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Flashcards in RNA Processing Deck (72):

What is RNA made up of?

- Ribose sugar ( 5 carbon sugar)
-a base - A,G,C,u
- 2 hydroxyl group (OH) - key feature of RNA
- Phosphodiester backbone


Why is the 2 Hydroxyl Group important ?

- it acts as a nucleophile to break the phosphodiester backbone in RNA
- if there was a lack of a 2 ' hydroxyl group it makes the DNA chemically stable.


How is genetic information in prokaryotes trasnferred from genes to proteins?

- this is done via a 'messenger ' RNA (mRNA) which is a direct copy of the DNA gene seduence.


How does eukaryotic protein coding occur?

- most genes in higher eukaryotes have their protein coding information interrupted by non- coding ' intervening' sequences called Introns. ( every gene in cells has many introns !)
the sequence expressed are called Exons.


What are the coding and non coding parts of DNA called?

introns - non coding
exons- coding expressed


Why are eukaryotic genes split ?

- Eukaryotic genes contain introns and the protein coding regions of the genes are thus not continuous !

- in lower eukaryotes - (e.g. Yeast) only a small fraction of genes have introns which are usually located near the 5' end of the gene.

- in multicellular eukaryotes ( including insects) , mammals and plants - most genes have introns which can occur throughout the gene in both protein coding and non coding regions


Why must introns be removed?

- the introns often contain STOP codons that would prematurely terminate translation
- even it no STOP codons are present the intron sequence may shift the translational reading frame of downstream exons.

-sequence of intron regions vary more than protein coding regions!


Why is splicing essential in Eukaryotes?

- splicing is when introns are removed , and exons are joined together

- splicing inhibited = cells stop growing and die because they cant make new proteins !

- RNA splicing is also essential for the growth of most eukaryotic viruses - most viral genes have introns which are removed by the cellular splicing machinery

- the reason that splicing was discovered was because researchers were studying the adeno virus.

- bacteria DO NOT require RNA splicing to make proteins - no known natural antibiotic blocks splicing.


why is it not as simple to say ' one intron to one gene'?

- because in higher eukaryotes ( including humans) most genes contain multiple introns

- usually all introns must be removed before the mRNA can be translated to produce protein.

However multiple introns may be spliced differently in different circumstances - e.g. in different tissues. ( proteins encoded do not have to identical)

therefore one gene can encode more than one protein!! - the proteins are not identical and may have distinct properties ( this is very important in complex organisms)
- multiple introns do NOT have to be removed in the same pattern.
- introns are recognised independently
( ribosomal processing occurs)


what is Recursive Splicing in Drosophila ?

- the removal of introns by sequential re-splicing at composite 3'/5' spli.e sites


What is snoRNA?

- small nucleolar RNA
- small group of RNA
- they guide chemical modifications of other RNA ( mainly rRNA ,tRNA etc)


are stop Introns just junk ?

- No they may play an important role in cell development - even though they don't code for any instructions.


What are the two types of snoRNA ?

- C/D Box snoRNA
- H/ACA box snoRNA


What are the functions of snoRNA?

-gene expression
- alternative splicing
- stress
- processing of different RNA


What is the role of intron sequences?

-not all introns are junk sequences

-same RNA sequence can act as an intron in one transcript and an exon in another transcript.( depending on the alternative splicing pattern)

- some introns contain functional RNA products that are processed out of the intron sequence after splicing ( e.g. miRNAs and snoRNAs

- most snoRNAs and a large fraction of miRNAs are encoded in introns of RNA polymerase 2 transcripts.


What is the Spliceosome ?

- splicing of introns from pre-mRNA's is catalysed by the ' spliceosome' - an RNA protein - complex!
- it has 300 proteins and 5 small RNAs
- the premRNA goes into it and comes out spliced mRNA
- it functions in the nucelus
- splicing works similarly in different organisms (e.g. yeast ,flies, worms, animals , humans , plants )
the spliceosome is like a ribosome but functions in the nucleus - NOT the cytoplasm!!


How are introns recognized?

- splice site consensus sequences.


What is similar between introns?

- most introns have the same general structure and are removed by the same splicing machinery - the major spliceosome


give an example of the splicing of a small subset of introns?

- a small subset of introns - called 'AT-AC' introns have a different consensus sequences and are recognised and removed by a separate splicing machinery - the 'minor' spliceosome


There re two types of spliceosomes?

- the major spliceosome ( most introns have same general structure so use the same splceosome )
- the minor spliceosome ( a small subset of introns - 'AT-AC' use a different splicing machine.


What are snRNPS ?

