Gene expression is the process where instructions in a gene are used to create a functional product, typically a protein. This starts with transcription, copying the gene’s DNA sequence into precursor messenger RNA (pre-mRNA). Before translation, pre-mRNA undergoes RNA splicing, a critical editing step that removes non-coding sections. The splice acceptor site acts as a precise boundary marker, signifying where the editing machinery must cut to ensure the final protein sequence is correct.
The Blueprint of a Gene
A gene’s primary RNA transcript is interrupted by non-coding segments. The coding segments are called exons, which contain instructions for building the protein. Interspersed between exons are introns, which are non-coding sequences that must be removed during processing.
The splice acceptor site is located at the very end of an intron, marking the exact spot where the intron sequence stops and the next exon sequence begins. It is also known as the 3′ splice site, defining the boundary at the downstream end of the intron.
Splicing removes the introns and seamlessly joins the exons to create a final, coherent message. This precise removal relies on recognizing specific sequence signals at both ends of every intron. The splice acceptor site is the final marker, ensuring the intron is cut away before the next exon is added.
How the Splice Acceptor Site Directs RNA Processing
The splice acceptor site is a highly conserved sequence located just before the start of the downstream exon. This site is almost always terminated by the two-nucleotide sequence AG, which acts as the ultimate recognition signal for the splicing machinery. The AG dinucleotide is preceded by a stretch of pyrimidines (C and U nucleotides).
The operation is carried out by the spliceosome, a massive molecular complex composed of small nuclear ribonucleoproteins (snRNPs) and other proteins. The spliceosome recognizes the splice acceptor site, the splice donor site (5′ site), and an internal branch point sequence. Recognition of the acceptor site is mediated by protein factors like U2AF, which bind to the polypyrimidine tract and the AG sequence.
The spliceosome executes a two-step reaction to remove the intron. The second step involves cleaving the RNA chain precisely at the splice acceptor site and joining the upstream exon to the downstream exon. This precision is necessary because the protein-coding sequence is read in groups of three nucleotides (codons). An error of even a single nucleotide at the splice acceptor site results in a frameshift, scrambling the entire downstream protein sequence.
Consequences When the Site is Defective
A single mutation within the splice acceptor site’s consensus sequence can prevent the spliceosome from correctly identifying the boundary. If the spliceosome cannot recognize the AG signal, it fails to cut the intron out correctly, leading to defective mature mRNA. A substantial portion of disease-related mutations are linked to such splicing problems.
A defective splice acceptor site can lead to several outcomes:
- Exon skipping, where the spliceosome skips the adjacent exon entirely.
- Intron retention, where the entire intron or part of it remains in the final mRNA transcript.
- Activation of a cryptic splice site, which is a sequence resembling a normal splice site that is not typically used.
These outcomes drastically alter the messenger RNA’s coding sequence. This results in a highly altered or truncated protein that is non-functional because the sequence is incomplete or out of frame. Errors in the splicing process cause genetic disorders such as beta-thalassemia and certain types of cancer and neurodegenerative conditions.