Unresolved Questions in Chromatin Dynamics & Transcription Regulation
Transcription needs to be highly regulated in order to orchestrate the complexity of cell types and expression patterns observed in higher eukaryotes. Perhaps the most common mechanism of tissue-specific expression is the regulation of a gene by distal enhancers – DNA sequences bound by various regulatory factors located sometimes hundreds of kbps away. Modular expression of a gene can be achieved with multiple enhancers, each activating expression in a given tissue. Even in this simplified picture, many fundamental questions remain unknown. Do promoters and enhancers form a stable complex? Is it dynamic? How frequently do such interactions take place? What mechanisms help achieve robust expression patterns?
These questions cannot be addressed without tackling the complex question of the structure and dynamics of chromatin in the nucleus. Various postulated polymer models exist, but a definitive consensus bridging data from imaging to biochemistry remains to be reached. We believe super-resolution techniques have an important role to play in understanding chromatin architecture and promoter/enhancer function. The nature of the nuclear space also has profound implication for the mobility of how fast and how far TF can diffuse to find their target in the genome.
In addition to chromatin architecture and TF mobility, the core transcription machinery itself is highly regulated: some Pre-Initiation Complex (PIC) components are required for transcription of subsets of genes or cell types (Goodrich and Tjian 2010, Juven-Gershon and Kadonaga 2010). The rules governing the specificity of this large complex (tens of polypeptides) are still poorly understood: what are the assembly paths? How is pausing regulated (Adelman and Lis 2012)? Do the transcription bursts observed in vivo reflect PIC assembly dynamics (Lionnet and Singer 2012)? In spite of recent single molecule in vitro experiments (Revyakin, Zhang et al. 2012), many questions remain.