Information

2: DNA Polymerase, RNA Polymerases, Transcription - Biology


Compare and contrast bacterial DNA polymerases and RNA polymerases

Note: ss=single strand ds=double strand P=phosphate

Overview:

DNA polymerases synthesize complementary DNA using a DNA template/guide

___________________DNA

E.g., ssDNA template base sequence: A T A G G C

Complementary DNA sequence T A T C C G DNA

synthesized by DNA polymerase

RNA polymerases synthesize complementary RNA sequences using DNA as a template/guide

___________________DNA

E.g., ssDNA template base sequence: A T A G G C

Complementary RNA sequence U A U C C G RNA

synthesized by RNA polymerase

Synthesis of DNA and RNA require input of energy, both ATP and charged precursors (see below)

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DNA Polymerase RNA Polymerase

Template/guide ss DNA ssDNA

Synthesize complementary DNA complementary RNA

Charged precursors deoxyadenosine tri-P= dATP adenosine tri-P= ATP

deoxythymidine tri-P=dTTP uridine tri-P=UTP

deoxycytodine tri-P= dCTP cytodine tri-P=CTP

deoxyguanosine tri-P=dGTP guanosine tri-P=GTP

primer required? Yes No

proofreading/editing? Yes* No

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*DNA polymerase proofreading/editting

Polymerases have a ”normal” or “intrinsic” mistake rate of approximately

10 -4 – 10 -5 nucleotides (this means the polymerases introduce the incorrect nucleotide every 10,000 to 100, 000 nucleotides). DNA polymerases have the ability to “proofread and edit” their mistakes. If they introduce the wrong nucleotide, they can remove or “excise” the wrong nucleotide and try again to make a correct match. This reduces the mistake rate of DNA polymerases to approximately 10-9 – 10 -10 (or only one incorrect nucleotide every 1,000,000,000 – 10,000,000,000 nucleotides). RNA polymerase cannot proofread or edit their work so RNA polymerase make many mistakes (one reason many RNA viruses, for example HIV, mutate so rapidly…..more later)

Transcription Prokaryotic repeated section

Review flow of information in cell

DNA--------> RNA ---------> Protein

replication transcription translation

I. Genetic Code: one to one relationship between specific codon (specific 3 base sequence) and an amino acid

II. Transcription: use of DNA as template/guide to synthesize complementary RNA. DNA info is rewritten in RNA sequence.

A. First step in gene expression

B. Products of transcription

1. messenger RNA=mRNA: will be translated into specific amino acid sequence of a protein

2. transfer RNA=tRNA: actual “translator” molecule, recognizes both a specific codon and specific amino acid

3. ribosomal RNA=rRNA: combined with ribosomal proteins, will form the ribosome, the “workbench” at which mRNA is translated into a specific amino acid sequence/polypeptide/protein

III. Promoters and RNA polymerases

A. Promoters: specific DNA sequences which signal the “start” points for gene transcription. Sigma factor/subunit of RNA polymerase binds to promoters to initiate transcription

B. RNA polymerases: enzyme complex which recognizes DNA promoters, binds to promoter and synthesizes complementary RNA copy using DNA as template/guide

E. coli RNA Polymerase: 2 subunits, sigma subunit and core

a. sigma subunit/factor= “brains” of RNA polymerase. Travels along DNA until it reaches a promoter, binds promoter

b. core subunit: binds to sigma attached at promoter. “Workhorse” of RNA polymerase, carries out actual RNA synthesis. Requires activated precursors and template strand, DOES NOT REQUIRE PRIMER (compare to DNA Polymerase). Synthesizes RNA in 5’ -to->3’ , similar to DNA polymerase. No proofreading ability therefore will make more mistakes than DNA Polymerase

c. sigma subunit will drop off after the first few ribonucleotides have been linked together, core continues alone. Note: core would start transcription randomly of DNA without direction of sigma subunit. Polycistronic mRNA (prok. only)

IV. Termination of transcription

terminators: DNA sequences which signal transcription stop signals. RNA polymerase releases DNA when transcription terminator sequence encountered


Every nucleated, diploid cell in the body contains the same DNA , or genome , yet different cells appear committed to different specialized tasks—for example, kidney cells absorb sodium, while pancreatic cells produce insulin . How is this possible? The answer lies in differential use of the genome in other words, different cells within the body express different portions of their DNA. This process, which begins with the transcription of DNA into RNA , ultimately leads to changes in cell function . Changes in transcription are thus a fundamental means by which cell function is regulated across species . In fact, even single-celled organisms, such as bacteria , regulate gene transcription depending on cues in their environments. Therefore, understanding how transcription is regulated is fundamental to deciphering the mysteries of the genome.

