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| Genetics Encyclopedia: Transcription |
Transcription is the process in which genetic information stored in a strand of DNA is copied into a strand of RNA. The sequence of the four bases in DNA, which are adenine (A), cytosine (C), guanine (G), and thymine (T), is preserved in the sequence of the four bases in RNA, which are A, C, G, and uracil (U).
Functions of Rna Transcripts
RNA molecules have various functions in the cell. Many of the functions are associated with translation, in which the genetic code of messenger RNA molecules is used to help the ribosomes synthesize a specific protein. In addition, ribosomal RNA is the main component of the ribosome, and transfer RNA does the actual translating from nucleotide sequence into amino acid sequence.
RNA molecules may also function as enzymes. They do so either alone or in association with proteins. RNA molecules associate with proteins, for example, when they serve as components of machinery that helps make other, newly formed RNA molecules functional.
RNA is chemically better suited to carry out certain tasks than is DNA. There are also other reasons RNA, not DNA, is used for these tasks. First, it is desirable to keep DNA available for replication and not tied up with other functions. Second, the small number of DNA molecules in the cell is often insufficient. Creating many identical RNA molecules that are copies of a single segment of DNA provides the necessary numbers. Third, RNA can be differentially degraded when it is no longer needed, providing an important regulatory mechanism that would be unavailable if there were only one type of nucleic acid.
Promoters
Transcription is initiated at regions of DNA called promoters, which are typically 20 to 150 base pairs long, depending on the organism. The sequence of bases at a promoter is recognized by RNA polymerase, the enzyme that synthesizes RNA.
The RNA polymerases in bacteria, as well as in viruses in bacteria, are able to recognize particular promoter sequences without the help of any other cellular proteins. However, in eukaryotes and Archaea, other proteins, called initiation factors, recognize the promoter sequence, "recruit" RNA polymerase and other proteins, help the RNA polymerase bind to the DNA, and regulate the enzyme's activity.
RNA polymerase is assembled on promoters in a particular orientation (Figure 1A). This allows RNA synthesis to start at a precise location and proceed in only one direction, "downstream" toward the gene (Figure 1B).
Rna Synthesis
RNA, like DNA, is a polymer of nucleotides. Each nucleotide consists of a sugar that is attached to a phosphate group and any one of four bases. The RNA polymerase, as it builds the chain of nucleotides, processes only one of the two complementary strands of DNA. This DNA strand is referred to as the template strand. The least confusing name for the other DNA strand is "the nontemplate strand."
The bases in the newly synthesized RNA are complementary to the bases in the template DNA strand and, therefore, identical in sequence to the bases in the nontemplate strand, except that the RNA contains U where the nontemplate strand of DNA contains T.
Before the nucleotides are linked together, they exist separately as ribonucleoside triphosphates (NTPs). As shown below, the NTPs contain one of the four common RNA bases, A, C, G, and U, linked to a five-carbon ribose sugar, linked, in turn, to a chain of three phosphate groups. During RNA synthesis, a covalent, "phosphodiester" bond is formed between one of the three phosphate groups on one NTP and a hydroxyl group on another. The two other phosphate groups that were part of the original NTP are released.
RNA synthesis is said to proceed in the 5′ to 3′ direction, reflecting the fact that the attachment of new nucleotides always occurs at the 3′ hydroxyl group of the growing RNA chain. RNA synthesis goes through phases that are typical of polymerization processes: initiation, elongation, and termination, yielding an RNA product of defined size and sequence.
Initiation
The first phase of RNA synthesis is initiation (Figure 1B). Initiation starts when the first phosphodiester bond is formed. At precise locations, determined by the promotor DNA sequence, the first and second RNA bases bind to the complex, and RNA polymerase catalyzes the formation of a covalent bond between them.
When the growing RNA chain reaches a length of about ten nucleotides, the complex loses contact with the promoter and starts moving along the DNA. This is referred to as promoter "clearance" or "escape."
Only a fraction of initiation events lead to promoter clearance. In many instances, an "abortive" RNA molecule, shorter than ten nucleotides, is released from the RNA polymerase, and RNA synthesis begins all over again. Such an abortive molecule is shown in the figure as a thick line.