- RNA- protein complexes snRNPs ( pronounces snurps) are the major sub units of the spliceosome
- the recognition of splice sites in mRNA precursors involves a complex set of RNA-RNA base pairing interactions between the intron branch point and intron-exon junctions and specific regions of complimentary RNA sequence in the Trans-acting snRNA components of the spliceosome snRNP subunits


How are introns recognised?

- intron recognition can occur by spliceosome snRNAs


What experimental evidence is there for base pairing between snRNAs and Intron sequences?

- experimental evicence for base pairing between snRNAs and intron sequences comes from both biochemical RNA X- linking data and from genetic compensatory mutation studies where intron mutations that block splicing are rescued by expressing suppressor mutations in snRNAs that restore sequence complimentarity with the mutant intron sequence.

- further evidence for base pairing between SnRNAs and intron sequences comes from the phylogenetic conservation in snRNA - intron sequences.

- even if sequences are different in species they can coevolve!


What the two steps in which introns are removed?

- splicing is a pre-mRNA and involves two sequential reactions - both of which are catalysed by the spliecosome

getting from step one to step two require intermediates !!!!

splicing step 1:
- trans - esterification
this is when the 2 - hydroxyl group of the branch site A residue attacks the phosphodiester bond between exon 1 and the 5' end of the intron.
( refer to page 7 of lecture 1 of RNA processing)

Splicing step 2:
- trans esterification
this is when the 3' hydroxyl group ( which was liberated by the first step) of the terminal ribose of the free 5' exon attacks the phosphodiester bond between the 3' end of the intron and the adjacent exon

(refer to page 8 of lecture 2 notes on RNA processing)


What are the products of the pre-mrna splicing?

- spliced mRNA
- intron lariat


What is the overview of the spliceosome cycle?

- the assembly of spiceosomes is dynamic
- the assembly of spliceosomes occurs on nascent premRNA in vivo - introns can be removed before the RNA polymerase has completed transcription of the gene !
- a seperate spliceosome assembles independently on each intron in a pre- mRNA - introns need not be removed in a 5' to 3' order
spliceosomes do not move along the pre-mrna removing each intron in turn


What energy is required for splicing?

- the splcing reaction is known as isoenergetic ( e.g. the two transesterification reactions swap phosphodiester bonds with no overall change in the number of chemical bonds formed or broken, in principle the chemistry of the splicing reaction therefore does NOT require energy !

- however the splicing reaction does require energy which is provided via coupled hydrolysis of ATP.

- energy is required to drive multiple assembly steps during the assembly of the spliceosome.

- this includes energy needed to ' remodel' the complex patterns of RNA-RNA base pairing between snRNAs and between snRNAs and pre-mRNA sequences- which change dynamically during the spliceosome cycle.


Do different eukaryotes have different numhers of protein coding genes ?

- YES !
- species with vastly different complexities have a comparable number of protein coding genes.
- in eukaryotes we have 1 gene to many proteins


alternative pre-mRNA splicing ?

- it is a frequent event in mammalian cells
- major mechanism for generating protein isoforms !
- genes coding for tens to hundreds of isonforms are common !
- 95% of human pre-mRNAs are alternatively spliced.


What is the alternative splicing pattern - of exon skipping?

- it is common to skip the exon - so one exon not joining to intron but instead the next exon!


what are the main alternative splicing patterns?

- mutually exclusive exons
- alternative 3'ss
- alternative 5'ss
- exitrons
- alternative promoters
- alternative polyadenylation
- intron retention


What are the function and consequences of alternative splicing?

***insertion/loss of protein sequences that affect:
- nucelic acid binding/ recognition
-protein targetting/stability
-protein-protein interactions
- post translational modifications and associated activites

*** major mechanism generating protein isoforms

*** regulation of at the level of RNA
- altering function of UTR sequences: RNA trafficking and stability

*** control of gene expression levels via couples NMD

*** on a global scale:
- modulating functions of entire networks of genes taht operate in specific pathways and processes
- cell type and organ specific differences
- specific - specific differences


Why is alternative splicing important for modulating mRNA expression?

alternative splicing events can modulate mRNA expression levels by introducing premature termination codons (PTC) that trigger 'NONSENSE MEDIATED mRNA DECAY' (NMD)

- this is important because 10% of alternative exons may regulate transcript levels via NMD

retention of the intron introduces a premature stop codon - recognition of this premature stop triggers destruction of the RNA by the NMD machinery
- normal stop codon downstream of protein coding sequences


What is a major mechanism for creating protein isoforms from a single gene?

- alternative splicing


coregulation of miRNA biogenesis and alternative pre-mRNA splicing of host gene ...

- a large fraction of miRNA's are encoded in introns of RNA polymerase 2 transcripts
- the production of mature mirNA occurs through a series of processing steps beginning with the cleavage from the primary transcript by the microprocessor complex.
- proteins of the spliceosome and theh microprocessor complex have been shown to be physically and functionally associated.


