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The transcription in eukaryotes, a much more complex process than in prokaryotes. In eukaryotes, transcription and translation take place in different cellular compartments:transcription takes place in the membrane-bounded nucleus, whereas translation takes place outside the nucleus in the cytoplasm. In prokaryotes, the two processes are closely coupled. Indeed, the translation of bacterial mRNA begins while the transcript is still being synthesized. The spatial and temporal separation of transcription and translation enables eukaryotes to regulate gene expression in much more intricate ways, contributing to the richness of eukaryotic form and function.

A second major difference between prokaryotes and eukaryotes is the extent of RNA processing. Although both prokaryotes and eukaryotes modify tRNA and rRNA, eukaryotes very extensively process nascent RNA destined to become mRNA. Primary transcripts (pre-mRNA molecules), the products of RNA polymerase action, acquire a cap at their 5′ ends and a poly(A) tail at their 3′ ends. Most importantly, nearly all mRNA precursors in higher eukaryotes are spliced. Introns are precisely excised from primary transcripts, and exons are joined to form mature mRNAs with continuous messages. Some mRNAs are only a tenth the size of their precursors, which can be as large as 30 kb or more. The pattern of splicing can be regulated in the course of development to generate variations on a theme, such as membrane-bound and secreted forms of antibody molecules. Alternative splicing enlarges the repertoire of proteins in eukaryotes and is a clear illustration of why the proteome is more complex than the genome.

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