Final answer:
Phosphorylation of RNA polymerase II is necessary for promoter clearance, after which the polymerase synthesizes RNA in the 5' to 3' direction within the transcription bubble, substituting uracil for thymine.
Step-by-step explanation:
Promoter clearance, which is the detachment of RNA polymerase from the promoter after the initiation of transcription, requires phosphorylation of the RNA polymerase II subunit. Once phosphorylated, the RNA polymerase dissociates from the mediator complex and other transcription factors. This transition from initiation to elongation phase allows the polymerase to synthesize the new RNA strand at the transcription bubble, moving in the 5' to 3' direction along the DNA template strand. The nascent RNA chain mirrors the DNA coding strand, with uracil (U) substituting for thymine (T). The phosphorylation process, as part of the transcription initiation complex, is crucial for the unwinding of the DNA strands to facilitate RNA synthesis.