Eukaryotic transcription and the ends of mRNA

Eukaryotes transcribe their genes in the same three stages as bacteria: initiation, elongation, and termination. The differences are in the crew. More proteins are needed to start, and the RNA that comes off a protein-coding gene needs finishing work before it can leave the nucleus.

Three RNA polymerases

A bacterium has a single RNA polymerase that transcribes all of its genes. Many bacterial species do have several sigma factors, though, each recognizing a different set of promoters.

Eukaryotes divide the work among three RNA polymerases, numbered I, II, and III:

• RNA polymerase II transcribes protein-coding genes, so it makes every pre-mRNA.
• RNA polymerases I and III transcribe the genes for non-coding RNAs, such as tRNAs and rRNAs.

Transcription factors replace sigma factor

Eukaryotes have no sigma factor. Instead, RNA polymerase II relies on transcription factors, the proteins from Chapter 9 that control whether a gene is transcribed. Six of them are needed to start transcription at a protein-coding gene.

The six transcription factors and RNA polymerase II assemble at the promoter into a large preinitiation complex. Once it has formed, the complex unwinds a short stretch of DNA into an open complex, and elongation proceeds as in bacteria.

Check yourselfIn eukaryotes, what does the job that sigma factor does in bacteria?

Transcription factors. Six of them assemble with RNA polymerase II at the promoter into a preinitiation complex, which positions the polymerase to begin transcription.

Finishing the pre-mRNA

The RNA that RNA polymerase II makes is a pre-mRNA, and it isn’t ready to use. Three modifications, all made in the nucleus, turn it into a mature mRNA, which then leaves for the cytosol.

The 5′ cap

Capping happens early, while RNA polymerase is still transcribing. An enzyme attaches a guanine nucleotide, modified with a methyl group, to the 5′ end of the RNA. This 7-methylguanosine is the 5′ cap. Proteins called cap-binding proteins recognize it, and through them the cap does three jobs:

• It lets the mRNA exit the nucleus properly.
• It protects the mRNA from being broken down once it’s in the cytosol.
• It lets the mRNA bind to a ribosome so it can be translated.

Check yourselfAn uncapped mRNA is injected straight into the cytosol of a eukaryotic cell. Will it be translated normally?

No. Without a cap, cap-binding proteins can’t bring the mRNA to a ribosome, and the mRNA would also be broken down faster.

The poly A tail

Most mature mRNAs end in a string of 100–200 adenine nucleotides at their 3′ end, the poly A tail. The tail isn’t spelled out in the gene. An enzyme adds the adenines one after another once the pre-mRNA has been fully transcribed, without reading any template.

The poly A tail has two jobs. It helps the mRNA leave the nucleus, and it stabilizes the mRNA so that it lasts longer in the cytosol.

Check yourselfCompare a mature mRNA with the DNA of its gene. What at the mRNA’s 3′ end has no match in the gene?

The poly A tail. An enzyme adds its adenines to the pre-mRNA after transcription, without a template, so the gene never codes them.