Transcription Units and the Structure of Genes

Transcription copies a selected region

Transcription is the synthesis of RNA using a DNA template. Unlike genome replication, which duplicates DNA across the genome, a transcription event uses a defined segment and one selected template strand of that segment. RNA polymerase moves along DNA, using ribonucleoside triphosphates to build RNA in the 5′→3′ direction. The RNA product is complementary to the DNA template and therefore matches the coding strand except that RNA has U in place of T. Which of a chromosome's strands is called the template depends on the particular gene's direction; there is no universal template strand for an entire chromosome.

Promoter, structural gene and terminator

A transcription unit includes a promoter at or near the start, a transcribed region containing the gene and a sequence that contributes to termination. Promoters help recruit and position transcription machinery and establish which direction polymerase travels. A terminator contributes to ending RNA synthesis and releasing the transcript in appropriate systems. Regulatory sites can occur elsewhere in nearby DNA and influence transcription. Upstream and downstream are defined relative to the selected gene's transcriptional orientation, not relative to a fixed left and right on a page.

Getting template and coding strands right

Consider a segment whose coding strand is 5′-ATGCCAT-3′ and whose template strand is 3′-TACGGTA-5′. RNA polymerase reads the latter from its 3′ end towards 5′ and produces 5′-AUGCCAU-3′. If one first writes the complementary DNA in the 5′→3′ direction, one must reverse the aligned string. A simple rule is: for a correctly oriented coding strand, replace every T with U to write the RNA. This rule fails if the sequence supplied is actually the template strand.

The meaning of a gene

A gene is a functional unit of hereditary information, but not all genes encode a polypeptide. Some encode functional RNA such as rRNA or tRNA. A cistron refers to a sequence specifying a polypeptide product. Many bacterial messenger RNAs are polycistronic: a single transcript can contain coding regions for several proteins. Most eukaryotic protein-coding mRNAs are monocistronic, specifying one main polypeptide. These terms describe transcript organisation rather than the total chromosome count.

Split genes and RNA processing

Many eukaryotic genes contain exons interrupted by introns. The initial RNA includes sequences that will remain in mature RNA and sequences that will be removed. RNA splicing removes introns and joins selected exon sequences. Exons are portions retained in the processed transcript, though not every exon nucleotide necessarily encodes amino acids: untranslated regions can also be exonic. This is why equating exon with protein-coding DNA is an oversimplification.

Regulatory sequences are not automatically protein genes

A DNA promoter or operator changes the use of nearby genetic information without necessarily producing an RNA or protein of its own. Such regions are functionally important but should not be confused with a conventional protein-coding gene. Regulation depends on the interaction of DNA sequences with proteins and sometimes RNAs, not only on the existence of the structural sequence.

Orientation is a property of the transcription unit

A DNA duplex contains two complementary strands, but naming one the coding strand is meaningful only with respect to a particular transcription unit. A gene oriented in the opposite direction along the same chromosome may use the other physical strand as its template. Promoter orientation determines which template the polymerase reads. When sketching the strands, label the 5′ and 3′ ends first, then identify the promoter and intended RNA product. This prevents confusing the two complementary sequences by accidentally reading one of them backward.

For example, let template DNA be 3′-TAC TTA CCG-5′. The RNA polymerase makes 5′-AUG AAU GGC-3′, while the coding DNA is 5′-ATG AAT GGC-3′. Only after identifying the coding frame should one infer amino acids: if the transcript is a protein-coding mRNA and initiation occurs at AUG, the first three codons would encode Met–Asn–Gly. Without an initiation site and context, a transcribed sequence is not automatically a complete protein-coding message.

The relationship among genes, transcripts and proteins

A functional gene is not necessarily a continuously translated DNA segment. Some genes produce tRNA or rRNA, and many eukaryotic protein-coding genes include untranslated exons, introns and regulatory DNA nearby. Pre-mRNA from a split gene contains introns that must ordinarily be removed before productive translation. A processed mature transcript can contain a 5′ untranslated region and a 3′ untranslated region on either side of the translated segment. These regions are exonic because they are retained, even though they do not encode amino acids.

In bacteria a polycistronic RNA can support translation of several separately initiated protein-coding segments. In most eukaryotic nuclear messenger RNAs, one major protein-coding region is translated, although biological exceptions exist. The difference concerns transcript architecture, not a claim that one chromosome carries only one protein or that all bacterial genes must reside in an operon.

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