RNA processing and modifications are crucial steps in gene expression. They transform raw RNA transcripts into functional molecules, ensuring proper protein synthesis and cellular function.

These processes include splicing, which removes introns from pre-mRNA, and modifications like 5' capping and 3' polyadenylation. RNA editing and non-coding RNA processing further enhance the complexity and diversity of the transcriptome.

RNA Splicing

Pre-mRNA Processing and Splicing

• Pre-mRNA is the initial transcript produced by RNA polymerase II
• Contains both coding regions (exons) and non-coding regions (introns)
• Introns are removed from pre-mRNA through a process called splicing
• Splicing involves the excision of introns and the joining of exons to form a mature mRNA molecule
• Occurs in the nucleus before the mRNA is exported to the cytoplasm for translation

Spliceosome and Alternative Splicing

• Splicing is carried out by a complex called the spliceosome
• Spliceosome is composed of small nuclear ribonucleoproteins (snRNPs) and other proteins
• Recognizes specific sequences at the boundaries between exons and introns (splice sites)
• Catalyzes the removal of introns and the ligation of exons
• Alternative splicing allows for the production of multiple protein isoforms from a single gene
• Occurs when different combinations of exons are included or excluded in the final mRNA (CD44 gene, which can produce over 100 distinct isoforms)

mRNA Modifications

5' Capping and 3' Polyadenylation

• Mature mRNA undergoes modifications at both the 5' and 3' ends
• 5' capping involves the addition of a 7-methylguanosine (m7G) cap to the 5' end of the mRNA
• 5' cap protects the mRNA from degradation and facilitates its translation by ribosomes
• 3' polyadenylation involves the addition of a poly(A) tail (a stretch of adenine nucleotides) to the 3' end of the mRNA
• Poly(A) tail enhances mRNA stability and facilitates its export from the nucleus to the cytoplasm

RNA Editing

• RNA editing is a process that alters the nucleotide sequence of an RNA molecule post-transcriptionally
• Can involve the insertion, deletion, or modification of specific nucleotides (adenosine-to-inosine editing in mammals)
• Editing can change the amino acid sequence of the encoded protein or alter the stability or localization of the RNA
• Allows for the generation of protein diversity beyond what is encoded in the genome (apolipoprotein B gene, which can produce two distinct isoforms through RNA editing)

Non-coding RNA Processing

tRNA and rRNA Processing

• Non-coding RNAs, such as transfer RNA (tRNA) and ribosomal RNA (rRNA), also undergo processing
• tRNAs are transcribed as precursors and undergo modifications, including the removal of 5' and 3' sequences, addition of CCA to the 3' end, and base modifications
• These modifications are essential for tRNA function in protein synthesis (anticodon loop modifications that enhance codon-anticodon interactions)
• rRNAs are transcribed as a single precursor that is subsequently cleaved and modified to produce mature 18S, 5.8S, and 28S rRNAs
• Processing of rRNAs involves the removal of spacer regions, base modifications, and the assembly of rRNAs with ribosomal proteins to form functional ribosomes (methylation and pseudouridylation of specific nucleotides in rRNAs)