Final answer:
The initiation step is the phase of eukaryotic transcription that shows the most significant differences from prokaryotic transcription due to the complex requirement of transcription factors and the impact of histone-DNA association.
Step-by-step explanation:
The step in eukaryotic transcription that differs the most from its prokaryotic counterpart is the initiation phase. During initiation in eukaryotes, there are complex processes involving the formation of an initiation complex with various transcription factors and enhancers. These components are crucial for the transcription machinery to correctly identify the start site of genes and begin transcription.
In contrast to prokaryotes, eukaryotic DNA is wrapped around histones, and this association affects the accessibility of the DNA for transcription initiation. Eukaryotic transcription also utilizes three different types of RNA polymerases for the transcription of various classes of genes, adding another layer of complexity. Moreover, unlike prokaryotic transcription—which occurs in the cytoplasm and can quickly be translated into proteins—eukaryotic transcripts (pre-mRNAs) undergo several processing steps, including splicing, before they are ready for translation.