Once the growing RNA chain has reached the critical length of about ten nucleotides, the initiation stage is considered to have ended, and elongation begins. In eukaryotes, the transition from initiation to elongation can be triggered by enzymes called kinases, which attach phosphate groups to RNA polymerase, facilitating promoter clearance.
Elongation
Genes range in length from about 80 base pairs of DNA, as is the case for those transcribed into transfer RNA, to more than 1 million base pairs, as is the case for those encoding very long proteins. An RNA polymerase molecule that has disengaged from DNA during elongation would be unable to finish synthesizing the RNA molecule. Thus the enzyme has to traverse even the longest genes (Figure 1C), without falling off.
Along the way, there are DNA sequences that the RNA polymerase traverses considerably more slowly than at its usual rate of about 50 nucleotides per second. At regions called pause sites, it may take longer than 1 second for a single nucleotide to be added to the growing polymer.
In eukaryotes, many genes contain blocks of DNA called introns, which disrupt the coding information of the gene. Introns are removed from the newly made RNA by a process called splicing. It is thought that the proteins which carry out the splicing are carried by the RNA polymerase as it is transcribing the gene, allowing the processing of the RNA to occur at the same time as the RNA molecule is synthesized.
Termination
When the RNA polymerase reaches a specific DNA sequence known as a terminator, it slows down and the transcription complex dissociates from the DNA, as shown in Figure 1D. The released RNA polymerase is then free to participate in a new initiation event.
At some terminators, primarily in bacteria, the RNA polymerase is able to respond to the release signal without being helped by any other proteins. Such sites are called intrinsic terminators. At other sites, termination is accomplished only with the aid of additional proteins. These proteins, called termination factors, are also instrumental in causing RNA to be released from the transcribing complex.
"Factor-dependent" terminators have been found in organisms from each of the three domains of life, the eukaryotes, bacteria, and Archaea. In eukaryotes, but usually not in bacteria, transcription of most genes proceeds past the end of the gene, as shown in Figure 1D.
The initial RNA molecules are often referred to as "primary" transcripts. In many instances, the primary transcripts must be processed to yield functional, or "mature," RNA. The processing can involve shortening them by removing their terminal or internal regions, or modifying specific nucleotides in other ways.
Regulation of Transcription
Only a few of an organism's genes are active or "expressed" at any particular time. Which genes are expressed in a particular cell depends on such factors as the nutrients available, the cell's state of differentiation, and the cell's age. There are intricate mechanisms that let the cell regulate the expression of many of its genes. Transcription, the first step in the expression of the genetic information, is an important point at which gene expression can be regulated.
There are two types of regulation: positive control, in which transcription is enhanced in response to a certain set of conditions; and negative control, in which transcription is repressed. Usually, positive control is used at promoters that are otherwise engaged in the initiation of few RNA molecules. Negative control is used at promoters where many molecules of RNA are initiated.
Activator proteins enable positive control by binding to the promoter to recruit RNA polymerase or other required initiation proteins. Such activator proteins usually bind upstream of the promoter (Figure 1). Increased recruitment then leads to an increased rate of synthesis of RNA for a particular gene. The more regulatory sites that are bound, the greater the increase in the rate of RNA synthesis. Repressor proteins can inhibit initiation of transcription by binding to the promoter and preventing RNA polymerase or a required initiation protein from binding.
In eukaryotes, DNA is "packaged" into nucleosomes by being wrapped around histone proteins. This can dramatically reduce the ability of genes to be transcribed, because the packaging may hide promoter sequences that are recognized by initiation factors.
Two mechanisms are used to alter the DNA packaging, to regulate transcription. First, enzymes called chromatin remodeling factors can move his-tone proteins around on the DNA, so that promoter sequences are more accessible or less accessible to the transcription initiation machinery. Second, enzymes can attach small chemical groups, including acetyl, phosphate, methyl or other groups, to the histone proteins. This modification of his-tone proteins may alter the interaction between the DNA and the histones, or between histones and other proteins, either facilitating or blocking the ability of initiation factors to bind DNA.
