Eukaryotic Transcription Is More Complex

EUKARYOTIC TRANSCRIPTION IS MORE COMPLEX

Several differences between eukaryotic and prokaryotic transcription occur because eukaryotic cells are more complex. The simple fact that eukaryotic mRNA is made in a nucleus makes the process more involved than bacterial transcription, but this is only one of the differences.

In contrast to the single RNA polymerase in prokaryotes, eukaryotes have three different RNA polymerases that each transcribe different types of genes. RNA polymerase I transcribes

the eukaryotic genes for large ribosomal RNA. These two rRNAs are transcribed as one long mRNA that is cleaved into two different transcripts, the 18S rRNA and 28S rRNA. These are used directly and not translated into protein. RNA polymerase III transcribes the genes for tRNA, 5S rRNA, and other small RNA molecules. RNA polymerase II transcribes the genes that encode proteins and has been studied the most.

Starting transcription of eukaryotic genes is more complex than in bacteria. The layout of the eukaryotic promoter is much different. RNA polymerase II needs three different regions, the initiator box, the TATA box, and various upstream elements that bind proteins known as transcription factors. The initiator box is the site where transcription starts and is separated by about 25 base pairs from the TATA box. The upstream elements vary from gene to gene and aid in controlling what proteins are expressed at what time.

Many proteins are involved in positioning eukaryotic RNA polymerase II at the transcriptional start site (Fig. 2.5 and Table 2.1). RNA polymerase II requires several general transcription factors to initiate transcription at all promoters. In addition, specific transcription factors are needed that vary depending on the particular gene (see later discussion). The TATA binding factor or TATA box factor (TBF) recognizes the TATA box. This factor is used by all three RNA polymerases in eukaryotes. For RNA polymerase II, TBF is found with other proteins in a complex called TFIID. (For the other RNA polymerases, TBF associates with different proteins.) After this complex

binds, TFIIA and TFIIB bind to the promoter, which then triggers the binding of RNA polymerase II. RNA polymerase is associated with TFIIF, which probably helps it bind to the promoter. Once RNA polymerase II has bound to the promoter, it still requires TFIIE, TFIIH, and TFIIJ to initiate transcription. In particular, TFIIH phosphorylates the tail of RNA polymerase II, which allows it to move along the DNA. As RNA polymerase II leaves the promoter, it leaves behind all of the general complexes except TFIIH.

Bacterial RNA polymerase can function with a promoter containing no upstream elements. But in eukaryotes the upstream elements are essential to RNA polymerase II function, and a promoter with no upstream elements is extremely inefficient at initiating transcription. These elements are from 50 to 200 base pairs in length and vary based on the gene being expressed. They bind regulatory proteins known as specific transcription factors, as opposed to the general transcription factors shared by all promoters that use RNA polymerase II.

For example, the specific transcription factors Oct-1 and Oct-2 proteins bind only to the Octamer elements. Oct-1 is found in all tissues, whereas Oct-2 is only found in immune cells. A plethora of specific factors exist that are beyond the scope of this discussion.

Eukaryotes have three different RNA polymerases that transcribe different genes. RNA polymerase II requires many different proteins to transcribe a gene.

Eukaryotes require specific transcription factors to initiate gene transcription. These are highly abundant, and each gene has a different set of factors that regulate its transcription.