Where is eukaryotic dna transcribed

This page has been archived and is no longer updated. In bacteria , mRNA is translated into protein as soon as it is transcribed. Unlike eukaryotic cells, bacteria do not have a distinct nucleus that separates DNA from ribosomes , so there is no barrier to immediate translation. Indeed, in high-magnification images of bacteria generated by electron microscopy, ribosomes can be seen translating messenger RNAs that are still being transcribed from DNA.

This process simply would not work in eukaryotic cells, mainly because eukaryotic RNAs contain introns and exons and must be edited before translation can begin. The eukaryotic nucleus therefore provides a distinct compartment within the cell, allowing transcription and splicing to proceed prior to the beginning of translation.

Thus, in eukaryotes, while transcription occurs in the nucleus, translation occurs in the cytoplasm. In other words, eukaryotic transcription and translation are spatially and temporally isolated. In contrast, bacteria, which have a comparatively streamlined genome , have no need to separate the processes of transcription and translation. In fact, several advantages may be provided by coupling these processes. One advantage involves the energy required for transcription and translation; specifically, the energy needed to drive the process of transcription could be provided by the large-scale expenditure of unstable nucleotide triphosphates during the process of translation.

Another advantage to coupled transcription and translation is that it provides a novel mechanism for gene regulation. At high concentrations of tryptophan, base pairing within the 5-prime UTR terminates transcription. At low concentrations of tryptophan, a different combination of base pairing within the 5-prime UTR allows transcription to occur. Genetics: A Conceptual Approach , 2nd ed.

All rights reserved. Colored regions along the cylinder represent important structural regions. In the 5-prime-UTR, a light green segment represents the ribosome binding site, a green segment represents the start codon, two dark blue segments represent region 1, two small light blue regions represent Trp codons, an orange segment represents region 2, a bright blue segment represents region 3, and a brown segment represents region 4.

In the trp E gene, a green segment represents the start codon and a pink segment represents the trp E gene. In the lower panel, the attenuation and anti-termination DNA conformations of the 5-prime UTR are shown in two side-by-side schematic illustrations.

In the attenuation conformation, the dark blue segments of region 1 base pair with the orange segment of region 2, and the bright blue segment of region 3 base pairs with the brown segment of region 4. Small hairpin loops are present between regions 1 and 2 and between regions 3 and 4. A large loop is present between regions 2 and 3. This conformation occurs in the presence of high levels of tryptophan, and it causes a termination of transcription. In the anti-termination conformation, regions 2 and 3 base pair, leaving regions 1 and 4 unpaired.

The loops between regions 1 and 2 and between regions 3 and 4 are larger than in the attenuation conformation, and the loop between regions 2 and 3 is smaller. This conformation occurs in the presence of low levels of tryptophan, and it allows transcription to proceed. This relationship can be exploited to provide a gene regulatory mechanism that is unique to prokaryotes. One example of this kind of regulation is provided by the trp operon , which has been well studied in E.

The trp operon is a cluster of genes involved in production of the amino acid tryptophan trp. In fact, an important mechanism by which the trp operon is regulated is called attenuation ; this clever feedback mechanism makes use of the fact that transcription and translation occur simultaneously in E. Attenuation, or dampening, of the trp operon is made possible by the fact that the rate of translation influences RNA structure, which in turn influences the rate of transcription.

Translation therefore interferes with transcription, making this an example of translation-mediated transcription attenuation. Mechanistically, this kind of attenuation is achieved because special sequences located near the beginning of the transcript, called the leader trpL , interact to create two possible RNA conformations: one that terminates transcription the terminator stem , and one that is permissive to transcription the anti-terminator stem Figure 1.

The mechanism by which formation of the terminator stem disrupts continued transcription is now understood. Interestingly, the choice between terminator and anti-terminator stem conformations depends on the speed of translation. This adds an additional layer of complexity to the system, as the rate of translation is affected by the availability of trp. Given that trp is an amino acid used to build proteins, the availability of trp will influence the rate at which proteins that contain a lot of trp residues are created.

Because the trpL region encodes a trp-rich polypeptide , its translation will be fast when trp is plentiful, and slow when it is not. In turn, quick translation of trpL leads to formation of the terminator stem and attenuation of continued expression of the trp operon.

Thus, when trp is plentiful, the coupled processes of transcription and translation respond and shut down. When it comes to gene regulation , prokaryotes and eukaryotes have evolved the best systems to suit their particular needs. While bacteria and other prokaryotes make use of paired transcription and translation on a variety of levels, eukaryotes have developed a more complex system, with different mechanisms of gene regulation.

