Post-Transcriptional Regulation Flashcards
What is RNAPII involved in?
capping, splicing and polyadenylation coupled to transcription
What does phosphorylation of the CTD of RNAPII do?
release RNAPII from the promoter to start RNA elongation which allows different sets of proteins to bind for capping, splicing and polyadenylation
What is mRNA capping?
5’ to 5’ addition of GMP to the 5’ end of the RNA transcript
When is the capping reaction started?
when an RNA is synthesised to ~25nt
What are the roles of capping?
- signals translation initiation by ribosome binding
- ensures correct processing and export of mRNA through binding a cap binding complex
- stabilises and protects 5’ end of mRNA from degradation
What are the 3 steps of capping?
- phosphatase removes a phosphate from 5’ end of primary transcript
- guanylyl transferase adds a GMP in a reverse linkage (5’-5’ instead of 3’-5’)
- methyl transferase adds a methyl group to the guanosine
What are all 3 enzymes for RNA capping associated with?
the CTD
What are the 3 splicing consensus sequences?
- 5’ GU - donor site
- 3’ CAG - acceptor site
- branch point - loose consensus
What are the 2 basic steps of RNA splicing?
- join the 5’ end of intron to a branch point A to form a lariat loop
- cut the 3’ end of intron and join the 2 exons
What type of reaction happens in RNA splicing?
transesterification
What are the 5 snRNAs and what are their functions?
- U1 - recognises 5’ splice site
- U2 - initial binding to branch site
- U4 - sequesters U6
- U5 - brings 2 exons together
- U6 - catalyses 2 transesterification reactions with U2
How are snRNPs formed?
each snRNA is complexed with more than 7 protein subunits
What does the spliceosome do?
- recognise the intron splice sites
- bring the two ends of the exon together
- remove the intron
What are the 4 steps of RNA splicing?
- U1 forms base pairs with the 5’ specific junction and the BBP and U2AF recognises the branch-point site
- U2 displaces BBP and U2AF and forms base pairs with the branch-point site consensus sequence
- U4/U5-U6 triple snRNP enters the reaction and once the U4/U6 base pairs are separated, U6 displaces U1 at the 5’ splice junction which creates the active site that catalyses the first phosphoryl-transferase reaction
- additional RNA-RNA rearrangements create the active site for the second phosphoryl-transferase reaction, which then completes the splice site
What does U1 RNA contain?
- several distinct stem-loop domains
- 8 core Sm proteins and 3 U1-specific proteins
What are Sm proteins?
8 common proteins constituting the core structure of snRNPs
What is Sm binding site required for?
interaction with common snRNP proteins
What is recognition of consensus sequences important for?
to ensure the accuracy of the position for RNA splicing
What are the 2 common types of splicing errors due to imperfect RNA pairing?
- exon skipping
- cryptic splice-site selection
How can splicing errors be minimised?
- coupling splicing to transcription to avoid exon skipping
- exon definition
What is the exon definition hypothesis?
the exon is bound by a group of SR proteins that serve as splice enhancers; they recruit U1 and U2 to define 3’ and 5’ exons respectively
What are SR proteins?
proteins rich in Ser and Arg
How are introns packaged into complexes?
by hnRNPs (heterogenous nuclear ribonucleoproteins)
What does abnormal processing of the β-globin primary RNA transcript in humans produce?
aberrant β-globins causing β-thalassemia disease
What are consequences of aberrant splicing?
- deletion or addition of amino acid sequence
- change of reading frame
- truncated protein due to premature termination codon
What does differential RNA splicing do?
increase product diversity
What are products of differential splicing?
- C-terminal truncation due to a premature termination codon
- change of reading frame
- missing of an internal part
- differential translation start sites
What are ways to generate multiple proteins from the same gene?
- alternative promoters but producing the same protein
- overlapping genes using different reading frames
- different N-termini using alternative promoters
Where is the polyadenylation termination signal?
10-30 nt before the polyA tail
What are the 5 steps of transcriptional termination?
- CstF and CPSF travel with RNAPII during transcription
- CPSF binds to the polyA signal and CstF binds to GU/U rich region
- cleavage occurs with additional cleavage factors to create 3’ end
- PAP adds ~200 A nucleotides to the 3’ end
- poly-A binding protein to aid polyadenylation and protect RNA from degradation
What is CstF and CPSF respectively?
- CstF = cleavage stimulation factor
- CPSF = cleavage and polyadenylation specificity factor
What does differential polyadenylation determine?
if an antibody is membrane-bound or secreted
What does increased CstF in activated B cells do?
cleave at the weak site to generate a short Ab without the membrane bound region
What does nuclear export receptor do?
guide the RNA to nuclear pore complex for export
What percentage of RNA is transported to the cytoplasm as a protein-RNA complex?
<10%
What does nonsense-mediated mRNA decay (NMD) do?
degrade newly synthesised mRNAs with a premature termination codon to prevent the production of truncated proteins that could result in disease
What happens in the first round of translation?
the ribosome removes EJCs to allow normal mRNA to continue onto translation
How do exon junction complexes (EJCs) activate NMD?
by binding to Upf
What are possible fates of mRNA after exportation?
- translated immediately in cytosol (common)
- directed to ER for synthesis of membrane and secreted proteins (common)
- sequestered in specific intracellular locations prior to translation (specific to certain mRNAs)
Where is the signal for mRNA localisation present?
in the 3’ UTR
What are the 2 main types of RNA editing?
- A to I affecting ~1,000 human genes
- C to U
What does an RNA editing complex do?
recognise a specific target sequence and/or secondary structure via its deaminase activity
What does RNA editing affect?
- protein sequence
- RNA splicing
- transport
- translation efficiency
