Final answer:
Phosphorylation of the C-terminal domain of RNA polymerase II occurs during the Initiation stage of eukaryotic transcription, right after the assembly of the preinitiation complex and before elongation begins.
Step-by-step explanation:
The C-terminal domain of RNA polymerase II is first phosphorylated during the Initiation phase of eukaryotic transcription. This step is an essential part of the process, enabling the transition from initiation to the elongation phase of transcription. After the assembly of the preinitiation complex, which includes various transcription factors and RNA polymerase II binding to the promoter region of the DNA, the C-terminal domain is phosphorylated. This phosphorylation event is critical as it changes the conformation of RNA polymerase II, allowing it to escape from the promoter and start synthesizing RNA during elongation.
The process of transcription initiation in eukaryotes begins with the transcription factors binding to the promoter, followed by the assembly of the preinitiation complex. Among the transcription factors, TFIIH has a kinase activity that is responsible for the phosphorylation of the C-terminal domain of RNA polymerase II. Once phosphorylated, transcription initiation is completed, and RNA polymerase II can proceed to transcribe the DNA into mRNA during the elongation process, as it moves away from the promoter.