Transcription

Transcription is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. In other words, it is the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, transcription is the beginning of the process that ultimately leads to the translation of the genetic code (via the mRNA intermediate) into a functional peptide or protein. The stretch of DNA that is transcribed into an RNA molecule is called a transcription unit. 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.


As in DNA replication, transcription proceeds in the 5' → 3' direction (i.e. the old polymer is read in the 3' → 5' direction and the new, complementary fragments are generated in the 5' → 3' direction). Transcription is divided into 3 stages: initiation, elongation and termination.




Initiation in prokaryotes
Transcription of RNA differs from DNA synthesis in that only one strand of DNA, the template strand, is used to make mRNA. Because transcription only proceeds in the 5' → 3' direction, it follows that the DNA template strand that is used must be oriented in 3' → 5' (complementary) direction. The strand that is not used as a template strand is called the non-template strand. Thus, DNA exists as a double strand, whereas RNA only exists as a single strand. The difference is due to the fact that DNA replication is semi-conservative, while transcription results in de novo production of a single strand of RNA.


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. Unlike DNA replication, transcription does not need a primer to start. The DNA unwinds and produces a small open complex and synthesis begins on only the template strand.

Elongation
Unlike DNA replication, mRNA transcription can involve multiple RNA polymerases, so many mRNA molecules can be produced from a single copy of the gene. This step also involves a proofreading mechanism that can replace an incorrectly added RNA molecule.

Termination
Upon seeing a termination codon within the DNA template, RNA transcription can stop by forming a secondary hairpin loop that lets it come off the DNA template. Alternatively, another protein designated "Rho" can pull the mRNA away from polymerase

Prokaryotic vs. eukaryotic transcription

Prokaryotic transcription occurs in the cytoplasm alongside translation.
Eukaryotic transcription is primarily localized to the nucleus, where it is separated from the cytoplasm (where translation occurs) by the nuclear membrane.

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.

Transcription initiation complex


Transcription factors mediate the binding of RNA polymerase and the initiation of transcription. The RNA polymerase only binds to the promoter after certain transcription factors are assembled. The completed assembly of transcription factors and RNA polymerase bound to the promoter is called the transcription initiation complex.

Reverse transcription

Some viruses (such as HIV, the cause of AIDS), have the ability to transcribe RNA into DNA in order to see a cell's genome. The main enzyme responsible for this type of transcription is called reverse transcriptase. In the case of HIV, reverse transcriptase is responsible for synthesising 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).

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