Transcription also is regulated by proteins that influence how quickly RNA polymerase moves along the DNA. These proteins, called regulatory elongation factors, may help the polymerase traverse pause sites, and they may facilitate elongation through packaged DNA. On the other hand, they may also facilitate the termination of transcription at specific sites.
Bibliography
de Haseth, Pieter L., Margaret Zupancic, and M. Thomas Record Jr. "RNA Polymerase-Promoter Interaction: The Comings and Goings of RNA Polymerase." Journal of Bacteriology 180 (1998): 3019-3025.
Lemon, Bryan, and Robert Tjian. "Orchestrated Response: A Symphony of Transcription Factors for Gene Control." Genes & Development 14 (2000): 2551-2569.
—David T. Auble and Pieter L. de Haseth
| Music Encyclopedia: Transcription |
Term for a written copy of a musical work involving some change. It may be a change of medium (thus meaning the same as ‘arrangement’); or it may mean that its notation has been changed (e.g. from tablature to staff) or its layout (e.g. from parts to score). The term may also include the writing down of music from a live or recorded performance, or its transference from sound to some graphic form by or mechanical means.
| Biology Q&A: What is transcription? |
Transcription is the synthesis of an mRNA
strand from a DNA template sequence, commonly known as a gene. The mRNA is then
used as a pattern for building a polypeptide.
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| Wikipedia: Transcription (genetics) |
This article is part of the series on: Gene expression |
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| Introduction to Genetics | |||
| General flow: DNA > RNA > Protein | |||
| special transfers (RNA > RNA, RNA > DNA, Protein > Protein) |
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| Genetic code | |||
| Transcription | |||
| Transcription (Transcription factors, RNA Polymerase,promoter) |
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| post-transcriptional modification (hnRNA,Splicing) |
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| Translation | |||
| Translation (Ribosome,tRNA) | |||
| post-translational modification (functional groups, peptides, structural changes) |
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| gene regulation | |||
| epigenetic regulation (Hox genes, Genomic imprinting) |
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| transcriptional regulation | |||
| post-transcriptional regulation (sequestration, alternative splicing,miRNA) |
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| post-translational regulation (reversible,irrevesible) |
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Transcription is the synthesis of RNA under the direction of DNA. RNA synthesis, or transcription, is the process of transcribing DNA nucleotide sequence information into RNA sequence information. Both nucleic acid sequences use complementary language, and the information is simply transcribed, or copied, from one molecule to the other. DNA sequence is enzymatically copied by RNA polymerase to produce a complementary nucleotide RNA strand, called messenger RNA (mRNA), because it carries a genetic message from the DNA to the protein-synthesizing machinery of the cell. One significant difference between RNA and DNA sequence is the presence of U, or uracil in RNA instead of the T, or thymine of DNA. In the case of protein-encoding DNA, transcription is the first step that usually leads to the expression of the genes, by the production of the mRNA intermediate, which is a faithful transcript of the gene's protein-building instruction. The stretch of DNA that is transcribed into an RNA molecule is called a transcription unit. A DNA transcription unit that is translated into protein contains sequences that direct and regulate protein synthesis in addition to coding the sequence that is translated into protein. The regulatory sequence that is before (upstream (-), towards the 5' DNA end) the coding sequence is called 5' untranslated region (5'UTR), and sequence found following (downstream (+), towards the 3' DNA end) the coding sequence is called 3' untranslated region (3'UTR). Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than DNA replication.[1]
As in DNA replication, RNA is synthesized in the 5' → 3' direction (from the point of view of the growing RNA transcript). Only one of the two DNA strands is transcribed. This strand is called the template strand, because it provides the template for ordering the sequence of nucleotides in an RNA transcript. The other strand is called the coding strand, because its sequence is the same as the newly created RNA transcript (except for uracil being substituted for thymine). The DNA template strand is read 3' → 5' by RNA polymerase and the new RNA strand is synthesized in the 5'→ 3' direction.
A polymerase binds to the 3' end of a gene (promoter) on the DNA template strand and travels toward the 5' end.
Transcription is divided into 5 stages: pre-initiation, initiation, promoter clearance, elongation and termination.
