Alternative splicing and one gene, many proteins
Alternative splicing changes exon inclusion or splice-site use to produce different RNA isoforms. Some encode different proteins. RNA-binding regulators, transcript sequence and cell conditions influence these choices.
What a learner can do afterwards
- Works out the possible mature transcripts from a stated exon arrangement.
- Explains what decides which splice sites are used in a given cell.
- Explains how an intronic splice-site variant can alter RNA processing and protein sequence without directly changing coding DNA.
1 · Read
Many pre-mRNAs contain introns between exons. Exons are retained RNA regions and can include untranslated sequence as well as coding sequence. The spliceosome recognises a 5 prime splice site, a branch point adenosine and a 3 prime splice site. Two transesterification reactions remove an intron and join adjacent exons. Splicing can begin during transcription.
Alternative splicing changes exon inclusion or splice-site use. Patterns include exon skipping, intron retention and alternative 5 prime or 3 prime sites. Copies of the same pre-mRNA can yield different RNA isoforms. These need not encode different proteins: untranslated regions may differ, or an RNA may be degraded. An exon does not necessarily encode one whole protein domain.
Count only allowed arrangements and preserve exon order. Four independent optional exons, each kept or skipped with every combination allowed, give 2 times 2 times 2 times 2 = 16 arrangements. If exactly one of three alternatives must be retained, there are three arrangements instead. RNA counts do not by themselves give protein counts.
RNA-binding regulators influence splice-site use. Many SR proteins promote splicing and many hnRNP proteins repress particular sites, but effects depend on the protein and binding position. RNA structure and transcription speed also contribute. For a local prediction, use the stated effect and whether binding at that site increases or decreases.
Disrupting a splice site can cause exon skipping, intron retention or use of a cryptic site, an alternative site normally used little or not at all. An intronic variant can alter processing without directly changing coding DNA. The mature RNA can then change the reading frame or protein sequence. Other splice-site variants lie in coding exons, so splicing and coding effects can overlap.
Splicing produces RNA isoforms. Count allowed arrangements, use stated regulator effects and assess protein consequences separately.
Lesson, questions and flashcards written for this dataset.
Readings and flashcards written for this dataset. Transcription and mRNA processing is a Khan Academy video linked through YouTube.
More to read
Exons are retained RNA
An exon is a retained region of spliced RNA. It can contain coding or untranslated sequence. During ordinary intron removal, the spliceosome removes the intervening intron and joins adjacent exons using two transesterification reactions.
Alternative splicing changes retained regions or junctions. Different isoforms may encode different proteins, but that is not automatic. Untranslated differences and RNA degradation can separate RNA diversity from protein diversity.
Site choice and sequence changes
Regulatory proteins bind RNA and influence splice-site use. Their effects depend on identity and binding position. RNA structure and transcription speed also affect processing choices.
Disrupting a normal splice site can lead to skipping, retention or use of a cryptic site. An intronic change can alter processing without directly changing coding DNA. A change within a coding exon may affect both coding information and splicing, so these categories can overlap.
Counting allowed isoforms
Begin with the fixed exon order and the question's allowed choices. Independent optional exons each supply a keep-or-skip choice. Mutually exclusive exons follow a different rule: when exactly one is required, combinations containing both or neither are excluded.
This calculation counts RNA arrangements under stated assumptions. To count proteins, additional information about coding regions, reading frames and RNA fate is needed. Cells may not produce every mathematical possibility.
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2 · Watch
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Where it sits
8 questions wait behind this lesson, each with its answer explained. Every answer feeds the sky: stars light as they are learned, and dim when it is time to come back.