8.9:
RNA Polymerase II Accessory Proteins
In the eukaryotic cells, the initiation of transcription is a complex process that needs meticulous coordination between certain DNA elements and protein components.
Besides RNA polymerase II and transcription factors, other regulatory factors are also involved in gene expression regulation during transcription initiation.
Enhancer sequences are one such transcriptional control element that can exert their effects independent of their distance from the promoter.
They are regulatory DNA segments of about 50 to 200 base pairs that contain multiple binding sites for gene regulatory proteins known as transcriptional activators.
Transcriptional activators are modular proteins consisting of two domains, a DNA binding domain and an activation domain.
The DNA binding domain anchors the protein to a specific enhancer sequence, while the activation domain interacts with different elements of the transcriptional machinery to stimulate transcription.
However, this interaction between the activator and the transcriptional machinery requires the presence of a multi-subunit complex called the mediator.
The structurally flexible network of proteins in the mediator relays signals from the activator to the RNA Polymerase II and transcriptional factors, which results in the upregulation of the transcription of a linked gene that would otherwise be only transcribed at a basal level.
In contrast to the activators, repressors regulate gene expression by inhibiting transcription.
Active repressors contain functional domains that interact with general transcription factors to interfere with their binding to the DNA.
Another repressor type binds near the transcription start site, blocking the interaction of RNA polymerase or general transcription factors with the promoter.
The third type of repressor competes with activators for binding to enhancers.
Overall, the combined actions of multiple different transcriptional regulatory proteins are responsible for gene expression control during embryonic development and cell differentiation.
8.9:
RNA Polymerase II Accessory Proteins
Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in prokaryotes, the catabolite activator protein or CAP directly interacts with the C-terminal domain of the alpha subunit of RNA polymerase to regulate gene expression. Strong evidence for direct interaction is the loss of function mutations in the activation domains of proteins that lead to suppression of transcriptional activity.
However, in some eukaryotic genes, regulation can happen via distal activation. Hence, the regulating elements may not lie in close proximity to the promoter or may not interact directly with the transcriptional machinery. Such interactions can be detected by (a) observing the rate of transcription in the presence or absence of the regulatory protein (b) mutations in the binding site of the regulatory protein that can disrupt gene expression (c) measuring the binding affinity between the regulatory protein and the promoter.
In addition, the transcription machinery also needs nucleosome remodelers to access the DNA within the chromatin. Hence, these nucleosome remodelers are also involved in regulating gene expression.
Suggested Reading
- Lee, David J., Stephen D. Minchin, and Stephen JW Busby. "Activating transcription in bacteria." Annual review of microbiology 66 (2012): 125-152.
- Busby, Steve, and Richard H. Ebright. "Transcription activation by catabolite activator protein (CAP)." Journal of molecular biology 293, no. 2 (1999): 199-213.
- Triezenberg, Steven J. "Structure and function of transcriptional activation domains." Current opinion in genetics & development 5, no. 2 (1995): 190-196.