Transcription is the synthesis of RNA from a DNA template. The product is an RNA copy of one strand of DNA.
Transcription elongation. RNA polymerase unwinds a short stretch of DNA, reads the template strand 3' to 5', and synthesizes RNA 5' to 3' using ribonucleotides. Credit: Wikimedia Commons, CC BY-SA
Template vs. Coding Strand
Only one of the two DNA strands is copied at each locus:
Template strand (antisense): the strand that RNA polymerase reads. The RNA is complementary to this strand (3’ to 5’ read, 5’ to 3’ written).
Coding strand (sense): the other strand. The RNA has the same sequence as the coding strand (except U replaces T).
The Three Stages
Initiation
RNA polymerase recognizes a promoter upstream of the gene. In bacteria, the sigma factor helps the polymerase find the promoter (-10 and -35 consensus boxes). In eukaryotes, general transcription factors (TFIID, TFIIB, etc.) assemble at the promoter (TATA box) and recruit RNA Pol II. The polymerase unwinds about 14 bp of DNA to expose the template.
Elongation
The polymerase reads the template 3’ to 5’ and synthesizes RNA 5’ to 3’. Each new ribonucleotide is added to the 3’-OH of the growing chain. The polymerase moves along the DNA, maintaining a short “transcription bubble” of unwound DNA. About 10-20 nucleotides are added per second in eukaryotes.
Termination
In bacteria: rho-independent termination uses a GC-rich hairpin followed by a stretch of U’s that destabilizes the RNA-DNA hybrid. Rho-dependent termination uses the rho protein to pull the RNA off the polymerase.
In eukaryotes: termination of Pol II is less clean - the polymerase transcribes past the polyadenylation signal (AAUAAA), and a cleavage factor cuts the RNA. The polymerase eventually falls off.
Does RNA polymerase need a primer to begin synthesis, and what direction does it read/write?
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No primer needed. RNA polymerase can start RNA synthesis from scratch at a promoter. It reads the template DNA 3' to 5' and synthesizes RNA 5' to 3'. This is unlike DNA polymerase, which requires a primer.
Which RNA polymerase in eukaryotes transcribes mRNA?
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RNA polymerase II. Pol I handles rRNA (in the nucleolus), and Pol III handles tRNA and 5S rRNA. Bacteria have just one RNA polymerase that handles all RNA types.
If the coding strand of a gene reads 5'-ATGGCATTC-3', what is the mRNA sequence?
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5'-AUGGCAUUC-3'. The mRNA has the same sequence as the coding strand but with U in place of T. The template strand (3'-TACCGTAAG-5') is what RNA polymerase actually reads; the resulting RNA is complementary to the template and matches the coding strand.