Central to the process of transcription is the complex of proteins known as the RNA polymerases. RNA polymerases have been found in all species, but the number and composition of these proteins vary across taxa. For instance, bacteria contain a single type of RNA polymerase, while eukaryotes (multicellular organisms and yeasts) contain three distinct types. In spite of these differences, there are striking similarities among transcriptional mechanisms. For example, all species require a mechanism by which transcription can be regulated in order to achieve spatial and temporal changes in gene expression . In order to fully understand what this means, it is first necessary to examine the mechanisms of RNA transcription in more detail.


1 Answer 1

As I have pointed out in my comment, it is not clear whether the sources mentioned relate to eukaryotes or prokaryotes, assuming they are correct. I am a translation man, rather than a transcription man, and so am answering this from the 2002 edition of Berg et al. ‘Biochemistry’, as I happen to have a copy of my own (a freebie from when I was still teaching) and this edition is freely available online. List members with more expertise in this area are encouraged to post comments to correct any errors in my answer or supply updates.

in neither prokaryotes nor eukaryotes is the DNA helicase that operates during DNA replication involved in transcription although other proteins necessary for transcription have DNA helicase activity.

In prokaryotes it appears that the RNA polymerase holoenzyme (made up of just four subunits) is responsible for unwinding about 17 base-pairs of template DNA. Quoting from Section 28.1.3:

Each bound polymerase molecule unwinds a 17-bp segment of DNA, which corresponds to 1.6 turns of B-DNA helix

There may be some ambiguity caused by the description of how this value was determined experimentally as it involved addition of topoisomerase II. However it is clear from discussion elsewhere that this is an enzyme of DNA replication and is not involved in transcription.

In eukaryotes transcription is much more complex, involving separate polymerases for different classes of RNA product and a variety of auxiliary transcription factors in the case of RNA polymerase II, which transcribes mRNA. According to Section 28.2.4:

The TATA box of DNA binds to the concave surface of TBP [the TATA-box-binding protein]. This binding induces large conformational changes in the bound DNA. The double helix is substantially unwound to widen its minor groove, enabling it to make extensive contact with the antiparallel β strands on the concave side of TBP.

So the initial recognition of the TATA box causes some unwinding. However the major player appears to be transcription factor TFIIF:

an ATP-dependent helicase that initially separates the DNA duplex for the polymerase


Process of Transcription

Transcription begins with the binding of the RNAP enzyme to a specific part of the DNA, also known as the promoter region. This binding requires the presence of a few other proteins – the sigma factor in prokaryotes and various transcription factors in eukaryotes. One set of proteins called general transcription factors are necessary for all eukaryotic transcriptional activity and include Transcription Initiation Factor II A, II B, II D, II E, II F and II H. These are supplemented by specific signaling molecules that modulate gene expression through stretches of non-coding DNA located upstream. Often initiation is aborted multiple times before a stretch of ten nucleotides is polymerized. After this, the polymerase moves beyond the promoter and loses most of the initiation factors.

This is followed by the unwinding of double stranded DNA, also known as ‘melting’, to form a sort of bubble where active transcription occurs. This ‘bubble’ appears to move along the DNA strand as the RNA polymer elongates. Once transcription is complete, the process is terminated and the RNA strand is processed. Prokaryotic RNAP and eukaryotic RNA polymerases I and II require additional transcription termination proteins. RNAP III terminates transcription when there is a stretch of Thymine bases on the non-template strand of DNA.


