Within a single gene, only one of the two DNA strands, the template strand, is generally transcribed into RNA.
The transcription unit A transcription unit is a stretch of DNA that codes for an RNA molecule and the sequences necessary for its transcription. In eukaryotes, as discussed in Chapter 14, alternative RNA molecules can be produced from each transcription unit. How does the complex of enzymes and proteins that performs transcription—the transcription apparatus—recognize a transcription unit? How does it know which DNA strand to read, and where to start and stop? This information is encoded by the DNA sequence.
Included within a transcription unit are three critical regions: a promoter, an RNA coding sequence, and a terminator (IFigure 13.7). The promoter is a DNA sequence that the transcription apparatus recognizes and binds. It indicates which of the two DNA strands is to be read as the template and the direction of transcription. The promoter also determines the transcription start site, the first nucleotide that will be transcribed into RNA. In most transcription units, the promoter is located next to the transcription start site but is not, itself, transcribed.
The second critical region of the transcription unit is the RNA-coding region, a sequence of DNA nucleotides that is copied into an RNA molecule. A third component of the transcription unit is the terminator, a sequence of nucleotides that signals where transcription is to end. Terminators are usually part of the coding sequence; that is, transcription stops only after the terminator has been copied into RNA.
Molecular biologists often use the terms upstream and downstream to refer to the direction of transcription and the location of nucleotide sequences surrounding the RNA coding sequence. The transcription apparatus is said to move downstream during transcription: it binds to the promoter (which is usually upstream of the start site) and moves toward the terminator (which is downstream of the start site).
When DNA sequences are written out, often the sequence of only one of the two strands is listed. Molecular biologists typically write the sequence of the nontemplate strand, because it will be the same as the sequence of the RNA transcribed from the template (with the exception that U in RNA replaces T in DNA). By convention, the sequence on the nontemplate strand is written with the 5' end on the left and the 3' end on the right. The first nucleotide transcribed (the transcription start site) is numbered +1; nucleotides downstream of the start site are assigned positive numbers, and nucleotides upstream of the start site are assigned negative numbers. So, nucleotide + 34 would be 34 nucleotides downstream of the start site, whereas nucleotide —75 would be 75 nucleotides upstream of the start site.
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