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
Differences between sRNA and short eukaryotic RNA
Prokaryots: RNA-RNA interactions, bigger 50-200 nt
Eukaryotes: RNA-protein interactions, smaller 30-30 nt
Describe the three types of endogenous small RNAs that are found in eukaryotes; their biogenesis and how they exert their function. Also, point out some important differences between these types of RNA.
- miRNA, piRNA, esiRNA
- associate with argonaute family proteins
What are argonaute proteins? Which two subfamilies exist? How do AGO proteins exert their function?
- Ago and Piwi subfamilies
- Ago expressed ubiquotously, interacts with miRNA and siRNA, post-transcriptional regulators
- Piwi in germ cells, involved in transposon silencing
Three domains: PAZ, MID, PIWI
PAZ and MID anchors RNA, PIWI may posess slicer activity (can cleave target RNA)
Which domains exist in AGO proteins?
Three domains: PAZ, MID, PIWI
Biogenesis miRNA
- Generated from local hairpin structures by the action of two RNAase III-type proteins, Drosha and Dicer
- 22 nt
- ss
- function as guide molecules - base pairs with target mRNA
- binding usually leads to translational repression and exonucleolytic mRNA decay
- over 1/3 of human genes reported to be targets
- synthesized from stem loop structures
- found in both introns and exons, and coding and non-coding genes
- after processing of the first transcript in the nucleus, it exists as a pri-miRNA - a 33 nt stem loop structure
- drosha cleaves pri-miRNA in the stem, creating pre-miRNA
- pre-miRNA is transported to the cytosol where it is sliced by dicer and becomes a mature 21 nt miRNA
- then loaded onto the AGO containing RISC complex
- RISC has RNAase activity
Biogenesis piRNA
- Does not depend on dicer
- trancribed from intergenic repetitive elements, active transposons and piRNA clusters
- piRNA precursors then go through primary processing –> linear pathway in somatic cells
–> continues into ping-pong cycle in germ cells
piRNA first goes through primary processing
antisense precursor is the loaded onto MIWI where the precursor is used as a guide for cleaving sense retrotransposon transcripts, this generates the piRNA 5’ end which associates with MILI – it is the loaded onto MILI and leads MILI to cleave antisense retrotransposon transcripts which generates new antisense piRNAs with the 5’ end that is loaded onto MIWI. PING-PONG AMPLIFICATION LOOP!
Biogenesis esiRNA
- Derived from repetitve sequences, sense-antisense
pairs or long stem loop structures (long DS RNA) - cleaved by dicer 2 which associates with LOQS
- loaded onto AGO2
- dependent on Dicer, not Drosha
- 21 nt
- ubiquitously expressed (unlike piRNA)
- associates with AGO2 (not PIWI)
- differ from miRNA in that they are derived from long DS RNA and are only dependent on Dicer
what is the function of snoRNA and where is it found?
Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. Nucleolus
Altman and Czechs discovery
Catalytic RNA performs reactions involving cleavage or joining of phosphodiester bonds. Altman - the catalytic part of a ribonucleotid is RNA - RIBOZYME
Cech’s - self splicing of group I introns
