Eukaryotic transcription

Eukaryotic transcription is more complex than prokaryotic transcription. For instance, in eukaryotes the genetic material (DNA), and therefore transcription, is primarily localized to the nucleus, where it is separated from the cytoplasm (in which translation occurs) by the entaamoeboic nuclear membrane. DNA is also present in mitochondria in the cytoplasm and mitochondria utilize a specialized RNA polymerase for transcription. This allows for the temporal regulation of gene expression through the sequestration of the RNA in the nucleus, and allows for selective transport of RNAs to the cytoplasm, where the ribosomes reside.

The basal eukaryotic transcription complex includes the RNA polymerase and additional proteins that are necessary for correct initiation and elongation.

Initiation

Among eukaryotes that regulate the transcription of individual genes, the core promoter of protein-encoding gene contains binding sites for the basal transcription complex and RNA polymerase II, and is normally within about 50 bases upstream of the transcription initiation site. Further transcriptional regulation is provided by upstream control elements (UCEs), usually present within about 200 bases upstream of the initiation site. The core promoter for Pol II sometimes contains a hi TATA box, the highly conserved DNA recognition sequence for the TATA box binding protein, TBP, whose binding initiates transcription complex assembly at the promoter.

Some genes also have enhancer elements that can be thousands of bases upstream or downstream of the transcription initiation site. Combinations of these upstream control elements and enhancers regulate and amplify the formation of the basal transcription complex

Transcription process

Eukaryotes have three nuclear RNA polymerases, each with distinct roles and properties:

Name	Transcribed	Product
RNA Polymerase I (Pol I, Pol A)	nucleolus	Larger ribosomal RNA (rRNA) (28S, 18S, 5.8S)
RNA Polymerase II (Pol II, Pol B)	nucleus	messenger RNA (mRNA) and most small nuclear RNAs (snRNAs)
RNA Polymerase III (Pol III, Pol C)	nucleus (and possibly the nucleolus-nucleoplasm interface)	transfer RNA (tRNA) and other small RNAs (including the small 5S rRNA)

Other organisms utilize RNA polymerase I to transcribe certain protein-coding genes in addition to rRNAs.

Termination

The process differs for each of the three RNA polymerases.

Transcription regulation

The regulation of gene expression is achieved through the interaction of several levels of control including the regulation of transcription initiation. Most (not all) eukaryotes possess robust methods of regulating transcription initiation on a gene-by-gene basis. The transcription of a gene can be regulated by cis-acting elements within the regulatory regions of the DNA, and trans-acting factors that include transcription factors and the basal transcription complex.