RNA processing in eukaryotes is a complex dance of molecular modifications. After transcription, pre-mRNA undergoes several key steps: 5' capping, 3' polyadenylation, and splicing. These changes prepare the RNA for its journey from the nucleus to the cytoplasm.

The process involves removing non-coding introns and joining coding exons. This splicing allows for alternative forms of proteins from a single gene. Other RNA types, like tRNA and rRNA, have their own unique processing steps, all crucial for proper cellular function.

RNA Processing in Eukaryotes

Steps in eukaryotic RNA processing

1. Transcription

   • RNA polymerase synthesizes a pre-mRNA molecule using a DNA template as a guide
   • Pre-mRNA contains both exons which are coding sequences and introns which are non-coding sequences

2. 5' capping

   • 7-methylguanosine cap is added to the 5' end of the pre-mRNA molecule
   • Protects mRNA from degradation by exonucleases and facilitates translation initiation by recruiting ribosomes

3. 3' polyadenylation

   • Poly(A) tail consisting of multiple adenine nucleotides is added to the 3' end of the pre-mRNA
   • Enhances mRNA stability by preventing degradation and facilitates export from the nucleus to the cytoplasm

4. Splicing

   • Introns are removed from the pre-mRNA molecule by the spliceosome complex
   • Exons are joined together by the spliceosome to form the mature mRNA molecule ready for translation
   • The spliceosome recognizes specific splice sites at the intron-exon boundaries

5. Nuclear export

   • Mature mRNA is actively transported from the nucleus to the cytoplasm through nuclear pore complexes
   • In the cytoplasm, mature mRNA can be translated by ribosomes to produce functional proteins

Exons and introns in mRNA splicing

• Exons
  • Coding sequences that contain the genetic information necessary for protein synthesis (amino acid sequence)
  • Exons are joined together during splicing to form the mature mRNA ready for translation
  • Alternative splicing allows for the production of different protein isoforms from a single gene (CD44, tropomyosin)
• Introns
  • Non-coding sequences that interrupt the coding regions of a gene but are removed during mRNA processing
  • Introns are removed during the splicing process by the spliceosome complex
  • Some introns contain regulatory sequences like enhancers that influence gene expression levels
  • Self-splicing introns found in some organisms can catalyze their own removal from the pre-mRNA (group I, group II introns)
  • Introns contain a branch point, which is crucial for the formation of the lariat structure during splicing

Processing of mRNA vs tRNA vs rRNA

• mRNA processing
  • Pre-mRNA undergoes 5' capping, 3' polyadenylation, and splicing to remove introns
  • Mature mRNA is exported to the cytoplasm where it serves as a template for protein synthesis
• tRNA processing
  • Pre-tRNA is transcribed by RNA polymerase III and contains extra sequences on both ends
  • 5' leader sequence is removed by RNase P and 3' trailer sequence is removed by RNase Z
  • Introns, if present, are removed by splicing enzymes specific to tRNAs
  • CCA sequence is added to the 3' end by a nucleotidyltransferase enzyme as the amino acid attachment site
  • Nucleotide modifications occur at various positions (pseudouridine, dihydrouridine) to stabilize tRNA structure
• rRNA processing
  • Pre-rRNA is transcribed by RNA polymerase I (28S, 18S, 5.8S rRNAs) and RNA polymerase III (5S rRNA)
  • Pre-rRNA is cleaved by endonucleases and exonucleases to generate mature rRNA molecules
  • Nucleotide modifications like pseudouridylation and 2'-O-methylation occur at specific sites to facilitate rRNA folding
  • Mature rRNAs assemble with ribosomal proteins to form the small (40S) and large (60S) ribosomal subunits

Additional RNA processing mechanisms

• RNA editing: A process that alters the nucleotide sequence of an RNA molecule after transcription
• Ribonucleoproteins: Complexes of RNA and proteins that play various roles in RNA processing and function
• snRNPs (small nuclear ribonucleoproteins): Key components of the spliceosome that recognize and bind to specific RNA sequences during splicing