Contents |
Unlike DNA replication, transcription does not require primers for initiation. However RNA polymerase does require the presence of a core promoter sequence in the DNA, which it is able to bind to in the presence of various specific transcription factors.
Promoters are regions of DNA which promote transcription and are found around -10 to -35 bp upstream from the start site of transcription. Core promoters are sequences within the promoter which are essential for transcription initiation. The most common type of core promoter in eukaryotes is a TATA box, with a consensus sequence of TATA(A/T)A(A/T). The TATA box, as a core promoter, is the binding site for a transcription factor known as TATA binding protein (TBP), which is itself a subunit of another transcription factor, called Transcription Factor II D (TFIID). After TFIID binds to the TATA box via the TBP, five more transcription factors and RNA polymerase combine around the TATA box in a series of stages to form what is known as the preinitiation complex. One such transcription factor has helicase activity and so is involved in the separating of opposing strands of double-stranded DNA to provide access to a single-stranded DNA template.
However only a low, or basal, rate of transcription is driven by this preintiation complex. Other proteins known as activators and repressors, along with any associated coactivators or corepressors, may further enhance or inhibit transcription.
In bacteria, transcription begins with the binding of RNA polymerase to the promoter in DNA. The RNA polymerase is a core enzyme consisting of five subunits: 2 α subunits, 1 β subunit, 1 β' subunit, and 1 ω subunit. At the start of initiation, the core enzyme is associated with a sigma factor (number 70) that aids in finding the appropriate -35 and -10 basepairs downstream of promoter sequences.
Transcription initiation is far more complex in eukaryotes, the main difference being that eukaryotic polymerases do not directly recognize their core promoter sequences. In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription. Only after certain transcription factors are attached to the promoter does the RNA polymerase bind to it. The completed assembly of transcription factors and RNA polymerase bind to the promoter, called transcription initiation complex. Transcription in archaea is similar to transcription in eukaryotes.[3]
After the first bond is synthesized the RNA polymerase must clear the promoter. During this time there is a tendency to release the RNA transcript and produce truncated transcripts. This is called abortive initiation and is common for both eukaryotes[4] and prokaroytes[5]. Once the transcript reaches approximately 23 nucleotides it no longer slips and elongation can occur. This is an ATP dependent process.
Promoter clearance coincides with phosphorylation of serine 5 on the carboxy terminal domain of RNA Pol in prokaryotes, which is phosphorylated by TFIIH.
One strand of DNA, the template strand (or noncoding strand), is used as a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy. Although RNA polymerase traverses the template strand from 3' → 5', the coding (non-template) strand is usually used as the reference point, so transcription is said to go from 5' → 3'. This produces an RNA molecule from 5' → 3', an exact copy of the coding strand (except that thymines are replaced with uracils, and the nucleotides are composed of a ribose (5-carbon) sugar where DNA has deoxyribose (one less oxygen atom) in its sugar-phosphate backbone).
Unlike DNA replication, mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be produced from a single copy of a gene. This step also involves a proofreading mechanism that can replace incorrectly incorporated bases.
Prokaryotic elongation starts with the "abortive initiation cycle". During this cycle RNA Polymerase will synthesize mRNA fragments 2-12 nucleotides long. This continues to occur until the σ factor rearranges, which results in the transcription elongation complex (which gives a 35 bp moving footprint). The σ factor is released before 80 nucleotides of mRNA are synthesized.
In Eukaryotic transcription the polymerase can experience pauses. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure. Often the polymerase pauses to allow appropriate RNA editing factors to bind.
Bacteria use two different strategies for transcription termination: in Rho-independent transcription termination, RNA transcription stops when the newly synthesized RNA molecule forms a G-C rich hairpin loop, followed by a run of U's, which makes it detach from the DNA template. In the "Rho-dependent" type of termination, a protein factor called "Rho" destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex. Transcription termination in eukaryotes is less well understood. It involves cleavage of the new transcript, followed by template-independent addition of As at its new 3' end, in a process called polyadenylation.
