Coupling of transcription and RNA decay Flashcards
What are we traditionally taught about gene expression in eukaryotes?
Transcription and RNA decay are independent events.
How many factors impact the fate of an mRNA?
7
How does polyA tail length impact the fate of an mRNA?
(In eukaryotes) transcripts with longer polyA tails are less susceptible to degradation because the 3’ end is protected.
How does splicing rate impact the fate of an mRNA?
Slow splicing = more frequent degradation. E.g. ribosomal proteins are spliced quickly and not degraded.
How does rate of nuclear export impact the fate of an mRNA?
Slow export = more frequent degradation.
How does RNA sequence impact the fate of an mRNA?
Specific sequences recruit RBPs e.g. which help recruit decay machinery to RNA. Often in the 3’ UTR.
How does RNA structure impact the fate of an mRNA?
Highly structured mRNAs tend to have longer half-lives e.g. stable stem loop at the beginning or end blocks nucleases.
How does codon sequence impact the fate of an mRNA?
mRNAs with many rare codons are not efficiently translated due to low frequency of these tRNAs; get degraded faster as ribosome pausing triggers decay.
How do ncRNAs impact the fate of an mRNA?
ncRNAs. miRNAs, bacterial sRNAs. Act in cis or in trans. Bind 3’ UTR and dictate translation efficiency and decay factor recruitment.
What are we traditionally taught about RNA decay in eularyotes?
Specific factors (RBPs) bind to sequences in the 3’ UTR, and they recruit or block nucleases ie promote or block decay.
What are new theories about RNA decay pointing to?
The fate of the mRNA can be dictated by cis-acting elements that are NOT part of the mRNA sequence (only the DNA).
What are theories coupling transcription to degradation?
- Polymerase subunits assist in mRNA degradation in the cytoplasm.
- The promoter sequence can determine the half-life of an mRNA.
- Transcription factors recruit RNA-binding proteins to mRNAs that regulate the decay of the mRNA in the cytoplasm.
- Transcription factor itself binds to mRNAs that regulate the decay of the mRNA in the cytoplasm.
- Promoter elements can determine the sub-cellular localisation of the mRNA and how well it is translated.
What are the mechanisms of nuclear and cytoplasmic RNA decay in eukaryotes?
- Nuclear RNA decay
- Cytoplasmic RNA decay (cytoplasmic decay factors and P bodies and stress bodies).
How does mRNA circularise?
The eIF cap binding complex interacts with the Pab1 proteins bound to the polyA tail.
Why does mRNA circularise?
To make translation circular; makes it easier for ribosomes to reinitiate translation by bringing them into close proximity with the promoter when they dissociate. Also allows cell to distinguish between faulty and correct mRNAs.
