Biology · Gene Expression: RNA & Proteins
RNA processing, alternative splicing and RNA stability
Two cells can share the same DNA region yet contain different mature RNAs from it. The difference may lie in how the transcript is processed or how long it remains available, rather than in a different inherited DNA sequence.
You need the ideas of DNA strands, complementary base pairing and cellular compartments. The DNA replication and repair chapter supplies that background. Here, direction labels and RNA base pairing are explained again before the worked examples; complete biochemical mechanisms need not be memorised.
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Trace selected RNA maturation steps and distinguish transcript form, abundance and lifetime.
A primary transcript is not always the finished RNA
For many nuclear eukaryotic mRNAs, a 5′ cap is added and the 3′ end is cleaved before a poly-A tail is attached. These features contribute to interactions involved in protection, export and translation. Processing can begin while transcription is still occurring. The diagram groups events for clarity; it does not impose a universal sequence in which every event waits for transcription to finish.
Splicing removes selected intron sequences from a precursor RNA and joins the retained exon sequences. Exon is not a synonym for protein-coding sequence: exons can include untranslated regions, or UTRs, that remain in a mature mRNA but are not read into amino acids. Nor does every eukaryotic protein-coding gene have introns or every mRNA use exactly the displayed end modifications.
Retained exons include untranslated regions
Read the diagram in words
A precursor RNA has three exon segments separated by two introns. A bracket marks the 5′ untranslated part within exon one and the 3′ untranslated part within exon three. A mature RNA row retains the exon segments, joins their boundaries, adds a 5′ cap and shows a 3′ poly-A tail. Introns are absent from this selected mature form; retained UTRs remain outside the translated coding-region bracket.
Precursor RNA
- Exon 1
- 5′ UTR
- Coding region begins
- Intron 1
- Exon 2
- Coding region
- Intron 2
- Exon 3
- Coding region ends
- 3′ UTR
Selected mature mRNA
- 5′ cap
- Exon 1
- 5′ UTR
- Coding region begins
- Exon 2
- Coding region
- Exon 3
- Coding region ends
- 3′ UTR
- 3′ poly-A tail
| Retained exon | Region |
|---|---|
| Exon 1 | 5′ UTR |
| Exon 3 | 3′ UTR |
| Retained exon | Region |
|---|---|
| Exon 1 | Coding region begins |
| Exon 2 | Coding region |
| Exon 3 | Coding region ends |
- Precursor RNA
- Selected mature mRNA
- Introns removed; retained exons joined
- 5′ cap
- 3′ poly-A tail
- Translation start
- Translation stop
- Translated coding region
- UTR: retained, not translated
- Processing events can overlap transcription
Different choices can change the mature product
Alternative splicing can retain different exon combinations or use different splice boundaries. In the constructed example, mature transcript one keeps A, B and C; transcript two joins A directly to C. The retained regions remain in their original order. The difference changes the RNA sequence without removing B from the DNA.
If these transcripts are translated, their protein products may differ. The result depends on the reading frame, start and stop positions, RNA stability and translation. An observed splice form is not automatically a useful protein isoform. Some processing choices affect only untranslated regions, and some transcripts may be degraded rather than yield a stable protein.
A splice choice can preserve or change a coding frame
Read the diagram in words
One constructed precursor arrangement contains coding-only exon fragments A, B and C with intervening introns. Two outcomes retain A–B–C or A–C. A contains AUG GCU, B contains UUU and C contains GAA UAA. Both outputs preserve the chosen reading frame here because omitted B has exactly three nucleotides. One short chain includes phenylalanine while the other omits it.
| Exon fragment | Bases from left to right | Nucleotide count |
|---|---|---|
| A | AUG GCU | 6 |
| B | UUU | 3 |
| C | GAA UAA | 6 |
Intervening intron — not sequenced here
Retain B
| Retained exon order | RNA read in the stated frame | Stop signal |
|---|---|---|
| A–B–C | AUG GCU UUU GAA UAA | UAA |
Constructed short amino-acid chain
- Methionine
- Alanine
- Phenylalanine
- Glutamate
Skip B
| Retained exon order | RNA read in the stated frame | Stop signal |
|---|---|---|
| A–C | AUG GCU GAA UAA | UAA |
Constructed short amino-acid chain
- Methionine
- Alanine
- Glutamate
- One precursor arrangement
- Intervening intron — not sequenced here
- Read 5′ → 3′ from the stated AUG
- Constructed short amino-acid chain
- Stop is not an amino acid
- Three-nucleotide omission preserves this frame
Amount is a balance, not a stopwatch
An RNA pool's abundance reflects production and removal, with processing, export and location affecting what is measured. A longer-lived mRNA can remain available for translation longer, but RNA amount alone does not determine protein amount. Translation rates and protein degradation also matter.
Sequence elements, RNA-binding proteins and regulatory RNAs can affect transcript fate. rRNAs and tRNAs also undergo processing and modification in both eukaryotes and prokaryotes; they do not bypass maturation merely because they are not translated. The nuclear mRNA model is one important route, not a universal recipe for all RNA.
Worked example
Keep a reading-frame condition in the comparison
In the hypothetical coding-only exon example, A is AUG GCU, B is UUU, and C is GAA UAA, all written 5′ to 3′. Keeping A–B–C gives AUG GCU UUU GAA UAA. Skipping B gives AUG GCU GAA UAA. Using the standard code and the stated start, the short chains are methionine–alanine–phenylalanine–glutamate and methionine–alanine–glutamate; the final UAA signals stop rather than adding an amino acid.
B contains three nucleotides, so this particular omission preserves the downstream triplet grouping. That is a condition of our example, not a rule that every exon can be skipped without a frame change. These tiny sequences illustrate decoding; they do not establish functional proteins or realistic splice-site signals. The separate maturation diagram includes UTRs that this coding-only example omits.
Check your understanding
Does alternative splicing remove the skipped sequence from the cell's DNA?
Show reasoning
No. It changes which regions are retained in the processed RNA. The underlying DNA region need not change.
Are all sequences retained in an mRNA translated into amino acids?
Show reasoning
No. Untranslated regions remain in mature mRNA and can affect its handling without being part of the translated coding region.
An RNA sample contains twice as much of one mRNA as another sample. Does that alone establish twice the transcription rate or twice the protein amount?
Show reasoning
No. RNA abundance depends on production and removal. Translation and protein removal add further steps between RNA amount and protein amount.
What to carry forward
RNA maturation, splice choice and turnover can change expression without changing the inherited DNA sequence.
References
Resources supporting this lesson’s explanations and examples.
Mary Ann Clark, Matthew Douglas and Jung Choi · OpenStax2 sources
National Human Genome Research Institute5 sources
- Talking Glossary — ExonNational Human Genome Research InstituteScientific reference
- Talking Glossary — IntronNational Human Genome Research InstituteScientific reference
- Talking Glossary — Alternative SplicingNational Human Genome Research InstituteScientific reference
- Talking Glossary — Messenger RNA (mRNA)National Human Genome Research InstituteScientific reference
- Ribonucleic Acid (RNA) Fact Sheet (Updated 24 May 2024)National Human Genome Research InstituteScientific fact sheet