Week 10 Flashcards
How does AU-rich element (ARE) - mediated decay regulate mRNA stability, and which protein families are involved in this pathway?
AREs in the 3’ UTRs recuit RNA-binding proteins like tristetraprolin (TTP) and HuR. TTP promotes decay via deadenylation and exosme recruitment, while HuR stabilizes transcripts by competing for binding.
What is the role of the CC4-NOT complex in mRNA decay, and how is it recruited?
CCR4-NOT is a major deadenylase complex that shortens poly(A) tails. It is recruited by proteins like TTP or directly via decapping enhancers such as DCP1/2.
Describe the sequence of events in the 5’ to 3’ mRNA decay pathway.
Deadenylation is followed by decapping then 5’ to 3’ exonucleolytic degradation by XRN1.
How does miRNA-mediated gene silencing differ between translational repression and mRNA degradation?
Partial complementarity leads to translational repression and eventual mRNA destabilization, perfect or near-perfect complementarity (rare in animals) triggers direct cleavage by Argonaute (AGO2).
What is the function of GW182 in the miRNA-induced silencing complex (miRISC)?
GW182 acts downstream of AGO, recruiting the CCR4-NOT complex and PABP to promote deadenylation and translational repression of target mRNAs.
Explain how mRNA secondary structure influences stability and susceptibility to RNAi.
Structured 3’ UTRs can hinder RISC access or ribonuclease activity, stabilizing transcripts. However, accessibility can also be increased by helicases or RNA-binding proteins that remodel these structures.
Differentiate between siRNA and miRNA in terms of origin, structure and function.
siRNAs arise from exogenous or long dsRNA, have perfect complementarity, and lead to cleavage. miRNAs are endogenously processed from pri-miRNAs, often have partial complementarity and lead to translational repression.
How does nonsense-mediated decay (NMD) recognize and degrade faulty mRNAs?
NMD targets mRNAs with premature stop codons >50-55 nt upstream of an exon-exon junction. UPF proteins (UPF1 are recruited during translation termination to trigger decay.
What determines the selectivity of Argonaute proteins in RISC assembly, and how does this affect RNA silencing?
Argonaute selects the guide strand based on the thermodynamic asymmetry of the siRNA/miRNA mix. AGO2 is the only human AGO with silencer activity, influencing whether mRNA is cleaved or repressed.
Describe the mechanism and biological significance of RNA-induced transcriptional silencing (RITS) in eukaryotes.
RITS complexes guided by siRNAs bind to nascent transcripts and recruit histone methyltransferases to promote heterochromatin formation and transcriptional silencing - a key mechanism in Schizosaccharomyces pombe and plants.
