Transcription

Initiation.

The first phase of RNA synthesis is initiation (Figure 1B). Initiation starts when the first phosphodiester bond is formed. At precise locations, determined by the promotor DNA sequence, the first and second RNA bases bind to the complex, and RNA polymerase catalyzes the formation of a covalent bond between them.

When the growing RNA chain reaches a length of about ten nucleotides, the complex loses contact with the promoter and starts moving along the DNA. This is referred to as promoter "clearance" or "escape."

Only a fraction of initiation events lead to promoter clearance. In many instances, an "abortive" RNA molecule, shorter than ten nucleotides, is released from the RNA polymerase, and RNA synthesis begins all over again. Such an abortive molecule is shown in the figure as a thick line.

Once the growing RNA chain has reached the critical length of about ten nucleotides, the initiation stage is considered to have ended, and elongation begins. In eukaryotes, the transition from initiation to elongation can be triggered by enzymes called kinases, which attach phosphate groups to RNA polymerase, facilitating promoter clearance.

Elongation.

Genes range in length from about 80 base pairs of DNA, as is the case for those transcribed into transfer RNA, to more than 1 million base pairs, as is the case for those encoding very long proteins. An RNA polymerase molecule that has disengaged from DNA during elongation would be unable to finish synthesizing the RNA molecule. Thus the enzyme has to traverse even the longest genes (Figure 1C), without falling off.

Along the way, there are DNA sequences that the RNA polymerase traverses considerably more slowly than at its usual rate of about 50 nucleotides per second. At regions called pause sites, it may take longer than 1 second for a single nucleotide to be added to the growing polymer.

In eukaryotes, many genes contain blocks of DNA called introns, which disrupt the coding information of the gene. Introns are removed from the newly made RNA by a process called splicing. It is thought that the proteins which carry out the splicing are carried by the RNA polymerase as it is transcribing the gene, allowing the processing of the RNA to occur at the same time as the RNA molecule is synthesized.

Termination.

When the RNA polymerase reaches a specific DNA sequence known as a terminator, it slows down and the transcription complex dissociates from the DNA, as shown in Figure 1D. The released RNA polymerase is then free to participate in a new initiation event.

At some terminators, primarily in bacteria, the RNA polymerase is able to respond to the release signal without being helped by any other proteins. Such sites are called intrinsic terminators. At other sites, termination is accomplished only with the aid of additional proteins. These proteins, called termination factors, are also instrumental in causing RNA to be released from the transcribing complex.

"Factor-dependent" terminators have been found in organisms from each of the three domains of life, the eukaryotes, bacteria, and Archaea. In eukaryotes, but usually not in bacteria, transcription of most genes proceeds past the end of the gene, as shown in Figure 1D.

The initial RNA molecules are often referred to as "primary" transcripts. In many instances, the primary transcripts must be processed to yield functional, or "mature," RNA. The processing can involve shortening them by removing their terminal or internal regions, or modifying specific nucleotides in other ways.