General Transcription Factors and Initiation of Transcription by RNA Polymerase II

Because RNA polymerase II is responsible for the synthesis of mRNA from protein-coding genes, it has been the focus of most studies of transcription in eukaryotes. Early attempts at studying this enzyme indicated that its activity is different from that of prokaryotic RNA polymerase. The accurate transcription of bacterial genes that can be accomplished in vitro simply by the addition of purified RNA polymerase to DNA containing a promoter is not possible in eukaryotic systems. The basis of this difference was elucidated in 1979, when Robert Roeder and his colleagues discovered that RNA polymerase II is able to initiate transcription only if additional proteins are added to the reaction. Thus, transcription in the eukaryotic system appeared to require distinct initiation factors that (in contrast to bacterial σ factors) were not associated with the polymerase.

Biochemical fractionation of nuclear extracts has now led to the identification of specific proteins (called transcription factors) that are required for RNA polymerase II to initiate transcription. Indeed, the identification and characterization of these factors represents a major part of ongoing efforts to understand transcription in eukaryotic cells. Two general types of transcription factors have been defined. General transcription factors are involved in transcription from all polymerase II promoters and therefore constitute part of the basic transcription machinery. Additional transcription factors (discussed later in the chapter) bind to DNA sequences that control the expression of individual genes and are thus responsible for regulating gene expression.

Five general transcription factors are required for initiation of transcription by RNA polymerase II in reconstituted in vitro systems (Figure 6.12). The promoters of many genes transcribed by polymerase II contain a sequence similar to TATAA 25 to 30 nucleotides upstream of the transcription start site. This sequence (called the TATA box) resembles the -10 sequence element of bacterial promoters, and the results of introducing mutations into TATAA sequences have demonstrated their role in the initiation of transcription. The first step in formation of a transcription complex is the binding of a general transcription factor called TFIID to the TATA box (TF indicates transcription factor II indicates polymerase II). TFIID is itself composed of multiple subunits, including the TATA-binding protein (TBP), which binds specifically to the TATAA consensus sequence, and 10-12 other polypeptides, called TBP-associated factors (TAFs). TBP then binds a second general transcription factor (TFIIB) forming a TBP-TFIIB complex at the promoter (Figure 6.13). TFIIB in turn serves as a bridge to RNA polymerase, which binds to the TBP-TFIIB complex in association with a third factor, TFIIF.

Figure 6.12

Formation of a polymerase II transcription complex. Many polymerase II promoters have a TATA box (consensus sequence TATAA) 25 to 30 nucleotides upstream of the transcription start site. This sequence is recognized by transcription factor TFIID, which (more. )

Figure 6.13

Model of the TBP-TFIIB complex bound to DNA. The DNA is shown as a stick figure consisting of yellow and green strands, with the site of transcription initiation designated +1. TBP consists of two repeats, colored light blue and dark blue. TFIIB repeats (more. )

Following recruitment of RNA polymerase II to the promoter, the binding of two additional factors (TFIIE and TFIIH) is required for initiation of transcription. TFIIH is a multisubunit factor that appears to play at least two important roles. First, two subunits of TFIIH are helicases, which may unwind DNA around the initiation site. (These subunits of TFIIH are also required for nucleotide excision repair, as discussed in Chapter 5.) Another subunit of TFIIH is a protein kinase that phosphorylates repeated sequences present in the C-terminal domain of the largest subunit of RNA polymerase II. Phosphorylation of these sequences is thought to release the polymerase from its association with the initiation complex, allowing it to proceed along the template as it elongates the growing RNA chain.

In addition to a TATA box, the promoters of many genes transcribed by RNA polymerase II contain a second important sequence element (an initiator, or Inr, sequence) that spans the transcription start site. Moreover, some RNA polymerase II promoters contain only an Inr element, with no TATA box. Initiation at these promoters still requires TFIID (and TBP), even though TBP obviously does not recognize these promoters by binding directly to the TATA sequence. Instead, other subunits of TFIID (TAFs) appear to bind to the Inr sequences. This binding recruits TBP to the promoter, and TFIIB, polymerase II, and additional transcription factors then assemble as already described. TBP thus plays a central role in initiating polymerase II transcription, even on promoters that lack a TATA box.

