Transcription

Transcription is the process by which one of the two strands of a DNA double helix, called the template strand, is used to direct the synthesis of a complementary RNA molecule, carried out by a family of enzymes called RNA polymerases. In eukaryotes, three distinct RNA polymerases divide the transcriptional workload: RNA Polymerase I transcribes the large ribosomal RNAs, apart from the small 5S rRNA; RNA Polymerase II transcribes the precursors of messenger RNA, called heterogeneous nuclear RNA (hnRNA); and RNA Polymerase III transcribes transfer RNAs, the 5S ribosomal RNA, and the small nuclear RNAs (snRNAs). Because in eukaryotes each mature mRNA molecule carries the coding information for only a single protein, eukaryotic mRNAs are described as monocistronic, in contrast to the multi-gene, polycistronic mRNAs typical of bacteria. Transcription itself always proceeds in the 5' to 3' direction, with RNA polymerase adding each new ribonucleotide to the growing 3' end of the RNA chain, while reading the template strand, which itself runs in the 3' to 5' direction, from a starting point defined by the promoter. A eukaryotic structural gene's promoter carries three essential features: regulatory elements, which can be enhancer sequences that increase the rate of transcription or silencer sequences that decrease it, and to which specific proteins called transcription factors bind (RNA polymerase itself cannot bind DNA directly and needs a transcription factor to guide it to the correct site); a TATA box (also called the Hogness box), a short conserved sequence found roughly 25 base pairs upstream of the actual start site; and the transcription start site itself, where synthesis of the RNA transcript actually begins. The DNA strand physically used as the template, which runs 3' to 5' relative to the RNA being made, is called the template strand, non-coding strand, or antisense strand, while the other DNA strand, which is not transcribed but has the same sequence as the resulting RNA (with U in place of T), is called the coding strand, non-template strand, or sense strand. Transcription ends when RNA polymerase reaches a specific termination sequence in the DNA that signals it to stop adding nucleotides. The raw product of this whole process, before any processing, is called the primary transcript, or pre-mRNA/hnRNA, and it still contains the introns that must be removed before the mRNA is mature; it is processed by capping (adding a modified guanosine nucleotide, methylguanosine triphosphate, to its 5' end, which protects the RNA from degradation and helps the spliceosome remove the very first intron), internal methylation of selected internal nucleotides at sites found across both coding and non-coding regions, splicing (removal of introns and joining of exons, covered in the next section), and tailing/polyadenylation (cleavage of the 3' end followed by addi …