What does alternative splicing regulate?

iit regulates the biogenesis of miRNAs located across exon-intron junctions.

- dozens of miRNAs have been shown to be located across active splice sites
- evidence that biogenesis of pri-miRNA located across splice sites are regulted by alternative splicing (e.g. splice site overlapping miR-412)

- mechanism of regulation:
- competition of tthe microprocessor and the spliceosome for processing the same RNA loci


What is needed by embryonic stem cell pluripotency?

- an alternative splicing switch controls transcriptional networks required for embryonic stem cell (ESC) pluripotency


What does regulated alternative splicing represent?

- a distinct layer of gene control


How do we systematically analyze alternative splicing patterns and compare them between different types of cells , organs and species?

- mining tissue regulated alternative splicing events using RNA sequence
- RNA - sequence profiling - alternative splicing (AS) in physiologically equivalent organs from vertebrae species spanning 350 million years of evolution.
- comparing AS complexity between the species using RNA sequence

( N.B primates do more alternative splicing than other species , especially in the brain and nervous system - alternative splicing techniques added to complexity in brain systems.


What is the statistic of splicing mutations and diseases?

- 15% of human diseases are caused by splicing mutations !


what do you know about mutations affecting specific genes ?

- mutations affecting specific genes - disturbs normal splicing patterns.
e.g. Cystic fybrosis , Duchenne muscular dsytrophy, B- thalassemia ( these are all inherent diseases)

- a single nucleotide difference alters ability of cell to recognise splice site !
- frequent exon slipping occurs - causing the diease...( e.g. Duchennes)
- altered ratios of alternatively spliced isoforms - many cancers


Splicing factors as proto-oncogenes?

SFRS1 (ASF/SF2) - proto oncogene
- over expressed in many tumour types

hnRNP A2/B1 - proto oncogene
- potent oncogene in glioblastoma development and tumour maintenance


Mutations affecting proteins involved in splicing?

- spinal muscular atrophy (e.g. major mutation inversion would cause infant mortality - affects muscles)
- retinitis pigmentosa
- myotonic dystrophy


What is a summary of SMA ( spinal muscular atrophy) ?

- SMA is the number one genetic cause of infant mortality
- about 10-16 out of every 100,000 children are born with SMA
- SMA causes weakness and wasting of muscles throughout the body


What are the three types of SMA?

type 1- severe
- onset evident from birth - problems eating , breathing etc

Type 2- intermediate
- onset between 6-18 months -not able to sit , stand or walk

Type 3- mild
- onset - 2-17 years - difficulty walking , or standing up from sitting, balance problems.


Developing thearpeutiic agents for splicing correction of SMA?

- druglike molecules added to increase concentration, and so cell solving machinery can be observed.

both the regulation of alternative splicing and the specificity of Intron recognition is mediated by the binding of specific trans- acting splicing factors to cis-acting RNA sequence elements.


What does Nova do?

- Nova regulates 7% of neural specific AS events
- the location and density of NOVA binding sites determine whether NOVA promotes exon inclusion or exon skipping ! - so many binding sites on exons and introns for NOVA.


What is caused by regulation of Pre mrna splicing?

- regulation of alternative splicing imposes requirements for signals that modulate splicing .

sequence elements within exons and introns control splice site selection!


there are two types of signals for modulating splicing - what are they?

- exonic splicing enhanver (ESE) usually purine rich and bound by SR proteins
-intronic splicing enhancer (ISE)

- intronic splicing silcencer (ISS) : PY rich and bound by hnRNP family (e.g. PTB)
- exonic splicing silencers (ESS) - not yet well charachterised !!!

these either activate or repress certain splices !


What is the importance of pre-mRNA intron Consensus sequences?

- no extensive sequence conservation of introns - only short conserved sequences at junctions and to some extent the positiions of sequence elements are conserved.

mutagenesis confirms importance of these sequences.

( refer alot to lecture 3 - RNA processing !!!)


What is the spliceosome composed of?

- 5 snRNPs (snRNA plus associated protein factors)- multiple RNA subunits

U1,U2,U4,U5,U6 ( in certain cases U1 and U2 , are replaced by U11, U12 )

- 200 polypeptides

initial recognition of the intron involves base pairing between U1 snRNA at the 5' intron-exon juncttion and between U2 snRNA a the branch site


What is the synamic pre-mRNA /snRNA interactions during spliceosome assembly ?

- snRNA -pre - mRNA base pairing interactions change as spliceosome assembly proceeds
transistions in base pairing require energy in the form of ATP hydrolysis

n.b. Prp8p- important protein component


is precision important in splicing ?

- splicing needs to be exact ! otherwise it interrupts the splicing ! ( no room for nucleotide mutations!!!!)


What is meant by splicing fidelity ?