Indeed, knowledge of the diversity of gene regulatory mechanisms deepens our appreciation of the diversity of nature. Although the enzymatic process of elongation is essentially the same in eukaryotes and prokaryotes, the DNA template is more complex. When eukaryotic cells are not dividing, their genes exist as a diffuse mass of DNA and proteins called chromatin. The DNA is tightly packaged around charged histone proteins at repeated intervals. These DNA—histone complexes, collectively called nucleosomes, are regularly spaced and include nucleotides of DNA wound around eight histones like thread around a spool.

For RNA synthesis to occur, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome. The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place 1,—2, nucleotides beyond the end of the gene being transcribed. Genes transcribed by RNA polymerase I contain a specific nucleotide sequence that is recognized by a termination protein.

OpenStax, Biology. OpenStax CNX. There are a number of different sigma subunits that bind to different promoters and therefore assist in turning genes on and off as conditions change.

Eukaryotic promoters are more complex than their prokaryotic counterparts, in part because eukaryotes have the aforementioned three classes of RNA polymerase that transcribe different sets of genes.

Many eukaryotic genes also possess enhancer sequences, which can be found at considerable distances from the genes they affect. Enhancer sequences control gene activation by binding with activator proteins and altering the 3-D structure of the DNA to help "attract" RNA pol II, thus regulating transcription. Because eukaryotic DNA is tightly packaged as chromatin , transcription also requires a number of specialized proteins that help make the template strand accessible.

The terms "strong" and "weak" are often used to describe promoters and enhancers, according to their effects on transcription rates and thereby on gene expression. Alteration of promoter strength can have deleterious effects upon a cell, often resulting in disease. For example, some tumor-promoting viruses transform healthy cells by inserting strong promoters in the vicinity of growth-stimulating genes, while translocations in some cancer cells place genes that should be "turned off" in the proximity of strong promoters or enhancers.

Enhancer sequences do what their name suggests: They act to enhance the rate at which genes are transcribed, and their effects can be quite powerful. Enhancers can be thousands of nucleotides away from the promoters with which they interact, but they are brought into proximity by the looping of DNA.

This looping is the result of interactions between the proteins bound to the enhancer and those bound to the promoter. The proteins that facilitate this looping are called activators, while those that inhibit it are called repressors. Transcription of eukaryotic genes by polymerases I and III is initiated in a similar manner, but the promoter sequences and transcriptional activator proteins vary. In eukaryotes, termination of transcription occurs by different processes, depending upon the exact polymerase utilized.

For pol I genes, transcription is stopped using a termination factor, through a mechanism similar to rho-dependent termination in bacteria. Transcription of pol III genes ends after transcribing a termination sequence that includes a polyuracil stretch, by a mechanism resembling rho-independent prokaryotic termination.

Termination of pol II transcripts, however, is more complex. Transcription of pol II genes can continue for hundreds or even thousands of nucleotides beyond the end of a noncoding sequence. The RNA strand is then cleaved by a complex that appears to associate with the polymerase.

Cleavage seems to be coupled with termination of transcription and occurs at a consensus sequence. Both polyadenylation and termination make use of the same consensus sequence, and the interdependence of the processes was demonstrated in the late s by work from several groups. One group of scientists working with mouse globin genes showed that introducing mutations into the consensus sequence AATAAA, known to be necessary for poly A addition, inhibited both polyadenylation and transcription termination.

They measured the extent of termination by hybridizing transcripts with the different poly A consensus sequence mutants with wild-type transcripts, and they were able to see a decrease in the signal of hybridization , suggesting that proper termination was inhibited.

They therefore concluded that polyadenylation was necessary for termination Logan et. Another group obtained similar results using a monkey viral system, SV40 simian virus The exact relationship between cleavage and termination remains to be determined. One model supposes that cleavage itself triggers termination; another proposes that polymerase activity is affected when passing through the consensus sequence at the cleavage site, perhaps through changes in associated transcriptional activation factors.

Thus, research in the area of prokaryotic and eukaryotic transcription is still focused on unraveling the molecular details of this complex process, data that will allow us to better understand how genes are transcribed and silenced. Connelly, S. Genes and Development 4 , — Dennis, P. Journal of Molecular Biology 84 , — Nature , — doi Izban, M. Journal of Biological Chemistry , — Kritikou, E.

Transcription elongation and termination: It ain't over until the polymerase falls off. Nature Milestones in Gene Expression 8 Lee, J. Methods in Molecular Biology , 23—37 Logan, J. A poly A addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene. Proceedings of the National Academy of Sciences 23 , — Nabavi, S.

Restriction Enzymes. Genetic Mutation. Functions and Utility of Alu Jumping Genes. Transposons: The Jumping Genes.