Mechanisms for RNA localisation in eukaryotes Flashcards
How can you see where mRNAs are located within cells? (2)
- Make a piece of DNA made of Ts with a fluorescent probe
- Binds to polyA tails on mRNAs
What are nuclear speckles?
Structures containing RNAs and proteins in the nucleus, located between the chromatin
What needs to happen before mRNA export? (2)
- Pre-mRNA must be fully processed before export (5’ cap, splicing, 3’ cleavage and polyA)
- RNA polymerase II acts as a tether as it is bound to DNA as RNA is coming out of it, therefore 3’ cleavage and polyA is essential
How is the TREX complex recruited to the 5’ end of mRNA? (2)
- TREX complex is conserved from yeast to man and promotes mRNA export
- Key component ALYREF binds the CBP80 subunit of the nuclear cap binding complex which anchors TREX complex on the 5’ end of mRNA
Which way does mRNA exit the nucleus?
Goes through nuclear pore 5’ end first
What is the nuclear cap binding complex?
Heterodimer made of CBP80 and CBP20 which binds to the 5’ cap of RNA transcripts
What is U2AF35?
Splicing factor which recognises the branch point sequence in intron of pre-mRNA (not spliced)
What is UAP56? (2)
- RNA helicase
- Component of the TREX complex
Why is TREX specifically bound to spliced mRNA? (4)
- TREX is first recruited to the 5’ cap of mRNA then jumps to internal sites next to the exon junction complex (EJC)
- EIF4A3 in EJC binds to ALYREF in TREX
- mRNA ends up with multiple TREX complexes bound to 5’ cap and internally next to EJC
- Therefore TREX is specifically bound to spliced mRNA because it is dependent on the EJC which is only present after splicing
What is the exon junction complex (EJC)?
Protein complex deposited 20-24 nucleotides upstream from the exon-exon boundary in spliced mRNA
What is EIF4A3? (2)
- RNA helicase
- Component of the EJC
What is polyA binding protein (PABP)?
Binds to the polyA tail of mRNA in the nucleus and encourages recruitment of TREX to the 3’ end
What are the 3 ways in which TREX is recruited to mRNA?
- 5’ cap via CBP80
- Internal EJCs via EIF4A3
- PolyA tail via PABP
What is the TREX complex?
Intermediate complex in mRNA export
What is Nxf1 (Tap) protein? (3)
- Nuclear RNA export factor 1
- The major mRNA export receptor
- Binds to RNA and the nuclear pore
What is the structure of Nfx1? (2)
- N-terminal cargo-binding domain which contains RNA binding domain (RBD) and leucine-rich repeat (LRR)
- C-terminal nuclear pore complex (NPC) binding domain which contains NTF2 scaffold and UBA-like domain
What is the function of the NPC-binding domain of Nxf1? (2)
- Nxf1 heterodimerises with p15 (Nxt1) via NTF2 scaffold
- NTF2 and UBA-like domain recognise phenylalanine-glycine (FG) repeats in nucleoporins
What are nucleoporins?
Proteins which line the nuclear pore
How is mRNA licenced for export? (3)
- Free Nxf1 doesn’t bind RNA in the nucleus because it sequesters its own RNA binding domain
- ALYREF in TREX binds to RBD in Nxf1 and THOC5 or Chtop in TREX binds to NTF2 in Nxf1 = causes Nxf1 to flip open and now will bind RNA with high affinity
- Nxf1 binds to the nuclear pore = export
How is Nxf1 linked to TREX? (2)
- TREX drives Nxf1 into a conformation which allows it to bind RNA with high affinity
- Only get TREX on mRNA after processing and only get Nxf1 after TREX
How does RNA length determine export route? (5)
- Some RNAs need to be kept in the nucleus
- Short RNAs (less than 200-300nt) e.g. snRNAs (splicing - nucleus) aren’t exported via mRNA export pathway (TREX and Nxf1)
- hnRNPC can wrap ~230-240nt of RNA around it
- If RNA is too short for hnRNPC, instead recruits Phax, Crm1 and Ran-GTP and this complex exports the mRNA
- If RNA is long enough to wrap around hnRNPC, recruitment of Phax/Crm1/Ran-GTP is blocked, binds ALYREF (TREX) and Nxf1 and is exported normally
What is hnRNPC?
Molecular ruler
How are mRNA export factors recycled? (5)
- Dbp5 RNA helicase forms a complex with ATP and binds to RNA in the nucleus with Met67 (Nxf1) and Mtr2 (p15)
- Complex goes through the nuclear pore, Gle1 joins, ATP hydrolysis triggers mRNA release into the cytosol leaving ADP bound
- Gle1 drives release of ADP and Dbp5 which triggers release of Met67 and Mtr2
- Nup159 joins and drives recycling of Dbp5
- Export factors have nuclear localisation signals so are imported via normal pathway without mRNA bound
Why is packaging of mRNA for export important? (2)
- Protects the mRNA
- Proteins packaging the RNA prevent it from re-annealing to the template DNA strand and prevent formation of R loops
How are R loops formed? (3)
- RNA polymerase II transcribes RNA
- The RNA being produced re-invades the transcription bubble forming a DNA:RNA duplex
- Dangerous because the affected DNA strand can’t base pair with its other strand that is being transcribed so is vulnerable to cleavage/mutagenesis so causes genome instability
What happens if TREX is depleted?
Lots of R loops and lots of DNA damage
How does SMN1 cause spinal muscular atrophy? (5)
- SMN1 mRNA includes exon 6, 7, 8 and the resulting protein forms oligomers
- SMN2 gene has C>T mutation in exon 7 causing skipping of exon 7 and the resulting protein can’t form oligomers but if you have WT SMN1 its fine
- SMN1 mutations cause spinal muscular atrophy, no functional SMN1 protein
- Cure is antisense oligos which binds SMN2 pre-mRNA and forces splicing to include exon 7 so makes functional SMN protein
- SMN complex is required for maturation of snRNP complex for splicing, motor neurons are susceptible to loss of spliceosome
What is spinal muscular atrophy?
Genetic condition caused by SMN1 gene mutations which causes death of motor neurons
What is the life cycle of snRNAs? (6)
- Transcription of snRNA in the nucleus
- 150-200nt = too short for hnRNPC so Phax complex recruited and is exported to the cytoplasm for maturation
- Has Gemin5 bound in the cytoplasm and interacts with SMN complex (mutated in spinal muscular atrophy)
- SMN complex forms a ring (importance of oligomerisation) and recruits Sm proteins that also form a ring on the snRNA (don’t get ring of Sm proteins on snRNA in spinal muscular atrophy, can’t form snRNP complexes, can’t form spliceosomes, can’t do splicing properly)
- Cap gets hypermethylated (tri-methyl)
- snRNA recruited back into the nucleus into the Cajal body, drives final maturation of snRNP complex which can then be used in splicing
What genes tend to be mutated in motor neuron diseases?
RNA binding proteins e.g. FUS
How does FUS mutation cause disease? (5)
- Loss of function causes disregulation of splicing, motor neurons are particularly susceptible to loss of spliceosome
- FUS binds to U1 snRNP (5’ splice site), TDP43 and SMN (splicing factors)
- FUS mutants mislocalise in the cytoplasm instead of the nucleus so bound U1 snRNA is in the cytoplasm rather than nucleus
- RNA polymerase II binds to FUS which stabilises RNApolII interaction with U1 snRNP so loss of FUS means loss of coupling splicing and transcription
- Uncoupled splicing is less efficient
