Transcription copies genetic information encoded in DNA into a complementary RNA molecule, serving as the first step in gene expression. This mechanism is central to the flow of genetic information, known as the Central Dogma, which dictates that information moves from DNA to RNA to protein. The resulting RNA molecule, particularly messenger RNA (mRNA), carries the instructions needed to build specific proteins. Accurate transcription ensures the correct genetic message is prepared for subsequent protein synthesis.
The Initial Setup: Initiation
Transcription begins when the RNA polymerase enzyme recognizes a specific DNA sequence called the promoter. This promoter acts as a binding site, positioning the polymerase complex upstream of the gene’s coding sequence. In complex organisms, recognition is aided by transcription factors, which are proteins that bind to the promoter and recruit the RNA polymerase. Once positioned, the RNA polymerase forms the open-complex configuration necessary for synthesis. The enzyme locally unwinds the double-stranded DNA helix, separating about 12 to 14 base pairs to create the transcription bubble. Only one DNA strand, the template strand, is read by the polymerase to guide RNA synthesis, allowing the enzyme to position the first ribonucleotide triphosphate at the start site.
Building the Strand: Elongation
Following initiation, RNA polymerase shifts into the elongation phase, moving continuously along the DNA template strand. The enzyme travels in the 3′ to 5′ direction along the template, synthesizing the new RNA strand in the complementary 5′ to 3′ direction. This occurs by adding ribonucleotides one by one to the growing RNA chain’s 3′-hydroxyl group, forming phosphodiester bonds. The enzyme follows base pairing rules, matching guanine (G) with cytosine (C) and adenine (A) on the DNA template with uracil (U) in the forming RNA. As the polymerase advances, the growing RNA molecule peels away from the DNA template, and the DNA helix immediately re-forms behind the moving enzyme.
Stopping the Process: Termination
Elongation continues until RNA polymerase encounters a specific nucleotide sequence known as the terminator sequence. Two main mechanisms exist to release the newly formed transcript. Rho-independent termination occurs when the transcribed RNA forms an internal hairpin structure followed by uracil bases, causing the polymerase to stall and the RNA-DNA hybrid to dissociate. Rho-dependent termination utilizes the Rho protein factor, which binds to the nascent RNA transcript and moves toward the stalled polymerase. Rho uses its helicase activity to physically separate the RNA from the DNA template, releasing the complete RNA molecule. In complex organisms, termination is often coupled with 3′ end processing, where cleavage and polyadenylation signals lead to RNA release.
Refining the Message: Post-Transcriptional Processing
The initial RNA molecule produced in complex cells, called pre-mRNA, undergoes immediate modification before translation.
5′ Capping
One modification is the addition of a 7-methylguanosine cap to the 5′ end via a unique 5′-to-5′ triphosphate linkage. This cap protects the transcript from degradation and is recognized by the ribosome to initiate protein synthesis.
Poly-A Tailing
A sequence of 100 to 250 adenine nucleotides, known as the Poly-A tail, is added to the 3′ end. This addition is signaled by the AAUAAA sequence in the pre-mRNA and is catalyzed by Poly(A) Polymerase. The Poly-A tail contributes to the stability and lifespan of the mRNA and aids in its export from the nucleus.
Splicing
The most extensive modification is splicing, the removal of non-coding segments called introns and the joining of protein-coding segments, or exons. Splicing is carried out by the spliceosome, which precisely recognizes the boundaries between introns and exons. By excising the intervening introns, the spliceosome creates a continuous coding sequence, resulting in the mature mRNA ready for translation.
Contextualizing Complexity: Prokaryotes Versus Eukaryotes
Although the fundamental chemistry of transcription is conserved, the overall process differs between prokaryotes and eukaryotes. A primary distinction is cellular location: prokaryotic transcription occurs in the cytoplasm, while eukaryotic transcription is sequestered within the nucleus. This separation in eukaryotes necessitates the extensive post-transcriptional processing of pre-mRNA before transport to the cytoplasm for translation.
Prokaryotes utilize only a single type of RNA polymerase to transcribe all RNA classes. In contrast, eukaryotes employ three distinct RNA polymerases, with RNA Polymerase II dedicated to transcribing protein-coding genes. Furthermore, the lack of a nucleus in prokaryotes allows transcription and translation to occur simultaneously, a process known as coupled transcription-translation. Eukaryotic gene expression is temporally and spatially separated, requiring transcription to complete in the nucleus before translation begins in the cytoplasm.