Transcription of specific genes can be specified by particular combinations of the roughly 1400 transcription factors encoded in the human genome, giving rise to cell-type-specific gene expression. There are various ways in which the activities of transcription factors themselves are controlled to ensure that genes are expressed only in the correct cell types and at the appropriate time during their differentiation. The expression of eukaryotic protein-coding genes is regulated by multiple protein-binding DNA sequences, generically referred to as transcription-control regions. These regions include promoters containing several types of control elements located near transcription start sites, as well as enhancers distant from the genes they regulate, which also control the how frequently the gene is transcribed.

Initiation of transcription by RNA polymerase requires several initiation factors. These initiation factors position RNAP molecules at transcription start sites and help to separate the DNA strands so that the template strand can enter the active site of the enzyme. They are called general transcription factors because they are required at most, if not all, promoters of genes transcribed by RNA polymerase.

Most genes are regulated by multiple transcription factors that bind specific sites in DNA regulatory regions. For each target gene, alternative transcription-factor binding configurations result in varied transcriptional outputs, in turn leading to alternative cell fates and behaviors. A common framework describing and interpreting gene expression is the gene regulatory network system. What it focuses on is specific interplay among key genes including the effect of the promoter and the enhancer distant from the starting site. It should be pointed out that when we talk about the formalism of gene regulation, the basal transcription rate resulted from general transcription factor may sometimes not be considered since what we predict is the fold-change of genes, which is the added effect for basal rate as a way to measure the level of regulation from systematically tuning the parameters of that regulation (Weinert et al. 2014).

The level of expression depends on multiple factors: activators and repressors influence transcription through interactions with large multi-protein complexes and can often function either to activate or to repress transcription, depending on their associations. Some of these multi-protein complexes modify chromatin condensation, altering the accessibility of chromosomal DNA to transcription factors and RNA polymerases. Other complexes directly influence the frequency at which RNA polymerases bind to promoters and initiate transcription. The complicated scenario makes it rather difficult describing the behavior of gene regulation.

Firstly, capturing binding behaviors remains a challenge. The binding configuration of the promoter in DNA changes with the time and location. The gene copy number varies during the life cycle resulting in different binding properties. Each of copy might have its own promoter scenario and can be individually regulated (Sepúlveda et al. 2016). To make it worse, transcription-control regions regulating expression of a specific gene are not that conserved in different tissues. Not to mention that there exist higher-order dependency among multiple binding sites either from single transcription factor or entangling with one another.

For another, elucidating the linking between transcription-factor configurations and the resulting transcription strength is a crucial task. The fact that operator site strength effects the fold change in expression add difficulty to get completed information for whole cell modeling which means, the probability of RNAP binding may not be considerable (Weinert et al. 2014). Moreover, it has been studied that switching between promoter configurations is faster than mRNA lifetime(Sepúlveda et al. 2016), making it even harder to explore the mechanism of gene regulation from experimental sides. Despite the occupation status of the promoter, the combinatorial possibilities of heterodimeric transcription factors and their heterogeneous binding effects hold back further investigation of regulatory architectures as well. 

Reference:

Molecular Cell Biology eighth edition by Harvey Lodish

Sepúlveda, L.A. et al., 2016. Measurement of gene regulation in individual cells reveals rapid switching between promoter states. Science.

Weinert, F.M. et al., 2014. Scaling of gene expression with transcription-factor fugacity. Physical Review Letters.