5 Transcription and RNA Processing

Gene Structure and Transcription Landmarks

A gene is a stretch of DNA whose transcription produces a functional RNA. Genes can produce messenger RNA (mRNA), which may be translated into protein, or functional RNAs such as ribosomal RNA and transfer RNA, which are not translated.

A typical eukaryotic protein-coding gene includes regulatory DNA, a promoter, a transcription start site (TSS), a transcribed region, and termination and 3′-end signals. These regions have distinct roles:

• Regulatory DNA, including enhancers and silencers, helps control when and how strongly a gene is transcribed. It may be far from the coding region.

• The promoter is where transcription machinery assembles. It helps determine where transcription begins and which DNA strand is used.

• The TSS is the first DNA position copied into RNA. It is not necessarily where the protein-coding sequence begins.

• The transcribed region is copied into an initial RNA. It may contain exons separated by introns.

• Termination and 3′-end signals help end or process the transcript.

A simplified gene arrangement is:

Exons remain in mature RNA, but they are not always entirely protein-coding: they can include untranslated regions (UTRs). Introns are removed from most pre-mRNAs. UTRs are transcribed and retained in mature mRNA but are not translated. The start codon lies downstream of the TSS within the transcribed RNA, and the stop codon ends its protein-coding sequence. Gene organization varies, and some genes do not contain introns.

Takeaway: The TSS marks the beginning of transcription, while the start codon marks the beginning of the protein-coding sequence; these are different points.

How Transcription Copies DNA into RNA

Transcription copies information from DNA into RNA. RNA polymerase separates a short stretch of DNA and uses the template strand as a guide. It reads that strand from 3′ to 5′ and builds RNA from 5′ to 3′ by joining complementary RNA nucleotides. The RNA sequence matches the nontemplate, or coding, DNA strand except that RNA uses uracil (U) instead of thymine (T).

Transcription proceeds through three broad stages:

1. Initiation: RNA polymerase and associated proteins recognize the promoter and begin RNA synthesis at the TSS.

2. Elongation: RNA polymerase travels along the template and extends the RNA strand.

3. Termination: Transcription ends when signals cause the transcript to be released. In eukaryotic protein-coding genes, RNA cleavage and termination are linked, but are not always the same event.

In eukaryotes, transcription occurs in the nucleus. Bacteria lack a nucleus, so transcription occurs in the cytoplasm and can take place while ribosomes translate the RNA. Bacterial mRNAs typically undergo less processing than eukaryotic pre-mRNAs.

Takeaway: RNA polymerase reads the DNA template in one direction and synthesizes complementary RNA in the opposite direction.

Eukaryotic mRNA Processing

For many eukaryotic protein-coding genes, the first RNA product is pre-mRNA. It is processed—often while it is still being transcribed—before mature mRNA can leave the nucleus and be translated. The major processing steps are 5′ capping, splicing, and 3′-end cleavage and polyadenylation.

5′ capping

A modified guanine nucleotide is added to the pre-mRNA’s 5′ end. The cap helps protect the RNA from breakdown and supports export from the nucleus and recognition by translation machinery.

Splicing

The spliceosome, a complex of proteins and small nuclear RNAs, removes introns and joins neighboring exons. Splicing must occur at the correct positions to preserve the intended RNA sequence. In alternative splicing, different combinations of exons are joined, allowing one gene to produce multiple mature RNA forms.

3′-end processing and polyadenylation

The pre-mRNA is cut at a specific 3′-end site. Poly(A) polymerase then adds a stretch of adenine nucleotides called the poly(A) tail. The tail generally supports mRNA stability and export. It is added during processing rather than copied as a long string from the DNA template.

After processing, mature mRNA contains a 5′ cap, joined exons (including any UTRs), and a 3′ poly(A) tail. It can be exported to the cytoplasm, where ribosomes translate its coding sequence into protein.

Takeaway: Capping, splicing, and 3′-end processing turn pre-mRNA into mature mRNA, while splicing choices can produce different RNA forms from one gene.