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Questions and Answers
Which of the following are types of splicing regulatory elements?
Which of the following are types of splicing regulatory elements?
Splicing is a process that only occurs in prokaryotic organisms.
Splicing is a process that only occurs in prokaryotic organisms.
False
What is the role of the Exon Junction Complex (EJC) in splicing?
What is the role of the Exon Junction Complex (EJC) in splicing?
The EJC marks the site of correct splicing.
Introns in eukaryotic genes must be removed from pre-mRNA to produce _____
Introns in eukaryotic genes must be removed from pre-mRNA to produce _____
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Match the following terms related to splicing with their definitions:
Match the following terms related to splicing with their definitions:
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Which of the following best describes the function of the spliceosome?
Which of the following best describes the function of the spliceosome?
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Alternative splicing can result in multiple protein isoforms from a single gene.
Alternative splicing can result in multiple protein isoforms from a single gene.
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How many splice isoforms can the Drosophila Dscam generate?
How many splice isoforms can the Drosophila Dscam generate?
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What is the primary function of mRNA capping and polyadenylation?
What is the primary function of mRNA capping and polyadenylation?
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The spliceosome is a static complex that does not change during splicing.
The spliceosome is a static complex that does not change during splicing.
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Name one of the proteins or complexes that compose the spliceosome.
Name one of the proteins or complexes that compose the spliceosome.
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The human Titin gene has __________ introns.
The human Titin gene has __________ introns.
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Match the following genes with the number of introns they contain:
Match the following genes with the number of introns they contain:
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Which of the following describes the arrangement of introns in yeast compared to humans?
Which of the following describes the arrangement of introns in yeast compared to humans?
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The splicing reaction is characterized by the formation of a branched lariat structure from introns.
The splicing reaction is characterized by the formation of a branched lariat structure from introns.
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What are trans-esterification reactions utilized for in the splicing process?
What are trans-esterification reactions utilized for in the splicing process?
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What is the role of SMN in the splicing process?
What is the role of SMN in the splicing process?
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Alternatively spliced mRNAs allow for multiple protein isoforms from a single gene.
Alternatively spliced mRNAs allow for multiple protein isoforms from a single gene.
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What is the significance of splice site selection in mRNA splicing?
What is the significance of splice site selection in mRNA splicing?
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The current therapy for Spinal Muscular Atrophy (SMA) involves the small molecule __________.
The current therapy for Spinal Muscular Atrophy (SMA) involves the small molecule __________.
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Match the splicing regulators with their functions:
Match the splicing regulators with their functions:
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What is one way to manipulate mRNA splicing therapeutically?
What is one way to manipulate mRNA splicing therapeutically?
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Modified nucleotides in eukaryotic mRNAs do not contribute to mRNA stability.
Modified nucleotides in eukaryotic mRNAs do not contribute to mRNA stability.
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Explain the role of spliceosomes in mRNA processing.
Explain the role of spliceosomes in mRNA processing.
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Study Notes
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.
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