RNA processing Flashcards
Describe mG7 capping
Guanine is methylated which prevents degradation of mRNA at the 5’ end
mRNA without a cap is degraded in the cell
Important in RNA export and stability
Aids in quality control as mG7 is recognised by cap binding protein 20
Why is the RNA pol II CTD important?
Acts as a platform for co-factors
Can be phosphorylated to aid in certain processes, e.g splicing
What is the RNA pol II CTD heptapeptide that can be phosphorylated
YSPTSPS
(You should probably take some presents santa)
What does phosphorylated Ser on RNA pol II do?
S2- Phosphorylated by Cdk9/12/13 to help RNAPII elongate down the gene
S5- Phosphorylated by Cdk7 for capping and splicing
S7- Phosphorylated by Cdk7, function unknown
What does phosphorylating T on the RNAPII CTD do?
Used for histone mRNA processing
What does the exon junction complex do?
Links mRNA biogenesis to quality control
Enhances mRNA export, protein synthesis and NMD
Suppresses inappropriate recognition of splice sites
Outline the splicing process.
- U1 snRNP binds 5’ exon,
- U2 snRNP binds 3’ exon defined by SR proteins and branchpoint A. This displaces branchpoint A binding protein (BBP) and U2AF
- U5 and U4/U6 snRNP bind to these and form an intron lariat by binding together. Creates the active site of the spliceosome
- Intron lariat is cleaved and debranched from snRNPs and degraded
Describe 3’ RNA end formation
Poly A tail forms 10-30nt upstream of the cleavage site
PABP binds to this
During formation, CPSF binds RNAPII to pause it and do quality checks
How are introns and exons defined?
Introns are bundled into hnRNPs
What can alternative splicing do?
Skips exons/introns
Alternative 5’ or 3’ splice sites
Alternative promotors
Intron retention leading to decay and downregulation of mRNA
How are exons defined
Exons are bound by SR proteins to enhance splice sites as recognition sequence is 4bp
5’ exon cap is bound by the CBC complex.
PABP binds poly A tail
How does Duchenne muscular dystrophy come about?
Alternative splicing of dystrophin gene leads to it being truncated as exons are skipped
Dystrophin translation is halted altogether
How is sex determined
Governed by splicing
U2AF binds to exon, blocking U2snRNP and driving exon inclusionn of sex lethal in males
Without U2AF exons skip from 2 to 4, allowing Sxl expression for females
How does 3’ UTR shortening contribute to cancer
miRNA no longer recognises 3’ UTR and the gene is transcribed more
e.g, shorter poly A on the Ras oncogene means the miRNA Let7 no longer recognises it. Ras oncogene is upregulated, leading to lung cancer
How does U1 snRNP keep the poly A long?
U1 snRNP concentration determines length of mRNA
Suppresses polyadenylation cleavage in early poly A tails
How does mRNA <200-300nt export from the nucleus?
- hnRNP tetramers wrap 200-300 bases around it to act as a molecular ruler.
- RNA unravels when it gets to the NPC
- Once moved through, Dbp5 (RNA helicase) strips Nxf1 from mRNA
- Gle1 drives ATP hydrolysis of Dbp5, causing release
- Nup159 releases ADP from Dbp5
How does the TREX complex promote mRNA export?
- CBP80 subunit of nuclear cap binding complex allows ALYREF to bind. ALYREF allows TREX to bind 5’ mRNA and recruit Nxf1
- Exon junction complex stabilises TREX on mRNA, allowing mRNA to be marked for export
- TREX ensures free Nxf1 exports mRNA before processing by changing its conformation to autoinhibit RNA binding domain
How does spinal muscular atrophy come about?
Mutation in exon 7, means it is skipped.
Exon 6 and 8 join and the protein cannot bind oligomers
Antisense oligonucleotides that drive inclusion of exon 7 is treatment
Why is the SMN protein important?
Key to producing snRNPs in cajal bodies so snRNA can be produced
SMN forms a ring around snRNA in cytosol, trimming the hypermethylation on the 3’ cap and allowing it to move the cajal body and make an active snRNP complex
What is siRNA
short intefering RNA
21-25 nt
Mostly exogenous
dsRNA precursor
Target specific
How is the chalcone synthase gene in petunias post-translationally silenced?
Chalcone synthase is required for a deeper purple
Overexpressing the gene leads to white and variegated petunias
Silencing persists despite miRNA being easy to degrade
How is motor neuron disease caused?
Fus binds snRNP, TDP43 and SMN
Fus usually connects U1snRNP to RNAPII but is occupied
U1 snRNP is mislocalised to the cytosol in ALS as the Fus NLS is mutated
U1 snRNP depletion in nucleus leads to motor neuron cell death
Describe miRNAs
21-25nt
Encoded by endogenous genes
Hairpin precursors
Recognise multiple targets
Achieves post-translational gene repression by
deadenylation
proteolysis
blocking initiation
blocking elongation
Describe miRNA processing
- RNAPII generates pri-mRNA which contains hairpins
- DGCR8 and Drosha clamp the hairpin out of RNA
- Pre-miRNA is exported with exportin-5 to the cytosol
- Dicer cleaves pre-miRNA in the stem to generate an miRNA duplex. 5’ end has more A-T content, making it easier to unwind
- Dicer, TRBP and AGO form the RISC complex. AGO cleaves the passenger strand and unwinds DNA
How is RNA silenced via an RNA pathway?
- Long dsRNA activates 2’, 5’ OligoA synthetase.
- This activates RNase L which degrades RNA
- Long dsRNA acitvates PKR via phosphorylation
- PKR phosphorylates EIF2α which blocks protein synthesis initiation
What do lncRNAs do?
Regulate nearby genes when transcribed
Alter epigenetic chromatin modifications
Good transcriptional regulators
Involved in mRNA stability and histone modifications
What makes lncRNAs good transcriptional regulators?
Tightly controlled spatial and temporal expression
Rapidly turned over
Has RNA recognition motifs (RRM)
What protein-RNA binding domains exist?
RRM
hnRNP K-homology motif (KH)
Zinc finger domains (ZnF)
Non-canonical RNA binding domains- chromatin organisation
How are lncRNAs strucutred?
5’ ends have mG7 caps
3’ end processing less well defined
Mainly polyadenylated
Sometimes spliced
How do lncRNAs recruite genes?
Interact with nascent RNA during transcription
Base pair with another RNA and target DNA
How can lncRNAs inhibit transcription?
Block transcriptional regulation factors by
acting as a decoy
Blocking active site
Allosteric effects
What is Neat1?
lncRNA that regulates paraspeckle formation to localise transcriptional proteins
What is HOTAIR?
lncRNA that acts in trans
Acts as a scaffold to hold the REST complex (H3K4 demethylation) and PRC2 (H3K27) trimethylation
Activates/deactivates HOX genes
What is Xist?
lncRNA involved in X-inactivation
Coats inactive X-chromosome in cis to repress it
Silenced by Repeat A (RepA), which allows PRC2 to lay down trimethylation on the Xist promotor
What is the difference of cis and trans genes
cis- affects genes proximal of lncRNA locus
trans- acts as a signal, scaffolds, guides to express distant genes
