TRANSCRIPTION

Transcription is the transfer of information from a double stranded DNA molecule to a single RNA molecule. Like DNA, RNA is a linear polymer made up of four types of nucleotides linked together by phosphodiester bonds. It differs from DNA in that (1) its sugar units are riboses (OH attached to the 2'C) rather than deoxyriboses, (2) uracil is substituted for the base thymine (uracil lacks the methyl group which thymine has), (3) it is single stranded except in some viruses and (4) it does not form a double helix although it can fold back onto itself to form double helical regions.

Most of the genes which are transcribed into RNA specify the amino acid sequence of proteins. The RNA which is transcribed from such genes is referred to as messenger RNA (mRNA). However, the final product after transcription of many genes is not protein but rather the RNA itself. Like proteins, these RNAs serve as enzymatic and structural components for a wide variety of processes in the cell. 3 major classes of such RNAs are small nuclear RNA (snRNA) which direct the splicing of pre-mRNA to form mRNA, ribosomal RNA (rRNA) which form the core of ribosomes and transfer RNA (tRNA) molecules which serve in translation of the mRNA.

Transcription starts with the opening and unwinding of a small portion of the DNA double helix to expose the bases on each DNA strand. Transcription runs in the 5' to 3' direction so that the RNA produced by transcription starts from the 3' end. In contrast to DNA replication, the RNA single strand product does not remain hydrogen bonded to the DNA template but is rather displaced just behind the region where the ribonucleotides are being added. This release means that many RNA copies can be made from the same gene.

The enzymes which transcribe DNA are called RNA polymerases. They differ from DNA polymerases in that 1) they catalyze the linkage of ribonucleotides, not deoxyribonucleotides, 2) they can start an RNA chain without a primer and 3) they lack the high fidelity or accuracy of DNA polymerases (there is an error rate of about 1 of 10⁴ nucleotides copies into RNA in comparison of 1 of 10⁷ by DNA polymerase).

Eucaryotics have 3 types of RNA polymerases which transcribe different types of genes. RNA polymerase I transcribes the 5.8S, 18S and 28S rRNA genes. RNA polymerase II transcribes all the protein coding genes along with some snoRNA and snRNA genes. RNA polymerase III transcribes tRNA genes, 5S rRNA genes and some other snRNA genes.

RNA polymerase II requires the help of a large set of proteins called general transcription factors which must assemble at the promoter with the polymerase before transcription can begin. The proteins are called "general" because they must assemble on all promoters used by RNA polymerase II. The assembly starts with the binding of a short double helical DNA sequence composed mainly of T and A nucleotides about 25 nucleotides upstream from the transcription start site, referred to as the TATA box by a subunit, TBP (for TATA box binding protein), of one of the general transcription factors, TFIID (for transcription factor II). After RNA polymerase II has been guided onto the promoter DNA to form a transcription initiation complex, it gains access to the template strand by another general transcription factor, TFIIH which contains a DNA helicase. Some eukaryotes also use a GC box rather than a TATA box which serve as promoter sequences for the transcription factor SP1. Compare Bacteria

Transcription in the eukaryotic cell is very complex and requires more proteins than it does on purified DNA. Even other regulatory proteins called enhancers or transcriptional activators bind to specific sequences in DNA sometimes several thousand nucleotide pairs away from the transcription start site to help RNA polymerase and the general factors assemble at the promoter. The enhancers which can be located anywhere with respect to the gene (5' of the promoter, 3' of the gene or even in an intron of the gene). In addition, enhancers attract ATP-dependent chromatin remodeling complexes and histone acetylases which allow greater accessibility to the DNA present in chromatin and thereby facilitate the assembly of the transcription ininitiation machinery on DNA.

These proteins bind to specific nucleotide sequences within promoters and enhancers and act either to enhance or suppress their activity. Such proteins have been identified by a variety of techniques like DNA footprinting.

Once transcription has started, RNA polymerase also require elongation factors which are proteins that help polymerases move along the DNA template. In order to deal with DNA supercoiling (1 large DNA supercoil will form to compensate for each 10 nucleotide pairs that are unwound, DNA topisomerase enzymes are necessary to remove this tension. Click Here to see what happens to a mRNA after transcription

Ribosomal RNA genes exist in multiple copies in order to produce necessary quantities of rRNA. This is important because, unlike mRNA, rRNAs are not translated. The final produce from transcription in the case of rRNA is the rRNA itself and thus amplification can not be achieved through multiple rounds of amplification. There are 4 types of eukaryotic rRNA. 3 of the 4 types (18S, 5.8S, and 28S) which are transcribed by RNA polymerase I, are made by chemically modifying and cleaving a single large precursor rRNA and the 4^th (5S) is transcribed by a different polymerase RNA polymerase III. The specific positions at which chemical modifications are made as well as the cleavage of the precursor rRNA into the mature rRNA are made by a large class of RNAs called small nucleolar RNAs (snoRNAs) so named because they perform their functions in a subcompartment of the nucleus called the nucleolus which is a large aggregate of macromolecules including the rRNA genes, snoRNPs and other proteins.