Everything about Transcription Genetics totally explained
Transcription is the synthesis of RNA under the direction of DNA. Both nucleic acid sequences use the same 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's transcribed into an RNA molecule is called a
transcription unit. A transcription unit that's translated into protein contains sequences that direct and regulate protein synthesis in addition to coding the sequence that's translated into protein. The regulatory sequence that's before, or 5', of the coding sequence is called 5' untranslated region (
5'UTR), and sequence found following, or 3', of the coding sequence is called 3' untranslated region (
3'UTR).
Transcription has some proofreading mechanisms, but they're fewer and less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than
DNA replication.
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
thymine being substituted for
uracil). The DNA template strand is read 3' → 5' by RNA polymerase and the new RNA strand is synthesized in the 5'→ 3' direction. RNA 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.
Prokaryotic vs. eukaryotic transcription
Pre-Initiation
Unlike
DNA replication, transcription doesn't need a
primer to start. RNA polymerase simply binds to the DNA and, along with other cofactors, unwinds the DNA to create an initiation bubble so that the RNA polymerase has access to the single-stranded DNA template. However, RNA Polymerase does require a promoter like sequence.
Proximal (core) Promoters:
TATA promoters are found around -30 bp to the start site of transcription. Not all genes have TATA box promoters and there exists TATA-less promoters as well. The TATA promoter consensus sequence is TATA(A/T)A(A/T).
The following are the steps involved in TATA Promoter Complex formation:
1.General transcription factors bind
2. TFIID, TFIIA, TFIIB, TFIIF (w/RNA Polymerase), TFIIH/E
The complex is called the closed pre-initiation complex and is closed. Once the structure is opened by TFIIH initiation starts.
Initiation
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 and
archaea, the main difference being that eukaryotic polymerases don't recognize directly 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.
Once the complex has been opened, Initiation starts and the first phosphodiester bond is formed. This is the end of Initiation.
Promoter Clearance
After the first bond is synthesized the RNA polymerase must clear the promoter. During this time there's a tendency to release the RNA transcript and produce truncated transcripts. This is called abortive initiation and is common for both Eukaryotes and Prokaroytes. Once the transcript reaches approximately 23 nucleotides it no longer slips and Elongation can occur. This is an ATP dependent process.
Promoter clearance also coincides with Phosphorylation of serine 5 on the carboxy terminal domain which is phosphorylated by TFIIH.
Elongation
One strand of DNA, the
template strand (or non-coding 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.
Termination
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.
Measuring and detecting transcription
Transcription can be measured and detected in a variety of ways:
Nuclear Run-on assay, measures the relative abundnace of newly formed transcripts
RNase protection assay and ChIP-Chip of RNAP, detect active transcription sites
RT-PCR, measures the absolute abundance of total or nuclear RNA levels, which may however differ from transcription rates
DNA microarrays measures the relative abundance of the global total or nuclear RNA levels, which may however differ from transcription rates
In situ hybridization, detects the presence of a transcript
Transcription factories
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 factory 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 factory.
History
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".
Reverse transcription
Some viruses (such as HIV, the cause of AIDS), have the ability to transcribe RNA into DNA. HIV has an RNA genome that's 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's 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's 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 can be part of the process that allows cancer cells to become immortal.
Further Information
Get more info on 'Transcription Genetics'.
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