- the rate of transcription through each conformational state is linked to ATP hydrolysis and is in competition with substrate rejection.


What controls splicing site selection?

- sequences within exons , introns and bound trans-acting factors control splice site selection.


What do silencers and enhancers promote?

- enhancers promote inclusion of an alternative exon
- silencers promote skipping of an alternative exon


How does enhancer and silencer motifs in exons and introns function?

- enhancer and silencer motifs in exons and introns function to specify correct pairs of splice sites and regulate alternative splicing


give a few examples of proteins importance for splicing ? ( these are known as splicing factors )

- SR proteins ( serines in RS repeats are subject to regulated phosphorylation/ dephosphorylation
- hnRNP proteins ( highly abundant proteins in the cell !!)


What are zinc fingers?

-a finger-like loop of peptides enclosing a bound zinc ion at one end, typically part of a larger protein molecule (in particular one regulating transcription).
- made up of histidines


What are transformer proteins?

- they regulate sex determination in proteins


what do you know about the SR family and the SR related proteins (e.g. RS)?

SR proteins are generally widely expressed but vary in relative levels between different cell and tissue types
- SR domains can react together to cause protein >> protein related domains !!!

the RS domain = rich in alternating Arg/ Ser residues - expressed in different tissues.
- RS domains interact with each other and with pre mRNA during spliceosome assembly
- differential phosphorylation of RS domains via upstream signalling , pathways affects SR protein localization and function.


What differences do we see with exons and introns in higher eukaryotes?

- introns are often much longer than exons and then the unit of initial recognition / definition by the splicing machinery may be the exon rather than the intron.

ESE= exon splicing enhancer- these are usually purine-rich sequences and are bound by SR proteins.

- if you look at average length of exons and introns - they are not the same - exons are usually smaller than introns! a few introns can vary over enormous size 60-70 nucleotides to 10,000 nucleotides !!
there is a big size difference between exons and introns.

N.B. alternative splicing is very important in brain cells.!


what is the relation between splicing enhancers and exons?

- splcing enhancers promote exon definition

exon definition is important for mammalian transcripts with long introns.

exon definition can be inhibited by intron silencers !


What antagonises exon definition?

- PTB - polypyrimidine tract binding proteins
- neaural cells produce higher levels of nPTB ( neurone specific PTB) whcih promotes the inclusion of the N1 exon
- other splicing activators are involved including members of the FOX family- these bind to enhancer elements downstream of the N1 exon to stimulate its splicing!


What is the relationship between sex determinination in drosophila and RNA splicing?

- sex determination in drosophila is regulated through RNA splicing.

N.B. Sxl is an RNA binding protein and promotes female specific splicing of its own transcript.- functional Sxl protein is only produced in females.


What is negative and positive control of alternative pre-mRNA splicing?

negative control - is when a repressor is involved (e.g. sex lethal regulates splicing of tra intron 1)

positive control- is when an activator is involved

( could be in exam !! so refer to page 7 of lecture 3 of RN processing notes)


what is the important role of alternative splicing in gene expression?

- interpreting genomic information in terms of protein production depends on how transcripts are spliced under different circumstances.

- bioinformatic analyses are identifying ' splicing codes' that allow predicitions to be made based on RNA sequence elements - but this alone is insufficient to explain all of the specificity and much remains to be learned


What regulatory elements and alternative splicing do you know?

- RNA binding proteins can mediate long range interactions between splice sites and can either stimulate or inhibit the selection of specific intro-exon junctions.


How does pre- messenger RNA processing occur?

- pre -RNA processing occurs with difference processes all coodinated !


What is co-transcriptional splicing?

the splicing mechanism often occurs co-transcriptionally so that splicing factors assemble on the pre-mRNA as it emerges from RNA polymerase 2 (RNAPII)

- a coupling of transcription and pre mRNA is seen !


Can the rate of transcription influence splice site selection?

- Yes - a fast RNAPII that transcribes both a weak and a proximal and strong distal
- exon skipping will occur as the two will compete and the stronger one can be used despite the fact that it is more distal than the weak one!

Kinetic coupling:

- if the RNAPII is slow - ( refer to page 9 of lecture 3 of RNA processing)

The rate of transcription can influence splice site selection
the ability of RNA to fold in different ways may also be affected by the rate of transcription and may in turn affect splice site recognition!


What is the correlation between nucleosome density and introns/ exons ?

- nucelosome density is higher on exons and depleted over introns
nucleosome enrichment is inversely correlated with strength of splice sites.

- exons are found to be rich in ( GC0 rich ) sequences favoured by nucleosomes and introns contain features at their ends that disfavour nucleosomes assembly - this pattern is conserved from worms to humans

N.B. individual steps in gene expression are highly coordinated and can influence each other.