Transcription can be measured and detected in a variety of ways:
Active transcription units are clustered in the nucleus, in discrete sites called ‘transcription factories’. Such sites could be visualized after allowing engaged polymerases to extend their transcripts in tagged precursors (Br-UTP or Br-U), and immuno-labeling the tagged nascent RNA. Transcription factories can also be localized using fluorescence in situ hybridization, or marked by antibodies directed against polymerases. There are ~10,000 factories in the nucleoplasm of a HeLa cell, among which are ~8,000 polymerase II factories and ~2,000 polymerase III factories. Each polymerase II factor contains ~8 polymerases. As most active transcription units are associated with only one polymerase, each factory will be associated with ~8 different transcription units. These units might be associated through promoters and/or enhancers, with loops forming a ‘cloud’ around the factor.
A molecule which allows the genetic material to be realized as a protein was first hypothesized by Jacob and Monod. RNA synthesis by RNA polymerase was established in vitro by several laboratories by 1965; however, the RNA synthesized by these enzymes had properties that suggested the existence of an additional factor needed to terminate transcription correctly.
In 1972, Walter Fiers became the first person to actually prove the existence of the terminating enzyme.
Roger D. Kornberg won the 2006 Nobel Prize in Chemistry "for his studies of the molecular basis of eukaryotic transcription".[6]
Some viruses (such as HIV, the cause of AIDS), have the ability to transcribe RNA into DNA. HIV has an RNA genome that is duplicated into DNA. The resulting DNA can be merged with the DNA genome of the host cell. The main enzyme responsible for synthesis of DNA from an RNA template is called reverse transcriptase. In the case of HIV, reverse transcriptase is responsible for synthesizing a complementary DNA strand (cDNA) to the viral RNA genome. An associated enzyme, ribonuclease H, digests the RNA strand, and reverse transcriptase synthesises a complementary strand of DNA to form a double helix DNA structure. This cDNA is integrated into the host cell's genome via another enzyme (integrase) causing the host cell to generate viral proteins which reassemble into new viral particles. Subsequently, the host cell undergoes programmed cell death (apoptosis).
Some eukaryotic cells contain an enzyme with reverse transcription activity called telomerase. Telomerase is a reverse transcriptase that lengthens the ends of linear chromosomes. Telomerase carries an RNA template from which it synthesizes DNA repeating sequence, or "junk" DNA. This repeated sequence of "junk" DNA is important because every time a linear chromosome is duplicated, it is shortened in length. With "junk" DNA at the ends of chromosomes, the shortening eliminates some repeated, or junk sequence, rather than the protein-encoding DNA sequence that is further away from the chromosome ends. Telomerase is often activated in cancer cells to enable cancer cells to duplicate their genomes without losing important protein-coding DNA sequence. Activation of telomerase could be part of the process that allows cancer cells to become technically immortal.
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| Translations: Transcription |
Dansk (Danish)
n. - afskrivning, afskrift, omskrivning
Nederlands (Dutch)
overzetting, bewerking, transcriptie
Français (French)
n. - (gén, Phon) transcription
Deutsch (German)
n. - Abschreiben, Abschrift, Übertragung, Tonaufnahme, Transkription, Umschrift
Ελληνική (Greek)
n. - μεταγραφή, αντίγραφο, αντιγραφή
Italiano (Italian)
versione, trascrizione
Português (Portuguese)
n. - cópia (f), transcrição (f), arranjo (m)
Русский (Russian)
копирование, расшифровка
Español (Spanish)
n. - transcripción, grabación
Svenska (Swedish)
n. - avskrift, kopia, avskrivning, utskrivning, återgivning, transkription, transkribering
中文（简体）(Chinese (Simplified))
抄写, 抄本
中文（繁體）(Chinese (Traditional))
n. - 抄寫, 抄本
日本語 (Japanese)
n. - 書き写すこと, 書き写したもの, 録音, 編曲, 複写, 筆写
العربيه (Arabic)
(الاسم) لحن مكيف بحيث يلائم أله لم تجعل له في ألأصل, نسخه
עברית (Hebrew)
n. - תעתיק, הקלטה, תעתוק, תסדיר, השמעת הקלטה, תסדיר - העברת יצירה מוסיקלית לכלים אחרים
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 | Archaea |
| Gene Expression: Overviewof Control |
| Nucleotide |
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