DNA transcription in eukaryotes

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

Question Is there a single type of RNA polymerase involved in eukaryotic transcription  

Eukaryotic RNA polymerases have been isolated from many tissues, and in all cases, three distinct enzymes have been found in the nucleus. All contain a number of polypeptide subunits and are complex in structure, RNA polymerase I is known to be involved specifically in the transcription of rRNA genes. RNA polymerase II gives rise to transcripts that are subsequently processed to yield mRNA. RNA polymerase 111 is responsible for the transcription of the tRNA genes and a small ribosomal RNA gene that yields a species called 55 RNA. The three polymerases are distinguishable from one another by their differential sensitivity to the drug a-amanitin (the toxic principle of the mushroom Amanita phalloides), which does not affect bacterial RNA polymerase. RNA polymerase 

II is very sensitive to a-amanitin, while RNA polymerase I is completely resistant. RNA polymerase 

III is moderately sensitive to this inhibitor. Mitochondria have yet another type of RNA polymerase, which is unaffected by a-amanitin but is sensitive to drugs that inhibit bacterial RNA polymerase. 

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Table 71.2 Summary and comparison of DNA transcription in eukaryotes and prokaryotes (see Chapters 66-69). 

The multiple sites that serve as origins for DNA replication in eukaryotes are poorly defined except in a few animal viruses and in yeast. However, it is clear that initiation is regulated both spatially and temporaUy, since clusters of adjacent sites initiate rephcation synchronously. There are suggestions that functional domains of chromatin replicate as intact units, implying that the origins of rephcation are specificaUy located with respect to transcription units. 

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). 

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... 

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

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)... 

Alternatively, RNA synthesis can be terminated by the action of rho, a protein. Less is known about the termination of transcription in eukaryotes. A more detailed discussion of the initiation and termination of transcription will be given in Chapter 28. The important point now is that discrete start and stop signals for transcription are encoded in the DNA template. 

We then turn to transcription in eukaryotes, beginning with promoter structure and the transcription-factor proteins that regulate promoter activity. A distinctive feature of eukaryotic DNA templates is the presence of enhancer sequences that... 

The process of transcription in eukaryotes is similar to that in prokaryotes. RNA polymerase binds to the transcription factor complex in the promoter region and to the DNA, the helix unwinds within a region near the startpoint of transcription, DNA strand separation occurs, synthesis of the RNA ffanscript is initiated, and the RNA transcript is elongated, copying the DNA template. The DNA strands separate as the polymerase approaches and rejoin as the polymerase passes. 

Montminy, M. Transcriptional Activation Something New to Hang Your HAT On. Nature SST, 654-655 (1997). [Transcription in eukaryotes requires opening the DNA/histone complex, which can be controlled by acetylation.]... 

Much less is known about termination of transcription in eukaryotes than in bacteria. Once transcribed, specific termination sequences of mRNA are bound by protein complexes (such as CPSF cleavage and poly(A)denylation specificity factor, and CstF cleavage stimulation factor) that process cleavage of the message and subsequent poly(A)denylation. RNA polymerase continues transcription for up to several hundred nucleotides before dissociating from the DNA. 

Real chromosomes, of course, come in the four-letter alphabet ACGT. A feature that has not found a use in GAs is the accumulation of junk DNA occurring in eukaryotic chromosomes. About 95% of our DNA resides in these noncoding regions, called introns. Presumably the reason that introns have never disappeared is that there is little selection pressure to get rid of them. However, except for some controversial ideas that introns contain signals for transcription, no positive use for them is known. 

Selective gene transcription in eukaryotes seems to rely more heavily on the specificity of the template sequences themselves rather than on the specificity of RNA polymerases. RNA polymerase specificity seems to be relatively restricted to the recognition of some specific nucleotide sequence or resulting structural arrangement which constitutes an initiation site on the DNA template of the chromosome. RNA transcription proceeds on those cistrons which are not repressed either by the proteins of the heterochromatin of the chromosome or by structural inhibition. This idea is supported by the demonstration of apparent transcriptional specificity in vitro of chromatin using bacterial RNA polymerase as the transcriptive agent (Paul and Gilmour, 1968 Smith et ah, 1969 Paul, 1970). 

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