Transcription

Transcription

Alternate meanings: transcription (linguistics) - conversion of spoken words into written language

Transcription is the process of copying DNA to mRNA by an enzyme called RNA polymerase (RNAP). Transcription is the first step of protein biosynthesis.

Table of contents
1 Bacterial transcription

1.1 Initiation
1.2 Elongation
1.3 Termination
2 Eukaryotic transcription

2.1 Initiation
2.2 Elongation
2.3 Termination

Bacterial transcription

A (simple) model for a bacterial gene to be transcribed looks like this :

   upstream        ~17 bp       The gene to transcribe     downstream
 5'----------|-35|---------|-10|----------------------|T|------------3'
 3'----------|-35|---------|-10|----------------------|T|------------5'
                                |
                                |--------------------->
                                         mRNA

where the region between -35 and -10 base pairs is called promoter, and |T| stands for terminator. The DNA between promoter and terminator is copied to mRNA, which is then translated into protein.

Promoters can differ in strength, that is, how attractive they are for RNAP. The more similar they are to a consensus sequence[?], the stronger they are. The "ideal" promoter in E. coli looks like this:

 5'----TTGACA---|17 bp|----TATAAT---|7bp|---|[[purine]]s|----3'

Initiation

The RNA polymerase holoenzyme consists of a core, made of four subunits (2&alpha, &beta, &beta'), &omega factor and the &sigma factor[?]. The followings steps occur upon initiation:

The RNAP recognizes the promoter region of the gene and binds to the DNA at that specific location. At this stage, the DNA is still double-stranded and called closed complex.
The DNA is unwound and becomes single-stranded at the initiation site (the -10 promoter region). This is called open complex.
The DNA is melted (the strands are locally separated), the &sigma-factor leaves the holoenzyme, and the transcription process begins. This is the elongation phase.

Elongation

The RNAP runs along the DNA, synthesizing mRNA in the process. In bacteria, the nascending mRNA is processed right away by ribosomes.

Termination

The elongation stops if:

The terminator is reached. The terminator is usually a palindromic DNA sequence that forms a hairpin.
A &rho factor[?] (a protein) binds and runs along the mRNA towards the RNAP. When &rho-factor reaches the RNAP, it causes RNAP to dissociate from the DNA, terminating transcription.
The RNAP comes across a region with repetitious base pairs (for example, TTTTTT). This will terminate transcription.

Eukaryotic transcription

Gene expression in eukaryotes is largely controlled by transcription via transcription factors. As eukaryotes are much more complex than prokaryotes, and have their genetic material stored in the nucleus, the transcription mechanisms are more complicated here. For example, eukaryotes have three RNA polymerases, in contrast to prokaryotes, which only have one.

RNA Polymerase I is located in the nucleolus and transcribes only rRNAs.
RNA Polymerase II is the "standard" RNAP.
RNA Polymerase III transcribes tRNAs and other small RNAs.

Also, eukrayotic RNAPs need specific accessory proteins to become active. The C-terminus of all RNAPs is highly conserved and contains the actual transctiptional mechanism.

Initiation

The core promoter of eukaryotic genes stretches from position -45 to 0. Additionally, there can be an upstream control element present at the -180 to -107 region, which can amplify the RNAP binding by a factor of up to 100. This UCE usually contains a TATA box[?], a highly conserved DNA sequence that reads

T A T A ^T/_A A

A similar sequence, thus not that highly conserved, is found in the INR element (initiator element, part of the complex core promoter).

Elongation

Termination

A major difference between prokaryotic and eukaryotic transcription is that the latter have splicing of the primary transcript, modifying the mRNA created during transcription.