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 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.
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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 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 | Location | RNA transcribed |
| 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) |
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. Splicing Two types of splicing, cis-splicing and trans-splicing, use the same splicing machinery to cleave RNAs at specific points and rejoin them to form new combinations once transcribed. Although most eukaryotes possess splicing machinery the extent of cis- and trans-splicing varies from organism to organism.
Cis-splicing
Primary (initial) mRNA transcripts are synthesized as larger precursor RNAs that are processed by splicing out introns (non-coding sequences) and ligating exons (non-contiguous coding sequences) into the mature mRNA. Primary transcripts for some genes can be large. The primary transcripts of the neurexin genes, for instance, are as large as 1.7 megabases (1,700,000 bases), while the mature (processed) neurexin mRNAs are under 10 kilobases (10,000 bases), with as many as 24 exons and thousands of possible alternative splice variants that produce proteins with different activities. Alternative splicing is now incorporated in as much as 60% of human genetic coding, drastically increasing the potential variety of actual proteins produced.
Trans-splicing
Observed in range of different eukaryotes (including most conspicuously the worm C. elegans and a group of parasitic protists called kinetoplastids), trans-splicing occurs whereby an exon from one RNA molecule is spliced onto the 5' end of a completely separate molecule post-transcriptionally. While relatively unimportant to many eukaryotes, the role of this process in the biology of some organisms is ubiquitous. In kinetoplastids, for example, every single nuclear-encoded message must be trans-spliced before translation of the message can occur.
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