BLOCK 3: MBG: (3.6) RNA Processing & The Spliceosome

SNRNA and mRNA

• SNRNAs and mRNAs are very similar in structure and regulation
• Both have upstream and downstream sequences that control processing
• SNRNAs and mRNAs are both transcribed by RNA polymerase II

Distal and Proximal Sequence Elements in SNRNA

• Distal sequence elements (DSEs) are similar to enhancers and increase the affinity of RNA polymerase for the promoter
• Proximal sequence elements are similar to promoters and specify the location for RNA polymerase binding

SNRNA and mRNA Transcription

• SNRNA can be transcribed independently of mRNA
• SNRNA can be transcribed even when mRNA is not needed
• SNRNA can play a role in processing the mRNA transcribed before it

SNRNA Function

• SNRNAs are small, nuclear RNAs that are part of the spliceosome
• SNRNAs are involved in the splicing process (cutting and joining RNA sequences)
• SNRNAs are critical for processing mRNA molecules

Splicing

• mRNAs need SNRNAs to be processed
• In splicing, introns are removed from mRNA and exons are joined together
• Small nuclear ribonucleoproteins (SNRNPs) are composed of SNRNA and proteins
• SNRNPs are the functional units of splicing and determine where the splice occurs

SNRNP Function

• Different SNRNAs identify and bind to different splice sites
• SNRNPs are required for catalytic activity and splicing

Intron Removal

• Introns are removed during splicing
• Intron removal is a regulated process to prevent the destruction of all mRNA molecules
• The lariat structure that forms after initial splicing signals for the removal of introns

Regulation of RNA Processing

• Splicing involves both nuclear and cytoplasmic components
• SNRNAs are exported from the nucleus, processed in the cytoplasm, and then reimported to the nucleus
• This process helps regulate splicing and ensures that only appropriate SNRNAs are involved in splicing

Upstream and Downstream Elements in mRNA and snRNA

• Similar arrangement in DNA for both mRNA and snRNA
• DSE (distal sequence element) acts as enhancer
• PSE (proximal sequence element) acts as promoter

snRNA Processing

• LEC (little elongation complex) for snRNA
• GTFs (general transcription factors) are involved
• SNAPc (snRNA-activating protein complex) is used

mRNA Processing

• SEC (super elongation complex) for mRNA
• Splicing factors
• Spliceosome is used

snRNA Function

• Essential for spliceosome function
• Undergoes additional processing to become functional
• Requires both cytoplasmic and nuclear steps, including export and import

Spliceosome

• Contains proteins and specialized snRNAs
• snRNAs base pair with splice junctions for specificity
• snRNAs combine with proteins to form snRNPs
• snRNPs U1, U2, and U5 recognize splice donor and acceptor sites

Splicing Process

• 5' exon moves to 3' splice acceptor site
• Second cut is made by spliceosome
• Exon termini join and seal, forming a lariat structure
• Lariat is degraded
• Spliced mRNA contains fused exons with coding information

Alternative Splicing

• Enables production of multiple products from the same sequence
• Increases variety in products
• Same regulatory control mechanisms for transcription
• Provides additional regulatory or functional control at the transcript processing level

Spliceosome Assembly and Activity

• Occurs at sites of transcription
• Rearrangement spans neighboring intron
• snRNA associates with pre-processed mRNA transcript
• Forms pre-spliceosome complex A
• Requires helicases Prp5 and Sub2

Spliceosome Assembly Stages

• U1 and U2 snRNPs associate with 5' and 3' splice sites, forming complex A (pre-spliceosome)
• Complex B formed by the addition of U4/U6 and U5 snRNPs
• Complex B is catalytically active and requires multiple RNA helicases
• U4 and U1 are released, forming lariat precursor and complex C
• Complex C carries out the second catalytic step, forming the post-spliceosomal complex

Post-Spliceosomal Complex

• snRNPs U2, U5, and U6 are released
• Lariat intron is released and exons are spliced
• Spliced particle (mRNA) is released via helicase Prp22

Exon vs. Intron Spliceosomes

• Exons are smaller than introns in vertebrates
• ED (Exon Defined) spliceosomes form first, then rearrange to ID (Intron Defined) spliceosomes

Cryo-electron Microscopy of Spliceosomes

• Showed 4 unique states of ED spliceosomes
• Implies a maturation process for spliceosomes
• Provides insights into canonical splicing, back-splicing, and exon skipping

Regulation of Alternative Splicing

• Combination of cis-regulatory elements and trans-acting factors
• Cis-acting regulatory elements (SREs): ESE, ISE, ESS, or ISS; can promote or prevent splicing
• Trans-acting splicing factors: recruited to the site by SREs
• Activity of factors depends on the situation

Differences Between Prokaryotic and Eukaryotic Gene Sequences

• Prokaryotes have colinear genes (no introns), while eukaryotes have split genes (contain introns)
• Prokaryotic mRNA is translated immediately after transcription, while eukaryotic mRNA undergoes processing before translation

Key Terms

• Deamination: Loss of an amino group from a molecule
• Colinear: Genes where the sequence of nucleotides directly corresponds to the sequence of amino acids in the protein product
• Split: Genes with non-coding sequences (introns) interspersed between coding sequences (exons)
• Polyadenylation: Addition of a poly(A) tail to the 3' end of a transcript
• Methyltransferase: Enzyme that adds a methyl group to a molecule
• Exon: Coding sequence within a gene
• Intron: Non-coding sequence within a gene
• Lariat: Loop structure formed during splicing
• snRNA: Small nuclear RNA, involved in splicing
• snRNP: Small nuclear ribonucleoprotein, complex of snRNA and protein
• Spliceosome: Complex of snRNPs and proteins that removes introns from pre-mRNA
• Upstream Elements: Sequences located before (upstream) a gene's coding region, important for transcription
• Downstream Elements: Sequences located after (downstream) a gene's coding region, important for transcription
• Regulatory Elements: Sequences that control the expression of a gene

Explore the similarities and differences between SNRNA and mRNA in this quiz. Delve into their transcription processes, regulatory elements, and functional roles in splicing. Test your understanding of these essential molecular components involved in gene expression.