RNA Processing and Splicing

RNA Processing and Splicing: Overview - Transcript Makeover

• Eukaryotic pre-mRNA undergoes extensive post-transcriptional modifications in the nucleus to become mature mRNA.
• Essential for mRNA stability, nuclear export, and efficient translation.
• Key modifications ("transcript makeover"):
  • 5' Capping: Addition of $m^7G$ (7-methylguanosine) cap.
  • Splicing: Intron removal, exon ligation.
  • 3' Polyadenylation: Addition of poly(A) tail.
• Prokaryotes: Minimal processing; transcription-translation often coupled.

⭐ Most human genes contain introns; precise splicing is vital for correct protein synthesis.

RNA Processing and Splicing: 5' Cap & Poly‑A Tail - RNA's Hat & Tail

• 5' Cap ("Hat"):
  • Structure: Modified guanine (7-methylguanosine, m7G) linked via unusual 5'-5' triphosphate bridge.
  • Enzymes: RNA triphosphatase, guanylyltransferase, methyltransferase.
  • Functions: Protects mRNA from 5' exonuclease degradation; essential for nuclear export; promotes translation initiation (recognized by eIF4E).
• Poly-A Tail ("Tail"):
  • Structure: Chain of ~200-250 adenine nucleotides at 3' end.
  • Enzyme: Poly(A) polymerase (PAP), template-independent.
  • Signal: AAUAAA (polyadenylation signal) upstream of cleavage site.
  • Functions: Protects from 3' exonuclease degradation; enhances translation efficiency (PABP binding); aids nuclear export; regulates mRNA stability.

⭐ Poly(A) polymerase adds the poly-A tail post-transcriptionally without requiring a DNA template for the adenine residues a crucial distinction from DNA/RNA polymerases during transcription.

RNA Processing and Splicing: The Spliceosome Show - Introns Out!

• Splicing: Crucial post-transcriptional modification; precisely removes introns (non-coding regions) and ligates exons (coding regions) from pre-mRNA.
• The Spliceosome: Dynamic, large RNA-protein complex that orchestrates splicing.
  • Components: snRNPs (small nuclear ribonucleoproteins) - U1, U2, U4, U5, U6 - plus other proteins.
    • U1 snRNP binds the 5' splice site.
    • U2 snRNP binds the branch point A.
  • Consensus Sequences:
    • 5' splice site (donor): GU sequence.
    • 3' splice site (acceptor): AG sequence.
    • Branch Point: Adenine (A) within the intron, upstream of 3' site.
• Mechanism (Two Transesterification Reactions):
  1. The 2'-OH of branch point A attacks the 5' splice site → forms a lariat (loop) structure.
  2. The freed 3'-OH of the 5' exon attacks the 3' splice site → exons are joined; lariat intron is released.

• Alternative Splicing: Allows a single gene to produce multiple distinct mRNA (and thus protein) variants. Significantly expands proteomic diversity.

⭐ Mutations in splice sites or splicing factors are a common cause of genetic diseases (e.g., some β-thalassemias, spinal muscular atrophy, cystic fibrosis variants).

RNA Processing and Splicing: Splice Variants & Errors - Code Remix & Glitches

• Alternative Splicing: "Code Remix" - one gene, multiple protein isoforms.
  • Mechanism: Differential inclusion/exclusion of exons.
  • Impact: ↑ Proteome diversity; tissue-specific functions (e.g., tropomyosin).
• RNA Editing: Further sequence modification post-transcription.
  • Types: A-to-I (by ADARs), C-to-U (by APOBECs).
  • Example: ApoB mRNA editing (ApoB100 vs. ApoB48).
• Splicing Errors: "Code Glitches" - mutations disrupting normal splicing.
  • Targets: Splice sites (📌 GU-AG rule), enhancers, silencers.
  • Outcomes: Exon skipping, intron retention, cryptic splice site activation.
  • Diseases: β-thalassemia, Spinal Muscular Atrophy (SMA), Duchenne Muscular Dystrophy.

  ⭐ A significant proportion, estimated around 15-50%, of human genetic disease mutations affect pre-mRNA splicing.

High‑Yield Points - ⚡ Biggest Takeaways

• hnRNA is the primary transcript processed into mature mRNA.
• 5' capping with 7-methylguanosine protects mRNA and aids ribosome binding.
• 3' polyadenylation adds a poly(A) tail, increasing mRNA stability and export.
• Splicing, by spliceosomes (snRNPs), removes introns and joins exons.
• GU-AG rule: Introns typically start with GU (5' site) and end with AG (3' site).
• Alternative splicing generates diverse protein isoforms from one gene.
• RNA editing (e.g., APOBEC) post-transcriptionally alters RNA sequence.