Despite the development of in vitro systems and the characterization of several general transcription factors, much remains to be learned concerning the mechanism of polymerase II transcription in eukaryotic cells. The sequential recruitment of transcription factors described here represents the minimal system required for transcription in vitro additional factors may be needed within the cell. Furthermore, RNA polymerase II appears to be able to associate with some transcription factors in vivo prior to the assembly of a transcription complex on DNA. In particular, preformed complexes of RNA polymerase II with TFIIB, TFIIE, TFIIF, TFIIH, and other transcriptional regulatory proteins have been detected in both yeast and mammalian cells. These large complexes (called polymerase II holoenzymes) can be recruited to a promoter via direct interaction with TFIID (Figure 6.14). The relative contributions of stepwise assembly of individual factors versus recruitment of the RNA polymerase II holoenzyme to promoters within the cell thus remain to be determined.

Figure 6.14

RNA polymerase II holoenzyme. The holoenzyme consists of a preformed complex of RNA polymerase II, the general transcription factors TFIIB, TFIIE, TFIIF, and TFIIH, and several other proteins that activate transcription. This complex can be recruited (more. )


Conclusion:

In 1956, the first DNA polymerase was discovered by Arther Kornberg. Both polymerases are important for a cell.

Error in the function of the polymerase (either DNA polymerase or RNA polymerase) results in some abnormalities. These abnormalities may cause some serious genetic problems.

wrong nucleotide addition during replication of transcription results in an abnormal polypeptide chain and results in abnormal or non-function protein.


Difference Between DNA POLYMERASE and RNA POLYMERASE

The main function of a polymerase which is an enzyme is somehow similar to nucleic acid polymers like that of DNA and RNA. Polymer is a compound with repeating small molecules where it is a natural or synthetic compound that consists of large molecules made of many chemically bonded smaller identical molecules such as starch and nylon. In this section, we will disclose the differences between DNA polymerase and RNA polymerase.

DNA strands are well formed when the deoxyribonucleotides undergo polymerization with the help of DNA polymerases which are thought to be enzymes that hasten the polymerization process. It is clear that DNA polymerase plays a vital role in the replication of DNA wherein they serve as agents that detect undamaged DNA strands as prototypes which later on they may utilize to be able to create new strands. After that, a new fragment of DNA will be copied through this process. This molecule that was recently polymerized is the actual counterpart of the strand of the template which has exactly the same identity to that partner strand of the original template. On the other hand, RNA polymerase is known to be a complex enzyme involved in the production of RNA from DNA via the process of transcription. RNA polymerases are also in charge for supplying ribonucleotides to the growing transcripts of RNA in the end portion. This is carried out by way of catalyzing the development of these phosphodiester bonds which act as connectors of the ribonucleotides to hold them together. In contrast with the DNA polymerase, RNA polymerases do not necessarily require the so called primer to start the process and they actually have no proofreading systems. However, between these two types of enzymes there is a great difference: DNA polymerases are not capable of initiating a new strand while RNA polymerases have the capacity. There is no known DNA polymerase that is able to initiate a new chain. Consequently, in the course of replicating DNA, there is oligonucleotide (known as primer) that must be synthesized first by an enzyme that is different.

Going further, DNA polymerases are capable of adding up nucleotides that are free only to the end portion of the strand that was newly formed. This may actually lengthen the strand in a manner following 5′-3′. A nucleotide can be added to DNA polymerase only on a pre-existing 3’-OH group which requires a primer so that it may add to the nucleotide. The so called primers do contain DNA and RNA base. DNA has the base thymine while RNA has uracil as its base. DNA is double stranded whereas RNA is a single stranded. DNA contains the pentose sugar deoxyribose while RNA contains the pentose sugar ribose. DNA polymerase will be continuous till the work is finally done wherein RNA polymerases will continue but eventually may break in the event it will reach a “stop” cycle. Subunits contained in RNA polymerases must unwind the templates of DNA and the DNA polymerases do actually abide the helicase that the double helix may be open just in front of it. Lastly, it is said that RNA polymerase is a lot slower compared to DNA polymerase. 50 nucleotides in one second for RNA polymerase while 800 nucleotides for DNA polymerase in one second.

1.DNA polymerase synthesizes DNA while RNA polymerase synthesizes RNA.

2.In contrast with the DNA polymerase, RNA polymerases do not necessarily require the so called primer to start the process and they actually have no proofreading systems.

2.RNA polymerases are capable of initiating a new strand but DNA polymerases cannot.

