Genes can be switched on by DNA sitting far away
Copying a gene from DNA into RNA is the first step in using it, but what decides when that happens is often not next door. Stretches called enhancers, sometimes hundreds of thousands of letters away, loop around to touch their target gene and can boost its activity up to a hundredfold. One study of brain neurons counted 24,937 such loops.
Transcription is the copying of a DNA segment into RNA. Some transcripts become messenger RNA, the templates for proteins; others are non-coding RNAs with jobs of their own. An enzyme called RNA polymerase reads the DNA and assembles a complementary strand, the primary transcript, substituting uracil wherever DNA would have thymine. The process runs through initiation, promoter escape, elongation and termination.
Only one strand serves as the template. The polymerase reads it from the 3' end toward the 5' end while building RNA in the opposite direction, because new letters can be added only to the chain's 3' end. As a result the RNA matches the other strand, called the coding strand, which is the one written down by convention. Working from a single strand spares transcription the short Okazaki fragments and RNA primers that DNA replication requires. It also has fewer and weaker proofreading checks, so it copies less faithfully than replication does. A protein-coding unit includes untranslated regulatory stretches on either side of the coding sequence.
In mammals, core promoters near each gene, together with general transcription factors, can start the process but only at a low baseline. Distant control elements, including enhancers, silencers and insulators, do much of the steering, with enhancers taking the lead in determining which genes each cell type uses. The loop that brings an enhancer to its promoter is held by a pair of connector proteins, such as CTCF or YY1. Of roughly 1,600 transcription factors in a human cell, a small combination bound to an enhancer sets the level of output, and a complex of about 26 proteins called Mediator relays their signals to RNA polymerase II waiting at the promoter.
Viruses use the word too. Many RNA viruses carry negative-sense genomes that must first be copied into positive-sense messenger RNA by a viral RNA-dependent RNA polymerase before viral proteins can be made.
Source: Transcription (biology)
