Non-coding RNA Flashcards
Give a summary of the different roles filled by non-coding RNA.
tRNAs - Transfer RNA (translation)
Structural RNAs - the RNA components of
- telomerase
- splicing factors
- signal reconition particle
- ribosomes
Regulatory RNAs
- large (usually >200 nt)
- small (20-30 nt)
- riboswitthches
Catalytic RNAs
- endonucleolytic cleavage
- splicing
Guide RNAs
- RNA editing
- RNA modificatipn
Catalytic
Regulatory
- x-chromosome inactivation/dosage compensation
What does catalytic RNA do?
- Endonucleolytic cleavage
- Splicing
Catalytic RNA = Ribozyme
- cleavage or joining of phosphodiester bonds
What does regulatory RNA do?
interacts with target through basepairing
- long ncRNAs. xist
- small: miRNA, esiRNAs, piRNA
- short bacterial
- riboswitches
rRNA
ribosomal RNA (transcription)
- constitutes between 80-90% of the total RNA in eukaryotic cells
- tandemly repeated
- precursors to the major rRNA are divided by non-transcribed spacers
- assembeled into ribosomes with proteins
snRNA
Small nuclear RNA (splicing)
snoRNA
small nucleolar RNA (modification)
tRNA
transfer RNA (translation)
miRNA
micro RNA (regulation)
siRNA
small interfering RNA (regulation)
esiRNA
endogenous siRNA (regulation)
piRNA
piwi interacting RNA (regulation)
sNRA
small RNA (bacteria, regulation)
What are ribozymes and what reactions are they involved in?
Ribozymes are catalytic RNA that perform reactions involving cleavage and splicing of phosphodiester bonds
- RNA can fold into 3D structures which therefore can form active sites
- Low catalytic rate, but may have high affinity
- Hammerhead ribozymes
hammerhead ribozymes
Catalytic RNA that perform self cleavage
What is RNA editing? What types of reactions are involved?
- post-transcriptional change(s) in the RNA sequence - information changes at the level of mRNA
- occurs in mammals
- involves deamination of cytidine to uridine and of adenosine to inosines
Give som examples of RNA editing.
Cytidine deamination - APOBEC:
- tissue specific
- leads to an early stop codon and a tuncated protein
Adenosine deamination - ADAR:
- edits glur-B mRNA
- adenosine to inosine leading to a change from Arg to Gly - changes the conductivity of the channel which changes ion flow
EXTENSIVE in humans
Happens in some trypanosomes:
- mRNA in the mitochondria
- removal or insertion of U residues
- information on how mRNA should be edited is found in guide RNAs
- catalyzed by the editosome: endonuclease, exonuclease, terminal uridyltransferase activity and RNA ligase
RNA modification
- common
- post transcriptional
- more than one hundred different types described
- different enzymes are involved, som use guide RNAs
What are guide RNAs? In which processes are they involved?
- involved in modification
- encoded in the introns of precursor mRNA
- functions as a template in trypanosoma - RNA editing, uridine
- Ribose methylation and pseudouridylation - guide RNAs, together with proteins, generate these modifications
- rRNA modification -gRNA has conserved sequences + sequences complimentary to the site which is methylated
- same for pseudouridylation
- in addition to rRNA snRNA are also subject to methylation and pseudouridylation
List the 4 different types of regulatory RNA
- Riboswitches
- Log, non-coding RNA
- Short bacterial RNA
- short eukaryotic RNA (esiRNAs, miRNAs, piRNAs)
How does regulatory RNA interact with it’s targets?
Through base pairing
What are riboswitches?
- A riboswitch is an RNA domain that contains a sequence that can change it’s secondary structure to control its activity
is an RNA whose activity is controlled by a small ligand - May be a ribozyme
- ## most common in bacteria
Give an example of a riboswitch.
Genet GlmS codes for an enzyme that synthesizes glucosamine-6-fosfat. mRNAet fra dette genet har en lang 5’ UTS før den kodene regionen i mRNAet - i denne 5’UTR er det et ribozym som er en endonuklease som kløyver sitt eget RNA. Den aktiveres av glucosamine-6-fosfat og på denne måten vil ribozymet kløyve mRNA og hindre translasjon når GlcN6P akumullerer i cellen. RNA domenet som binder liganden kalles APTAMER. Når aptamer binder ligand vil endonukleaseaktiviteten aktiveres.
How big is long ncRNA?
> 200 nt
Give some examples of how genes can be regulated by long ncRNA in eukaryotes.
Can be targeted to specific loci in the genome by several mechanisms:
- Base pairing with mRNA
- Base pairing with genomic DNA
- Formation of secondary structures that base pair with genomic DNA
- binding to a protein which show sequence specific DNA binding
- Heterochromatin formation (xist)
- transcriptional control - form triplex DNA at the DHFR promoter, which inhibits transcription factor binding
- post transcriptional processeing (splicing)
Some promote heterochromatin formation by recruiting the polycomb complex
An example is Xist
