Untitled Quiz

RNA Processing

• RNA processing is a crucial step in the central dogma, converting a primary transcript into a mature RNA molecule.
• Multiple RNA species play key roles in the central dogma, including snRNA, snoRNA, rRNA, tRNA, mRNA, piRNA, and siRNA.
• DNA is transcribed into mRNA, which is then processed into a mature mRNA that codes for a protein.
• Different RNA polymerases (Pol I, Pol II, and Pol III) produce distinct RNA types: Pol I transcribes rRNA; Pol II produces mRNA, snRNAs, snoRNAs, and miRNAs; Pol III synthesizes tRNAs, 5S rRNA, U6, and other small RNAs.
• RNA processing is a multi-step pathway.
  • Co-transcriptional association with processing factors and ribosomal proteins occurs.
  • Multiple endonucleases (and exonucleases) remove or add sequences.
  • Processing factors associate and disassociate as rRNAs fold and bind proteins.
  • Maturation often occurs in the nucleolus (with some in the nucleoplasm).
• RNase III domains are crucial for rRNA and RNA processing.
• Specific endonucleases cleave double-stranded RNA and intramolecular stems, leaving 2-nucleotide 3' overhangs.
• Transfer RNA (tRNA) processing involves the removal of 5' and 3' trailers by RNaseP and RNaseZ respectively.
• CCA adding enzymes add the CCA sequence to the 3' end, and various nucleotide-modifying enzymes modify the bases.
• RNase P is a ribonucleoprotein (RNP) complex and one of the first discovered ribozymes. Other ribozymes include those involved in splicing.

mRNA processing

• The primary transcript is the initial RNA product of transcription.
• Cleavage, splicing, 3′ addition and editing produce mature functional RNA.
• Eukaryotic pre-mRNA undergoes extensive processing: 5′ capping, splicing and 3′ polyadenylation.
  • 5′ capping: protects the 5′ end of the mRNA molecule from degradation.
  • Splicing: removing introns and joining exons to form continuous coding sequences of mRNA.
  • 3′ polyadenylation: process of adding a poly(A) tail to the 3′ end of the mRNA molecule, aiding in mRNA stability and translation.

rRNA processing

• Ribosomal RNA transcription, processing, and assembly often occur coupled.
• Different organisms (bacteria vs eukaryotic cells) have different rRNA processing mechanisms but similarities exist across species.

tRNA modifications

• tRNAs undergo diverse modifications
• Nucleotide modifications have many implications ,including effects on mRNA stability and function

Introns and Splicing

• Introns are non-coding sequences within genes.
• Splicing is when introns are removed and exons are joined.
• A spliceosome, incorporating snRNPs (small nuclear ribonucleoproteins) and protein complexes, carries out the splicing reaction.
• This process proceeds through sequential trans-esterification reactions, resulting in ligated exons and intron removal.

mRNA splicing

• Spliceosome assembly begins with U1 and U2 binding
• Multiple helicases are used for RNA:RNA interactions and for energy.
• Splicing events can be altered by consensus and regulatory sequences.
• Exon junction complexes (EJCs) are important for correct splicing and are deposited during or after splicing

Alternative Processing

• Alternative processing creates diverse products from a single gene. - Alternative splicing, alternative 5′ or 3′ splice sites, alternative start sites and alternative polyadenylation, create significant regulatory effects.
• Multiple splice isoforms can occur

RNA Decay

• RNA decay is necessary for maintaining steady-state RNA levels.
• Bacterial mRNA decay includes endonucleolytic cleavage and 3' exonuclease degradation.
• Eukaryotic factors, including capping machinery, decapping enzymes, and exosomes, affect various phases of mRNA degradation.

RNA decay regulation

• Several mechanisms, including deadenylation and decapping, affect the rate of mRNA degradation.

RNA processing consequences

• RNA processing generates a wealth of applications as it produces functional RNAs and ribonucleoproteins (RNPs).

RNA processing and complexity

• Eukaryotic gene regulation is complex. RNA modifications likely evolved as a defense mechanism against parasitic elements.