Transcription in eukaryotes

The chemistry of transcription in eukaryotes is the same as in prokaryotes. However, the promoter structure and the mechanism for initiation are strikingly different. 

We have seen that prokaryotes have a single RNA polymerase that is responsible for the synthesis of all three kinds of prokaryotic RNA— mRNA, tRNA, and rRNA. The polymerase can switch a factors to interact with different promoters, but the core polymerase stays the same. The transcription process is predictably more complex in eukaryotes than in prokaryotes. Three RNA polymerases with different activities are known to exist. Each one transcribes a different set of genes and recognizes a different set of promoters  

RNA polymerase 1 is found in the nucleolus and synthesizes precursors of most, but not all, ribosomal RNAs. 

RNA polymerase If is found in the nucleoplasm and synthesizes mRNA precursors. 

RNA polymerase Iff is found in the nucleoplasm and synthesizes the tRNAs, precursors of 5S ribosomal RNA, and a variety of other small RNA molecules involved in mRNA processing and protein transport. 

All three of the eukaryotic RNA polymerases are lai e (500—700 kDa), complex proteins consisting of 10 or more subunits. Their overall structures differ. 

---

Figure 37-1. This figure illustrates that genes can be transcribed off both strands of DNA. The arrowheads indicate the direction of transcription (polarity). Note that the template strand is always read in the 3 to 5 direction. The opposite strand is called the coding strand because it is identical (except for T for L) changes) to the mRNA transcript (the primary transcript in eukaryotic cells) that encodes the protein product of the gene.

It is clear that the signals in DNA which control transcription in eukaryotic cells are of several types. Two types of sequence elements are promoter-proximal. One of these defines where transcription is to commence... 

Regulation of transcription is a central mechanism by which cells respond to developmental and environmental cues. RNA polymerase Il-mediated transcription in eukaryotes is to a large extent regulated at the level of chromatin, which forms a physical barrier for the binding of proteins to the promoter region of a target gene. The basic unit of chromatin is the nucleosome, which consists of an octamer of histone proteins around which the DNA is wrapped (see Fig. la). 

Acetylation of internal lysine residues of core histone N-terminal domains has been found correlatively associated with gene transcription in eukaryotes for more than four decades. Histone acetylation levels are the result of a competition between two families of enzymes histone acetyltransferases (HATs) and histone deacetylases (HDACs). 

Transcription factors (such as TFIID for RNA polymerase II) help to initiate transcription. The requirements for termination of transcription in eukaryotes are not well understood. All transcription can be inhibited by actinomycin D. In addition, RNA polymerase II is inhibited by a-amanitin (a toxin from certain mushrooms). These points are summarized in Table 1-3-1,... 

FIGURE 26-19 Two mechanisms for the alternative processing of complex transcripts in eukaryotes, (a) Alternative cleavage and polyadenylation patterns. Two poly(A) sites, A, and A2, are shown. 

A hairpin structure in bacterial mRNAs with a p-independent terminator (Fig. 26-7) confers stability against degradation. Similar hairpin structures can make some parts of a primary transcript more stable, leading to nonuniform degradation of transcripts. In eukaryotic cells, both the 3 poly (A) tail and the 5 cap are important to the stability of many mRNAs. Life Cycle of an mRNA... 

Initiation of transcription is a crucial regulation point for both prokaryotic and eukaryotic gene expression. Although some of the same regulatory mechanisms are used in both systems, there is a fundamental difference in the regulation of transcription in eukaryotes and bacteria. 

Because viruses contain small genomes, study of transcription of viral DNA and of replication of RNA viruses has played an important role in helping us to understand transcription in eukaryotes 47/686-688 An example is the discovery of the virus SV40 enhancer, which has been discussed in Section C,4. Study of viral life cycles is also essential to future progress in fighting viral diseases. Each of the many different viruses has its own often very complex life cycle. Only a few details can be given here. For lucid summaries see Voyles.259... 

How does transcription in eukaryotes differ from that in prokaryotes ... 

DNA-Binding Proteins that Regulate Transcription in Eukaryotes Are Often Asymmetrical The Homeodomain Zinc Finger Leucine Zipper Helix-Loop-Helix... 

There is no large difference in the frequency of histones in transcribed regions of the genome compared with untranscribed regions. Why don t nucleosomes interfere with transcription in eukaryotes ... 

Related topics DNA replication in bacteria (F3) Transcription in DNA replication in eukaryotes (F4) prokaryotes (G2) RNA structure (Gl) Transcription in eukaryotes an overview (G5)... 

Reeder, R.T. and Lang W.H. (1997) Terminating transcription in eukaryotes lessons learned from RNA polymerase I. Trends Biochem. Sci. 22(12), 473-477. 

RNA polymerase III transcribes the small genes for the many different tRNAs and the 5 S rRNA of the large ribosomal subunit. The primary tRNA transcripts in eukaryotes are transformed into mature tRNAs by endonuclease removal of a 5 -leader sequence, and replacement of a 3 -terminal UU by CCA. 

The process of transcription in eukaryotes is similar to that in bacteria, but there are important differences. 

---