The fact that proteins themselves largely determine a cell’s protein composition leads to complex regulatory networks that involve protein interactions and control of their activity.

Maintenance of genome integrity and faithful execution of gene expression programmes rely on interaction of proteins with nucleic acids, be it in the form of genomic DNA, or RNA on its way to being processed to serve as a template for the translation machinery. Protein-nucleic acid interactions are the single most important aspect of any advanced genetic system.

Epigenetic principles of gene regulation

Complex protein interactions with eukaryotic genomes define chromatin, a nuclear storage form of DNA that has intrinsic regulatory potential. The architecture of the chromosomes, far from being the result of random coiling of the chromatin fibre, is determined and itself a determinant of the organisation of a cell’s nucleus. Access to the genetic information, be it to transcribe genes, replicate the genome or locate and repair DNA damage involves a large number of enzymes that render chromatin either functionally repressive or permissive. The transcription of DNA in a chromatin environment poses steric and topological problems that are solved by the integrated action of numerous enzymes. Regulators of chromatin structure and the RNA polymerase machinery itself are targeted to genes by a combinatorial system of DNA–binding transcription factors. The resulting RNA is immediately bound by proteins that coordinate its stabilisation, processing, localisation, transport and finally translation into mature protein. However, it is becoming more and more obvious that non-coding, regulatory RNAs are integral parts of chromatin organisation and their expression, processing and interaction with proteins can have profound consequences on chromatin structure and function. Changes of the epigenome play a causal role in both normal and pathological development, including cancer.

Programming and reprogramming of cell identity

During embryonic development, pluripotent cells generate the diversity of cell types and tissues in different organs. During this process, stem cells give rise to cells with ever-more restricted fates. Cells can maintain this fate specification during many cycles of cell division and eventually develop into fully differentiated progeny. Neither the first, nor the last step in this cascade is understood at the molecular level at present – and we are far from manipulating these programs as would be required for a safe stem cell-based therapy. Plasticity of stem cells implies that they can generate a diverse set of cell types, in the extreme all cell types in the organism. While this extreme is not now attainable using adult stem cells, nuclear cloning experiments show that it can be reached if somatic, differentiated nuclei are exposed to an environment apt to induce their reprogramming into less determined cells allowing new fate decisions to be made. This highlights the need to understand the mechanisms of nuclear reprogramming and its potential in the directed differentiation of adult stem cells.

The key questions are how transcriptional regulators (both proteins and non-coding RNA) interact during progressive differentiation and how cell type specificity can be fixed or reversed. Understanding and manipulation of these developmental mechanisms e.g. using synthetic inhibitors provided by research area E in CIPSM will permit us to implement them in adult stem cells recovered from diverse organs or from the bloodstream. One of the central unsolved questions is how cell-type specific gene expression is controlled by the architecture of the epigenome in a cell’s nucleus. While the structures of eukaryotic genomes are at our disposition their epigenomes, i.e. the activity status that is dictated by DNA modification and packaging, is cell-type specific and hence changing during development.