3.DNA has the base thymine while RNA has uracil as its base.

4.DNA is double stranded whereas RNA is a single stranded.

5.DNA contains the pentose sugar deoxyribose while RNA contains the pentose sugar ribose.

6.DNA polymerase will be continuous till the work is finally done wherein RNA polymerases will continue but eventually may break in the event it will reach a “stop” cycle.

7.Subunits contained in RNA polymerases must unwind the templates of DNA and the DNA polymerases do actually abide the helicase that the double helix may be open just in front of it.


Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then help recruit the appropriate polymerase.

The Three Eukaryotic RNA Polymerases

The features of eukaryotic mRNA synthesis are markedly more complex those of prokaryotes. Instead of a single polymerase comprising five subunits, the eukaryotes have three polymerases that are each made up of 10 subunits or more. Each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template.

RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes (Table 1). The rRNA molecules are considered structural RNAs because they have a cellular role but are not translated into protein. The rRNAs are components of the ribosome and are essential to the process of translation. RNA polymerase I synthesizes all of the rRNAs except for the 5S rRNA molecule. The “S” designation applies to “Svedberg” units, a nonadditive value that characterizes the speed at which a particle sediments during centrifugation.

Table 1. Locations, Products, and Sensitivities of the Three Eukaryotic RNA Polymerases
RNA Polymerase Cellular Compartment Product of Transcription α-Amanitin Sensitivity
I Nucleolus All rRNAs except 5S rRNA Insensitive
II Nucleus All protein-coding nuclear pre-mRNAs Extremely sensitive
III Nucleus 5S rRNA, tRNAs, and small nuclear RNAs Moderately sensitive

RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. Eukaryotic pre-mRNAs undergo extensive processing after transcription but before translation (Figure 1). For clarity, this module’s discussion of transcription and translation in eukaryotes will use the term “mRNAs” to describe only the mature, processed molecules that are ready to be translated. RNA polymerase II is responsible for transcribing the overwhelming majority of eukaryotic genes.

Figure 1. Eukaryotic mRNA contains introns that must be spliced out. A 5′ cap and 3′ poly-A tail are also added.

RNA polymerase III is also located in the nucleus. This polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre-RNAs. The tRNAs have a critical role in translation they serve as the adaptor molecules between the mRNA template and the growing polypeptide chain. Small nuclear RNAs have a variety of functions, including “splicing” pre-mRNAs and regulating transcription factors.

A scientist characterizing a new gene can determine which polymerase transcribes it by testing whether the gene is expressed in the presence of a particular mushroom poison, α-amanitin (Table 1). Interestingly, α-amanitin produced by Amanita phalloides, the Death Cap mushroom, affects the three polymerases very differently. RNA polymerase I is completely insensitive to α-amanitin, meaning that the polymerase can transcribe DNA in vitro in the presence of this poison. In contrast, RNA polymerase II is extremely sensitive to α-amanitin, and RNA polymerase III is moderately sensitive. Knowing the transcribing polymerase can clue a researcher into the general function of the gene being studied. Because RNA polymerase II transcribes the vast majority of genes, we will focus on this polymerase in our subsequent discussions about eukaryotic transcription factors and promoters.

RNA Polymerase II Promoters and Transcription Factors

Eukaryotic promoters are much larger and more intricate than prokaryotic promoters. However, both have a sequence similar to the -10 sequence of prokaryotes. In eukaryotes, this sequence is called the TATA box, and has the consensus sequence TATAAA on the coding strand. It is located at -25 to -35 bases relative to the initiation (+1) site (Figure 2). This sequence is not identical to the E. coli -10 box, but it conserves the A–T rich element. The thermostability of A–T bonds is low and this helps the DNA template to locally unwind in preparation for transcription.

Instead of the simple σ factor that helps bind the prokaryotic RNA polymerase to its promoter, eukaryotes assemble a complex of transcription factors required to recruit RNA polymerase II to a protein coding gene. Transcription factors that bind to the promoter are called basal transcription factors. These basal factors are all called TFII (for Transcription Factor/polymerase II) plus an additional letter (A-J). The core complex is TFIID, which includes a TATA-binding protein (TBP). The other transcription factors systematically fall into place on the DNA template, with each one further stabilizing the pre-initiation complex and contributing to the recruitment of RNA polymerase II.

