Eukaryotic organisms such as humans store their genetic information in the structure of DNA molecules. Most of the genetic instructions in genes are used to specify the structures of proteins (Figure 1). The many proteins of cells function as molecular machines that produce the living state. Intermediate between DNA and protein is RNA. The process by which cells convert the structure of a gene into the structure of a mRNA molecule is called transcription. In eukaryotes, a large molecular complex of specialized proteins is required to achieve the careful control of which subset of genes is transcribed in each type of cell. At the core of this complex is the enzyme RNA polymerase II.
Roger Kornberg's laboratory has used biochemical techniques to isolate the large complex of proteins that allow RNA polymerase II to produce messenger RNA. Working with yeast cells as an experimental system, Kornberg's research team has isolated and purified the functioning RNA pol II protein complex with attached template DNA, product mRNA and substrate nucleotides and captured images of the complex using electron microscopy and X-ray crystallography  (see Figure 2)
General transcription factors 
There are three major forms of life on Earth, bacteria, archaea and eukaryotes (Figure 3). RNA polymerase in bacteria is less complex than RNA polymerase in eukaryotes. Some of the increased complexity of RNA polymerase in eukaryotes reflects differences between DNA in eukaryotes and DNA in bacteria. Two important differences are that eukaryotes organize their DNA into nucleosomes and have more complex mechanisms for regulation of gene transcription. Nucleosomes are a complex of DNA and histone proteins (Figure 4). In order for transcription to occur, DNA must be released from being tightly coiled in nucleosomes. Bacteria do not have nucleosomes. Another complication of eukaryotic gene expression regulation is that gene sequences controlling transcription are often distant from the DNA site where transcription starts. The RNA polymerase of bacteria is relatively small with a core of five protein subunits and one additional protein that recognizes the start points for transcription. In contrast, RNA polymerase II of yeast (Baker’s yeast Saccharomyces cerevisiae) has 12 protein subunits and requires five general transcription factor proteins (TFIIB, D, E, F and H). The general transcription factors are complex, for example, TFIIH has at least six protein subunits in various eukaryotic organisms from yeast to mammals.
Searching for a full understanding of transcription 
As discussed above, Kornberg has made important contributions to on-going attempts to discover the full complexity of transcription in eykaryotes. In addition to the polymerase core and its associated general transcription factors, another large protein complex called Mediator is involved in the control of RNA polymerase II . In some cells, Mediator is about 4 times larger than the RNA polymerase core complex (with as many as 20 different protein subunits) and is important for transmitting the effects of positive and negative regulators of gene transcription (often quite distant from the transcription start site) to the core polymerase. Efforts continue to reveal the details of how the Mediator complex functions.
Learning project; where to next? 
Explore one of the following questions and then describe what you learn on this page:
- How many types of RNA polymerase are there in humans and what does each type do?
- What is known about transcription in archaea? (hint)
- How do HIV proteins interact with RNA polymerase II and induce transcription from the HIV-1 promoter? (hint: search here)
- Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution by Averell L. Gnatt, Patrick Cramer, Jianhua Fu, David A. Bushnell and Roger D. Kornberg in Science (2001) Volume 292, pages 1876-1882.
- 2006 award at the Nobel Prize website.
- Advanced information on the Nobel Prize in Chemistry 2006: Molecular basis of eukaryotic transcription by Lars Thelander.
- "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya" by C. R. Woese, O. Kandler, and M. L. Wheelis in Proceedings of the National Academy of Sciences U.S.A. (1990) Volume 87, pages 4576-4579. Full text online.
- McDonald D, "Milestone 9, (1973-1974) The nucleosome hypothesis: An alternative string theory, Nature Milestones: Gene Expression. (2005)
- The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing by A. J. Dombroski, B. D. Johnson, M. Lonetto, and C. A. Gross in Proceedings of the National Academy of Sciences U.S.A. (1996) Volume 93, pages 8858–8862.
- "A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II" by Y. J. Kim, S. Bjorklund, Y. Li,, M. H. Sayre and R. D. Kornberg in Cell (1994) Volume 77, pages 599-608.
See also 
- This lesson on eukaryotic transcription is part of the Nobel Prize in Chemistry learning project.
- The Nobel Prize in Physiology or Medicine learning project.
- RNA polymerase II article at Wikipedia.