Transcription


Transcription is the process of producing an RNA transcript that is complementary to a DNA template. It can be thought of as DNA-dependent RNA synthesis.

In the case of protein biosynthesis, the type of RNA synthesised is messenger RNA (mRNA). However, DNA may also be transcribed into transfer RNA (tRNA) or ribosomal RNA (rRNA), among others. In eukaryotes, transcription occurs predominantly in the cell nucleus, where it is compartmentalised from protein translation in the cytoplasm; in prokaryotes it occurs freely in the cytoplasm and is coupled to protein translation. Translation also occurs in some organelles where proteins are synthesised, such as chloroplasts and mitochondria.

Transcription occurs in three major steps: initiation, elongation and termination, and these stages differ between prokaryotes and eukaryotes.

Initiation:

In bacteria, initiation simply involves the RNA polymerase complex binding correctly to the promoter sequence of the gene, with some assistance from bound proteins called sigma factors. This is because DNA in prokaryotes is naked and thus locating the promoter is comparatively easy. In eukaryotes, however, RNA polymerase instead binds to a complex of transcription factors called the preinitiation complex, which in turn is bound to the promoter sequence. The preinitiation complex unwinds the DNA and places the template DNA strand in the active site of RNA polymerase (the enzyme which goes on to catalyse transcription).

Elongation:

Elongation is then the writing of the RNA transcript, according to the complementary sequence of the DNA template strand. Elongation is essentially the same in both prokaryotes and eukaryotes: the RNA is synthesised in the 5' to 3' direction, complementary to the template strand of DNA. The template strand is also called the non-coding or antisense strand because it is complementary, but not identical, to the nascent RNA strand. The template DNA strand has polarity in the 3' to 5' direction. The opposite DNA strand is called the non-template, coding or sense strand. It is the coding/sense strand because it is identical to the sequence on mRNA (ignoring thymine/uracil differences), and it is non-template because RNA polymerase does not use this strand to synthesise mRNA. The non-template strand thus has polarity in the 5' to 3' direction. In prokaryotes, all types of RNA are transcribed by the same RNA polymerase; in eukaryotes, different RNA polymerases are responsible for different types of RNA transcription.

Termination:

In bacteria, transcriptional termination may be rho-independent or rho-dependent. In rho-independent termination, a palindromic G/C-rich hairpin loop forms in mRNA, causing RNA polymerase to stall. This is followed by a poly-U tract in the mRNA which destabilises the RNA-DNA duplex (a phenomenon known as attenuation). In rho-dependent termination, the G/C-hairpin loop is still present, but there is no poly-U tract. Instead there is a poly-C tract preceding the hairpin loop by about 70 nucleotides; an ATP-dependent helicase enzyme called rho binds to the poly-C tract (on the mRNA) and thereby destabilises the RNA-DNA duplex while RNA polymerase is stalled at the hairpin loop.

In eukaryotes, the mechanism of termination is less well understood, except that the newly synthesised RNA transcript is cleaved and then has a run of adenine residues added to it; a structure known as a poly-adenylated (poly A) tail (see: post-transcriptional modification of RNA transcripts).

Transcription factors:

In eukaryotes, the rate of transcription is modified by proteins called transcription factors, which bind to regions on DNA to either enhance or decrease the affinity of RNA polymerases for the promoter sequence of the gene. Transcription factors themselves are induced or repressed by micro-environmental cues, such as the action of nuclear hormones.