Figure 2. A generalized promoter of a gene transcribed by RNA polymerase II is shown. Transcription factors recognize the promoter. RNA polymerase II then binds and forms the transcription initiation complex.

Practice Question

A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene?

Some eukaryotic promoters also have a conserved CAAT box (GGCCAATCT) at approximately -80. Further upstream of the TATA box, eukaryotic promoters may also contain one or more GC-rich boxes (GGCG) or octamer boxes (ATTTGCAT). These elements bind cellular factors that increase the efficiency of transcription initiation and are often identified in more “active” genes that are constantly being expressed by the cell.

Basal transcription factors are crucial in the formation of a preinitiation complex on the DNA template that subsequently recruits RNA polymerase II for transcription initiation. The complexity of eukaryotic transcription does not end with the polymerases and promoters. An army of other transcription factors, which bind to upstream enhancers and silencers, also help to regulate the frequency with which pre-mRNA is synthesized from a gene. Enhancers and silencers affect the efficiency of transcription but are not necessary for transcription to proceed.

The Evolution of Promoters

The evolution of genes may be a familiar concept. Mutations can occur in genes during DNA replication, and the result may or may not be beneficial to the cell. By altering an enzyme, structural protein, or some other factor, the process of mutation can transform functions or physical features. However, eukaryotic promoters and other gene regulatory sequences may evolve as well. For instance, consider a gene that, over many generations, becomes more valuable to the cell. Maybe the gene encodes a structural protein that the cell needs to synthesize in abundance for a certain function. If this is the case, it would be beneficial to the cell for that gene’s promoter to recruit transcription factors more efficiently and increase gene expression.

Scientists examining the evolution of promoter sequences have reported varying results. In part, this is because it is difficult to infer exactly where a eukaryotic promoter begins and ends. Some promoters occur within genes others are located very far upstream, or even downstream, of the genes they are regulating. However, when researchers limited their examination to human core promoter sequences that were defined experimentally as sequences that bind the preinitiation complex, they found that promoters evolve even faster than protein-coding genes.

It is still unclear how promoter evolution might correspond to the evolution of humans or other higher organisms. However, the evolution of a promoter to effectively make more or less of a given gene product is an intriguing alternative to the evolution of the genes themselves. [1]

Promoter Structures for RNA Polymerases I and III

The processes of bringing RNA polymerases I and III to the DNA template involve slightly less complex collections of transcription factors, but the general theme is the same.

The conserved promoter elements for genes transcribed by polymerases I and III differ from those transcribed by RNA polymerase II. RNA polymerase I transcribes genes that have two GC-rich promoter sequences in the -45 to +20 region. These sequences alone are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from -180 to -105 upstream of the initiation site will further enhance initiation. Genes that are transcribed by RNA polymerase III have upstream promoters or promoters that occur within the genes themselves.

Eukaryotic transcription is a tightly regulated process that requires a variety of proteins to interact with each other and with the DNA strand. Although the process of transcription in eukaryotes involves a greater metabolic investment than in prokaryotes, it ensures that the cell transcribes precisely the pre-mRNAs that it needs for protein synthesis.

Elongation and Termination

Following the formation of the preinitiation complex, the polymerase is released from the other transcription factors, and elongation is allowed to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5′ to 3′ direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will focus on how this polymerase accomplishes elongation and termination.

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 146 nucleotides of DNA wound around eight histones like thread around a spool.

For polynucleotide synthesis to occur, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome. This is accomplished by a special protein complex called FACT, which stands for “facilitates chromatin transcription.” This complex pulls histones away from the DNA template as the polymerase moves along it. Once the pre-mRNA is synthesized, the FACT complex replaces the histones to recreate the nucleosomes.

The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place 1,000–2,000 nucleotides beyond the end of the gene being transcribed. This pre-mRNA tail is subsequently removed by cleavage during mRNA processing. On the other hand, RNA polymerases I and III require termination signals. Genes transcribed by RNA polymerase I contain a specific 18-nucleotide sequence that is recognized by a termination protein. The process of termination in RNA polymerase III involves an mRNA hairpin similar to rho-independent termination of transcription in prokaryotes.


References

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