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.