While it is known that signaling pathways are amongst the first players initiating the differentiation cascade, their effect can be short-lived and depends on the presence of ligands. Differential gene expression in specializing cells is maintained by the cis-regulatory sequences or modules (CRM) that consist of enhancer, insulator or repressor domains. The CRMs contain multiple transcription factor binding sites (TFBSs) for certain transcription factors (TFs) that change the rate of expression of genes located upstream or downstream of them.
The discoveries have shown that a big role in establishing and maintaining the complexity is played by genes – the simplest unit consisting of nucleic acid that is later converted into proteins that play a diverse array of functions in biological processes.
An important aspect of the role of proteins during the establishment of cell identities and differentiated cells lies at the very beginning of developmental processes, when the cells are assigned cellular fates. While the direct effect of signalling cascades on gene expression can be short-lived, the longer term effect is established by transcription factors.
Proteins are an important constituent of the living world. They are molecular entities that consist of aminoacids and play roles of molecular machines that perform the basic operations with other biologic entities such as DNA, RNA, other proteins, lipids, and carbohydrates. Proteins are classified into many different groups based on their molecular structure, molecular function, cellular compartment, biological processes they are involved in, time of engagement into biological processes in living organisms.
Among proteins the transcription factors are a separate functional class that is responsible for many key decisions during the developmental course including cell fate assignment and cellular identity establishment.
1.1.1 Mechanisms of regulation of transition of a cell by TFs from committed to differentiated state 1000- 725 more words needed
TFs bind to CRMs in order to alter the DNA accessibility, attract cooperating TFs, cofactors or even protein-binding ligands. The selective binding results in combinatorial occupancy of CRMs, which modulates activity of the RNA polymerase II (RNA Pol II). Initially certain TFs can bind to DNA alone and act as pioneers that initiate nucleosome repositioning8 and create less condensed chromatin for binding others. Some types of TFs can also engage chromatin remodeling complexes and DNA methyltransferases for the same purpose. The loosened chromatin can recruit other cooperating TFs to form complexes that change the bending angle of sequences near promoter and make it even more attractive to RNA PolII and its cofactors.
Depending on the requirement for other TFs to maintain functionality of the bound complex, several types of CRMs can be distinguished. Enhanceosomes are linear sequences of bound TFs that act as a unit. When one or more of the interacting molecules unbinds from CRM, it may cease functioning16. “Billboard” types of CRMs may have less strict requirements for activation given that at a given stage only a subgroup of bound TFs contributes to function of the enhancer. Autoregulative CRMs, as the name suggests, are under positive or negative feedback of the genes they regulate that often can encode a TF.
Given that nuclear lumen is crowded with various TFs and proteins competing for binding sites, and the fact that TF contribution to CRM activity depends on the context to which it binds, the slight changes in TFBS occupancy could have a dramatic effect on gene expression. Such complexity of regulatory interactions implies that more than one gene may be needed to regulate expression of a downstream gene, and that a mere information on the expression level of certain TFs is not sufficient to draw robust conclusions on their effect on transcriptional targets.