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Eukaryotic Genes and Genomes > Non-coding RNA > Flashcards

Non-coding RNA Flashcards

1
Q

Give a summary of the different roles filled by non-coding RNA.

A

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

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2
Q

What does catalytic RNA do?

A
  • Endonucleolytic cleavage
  • Splicing

Catalytic RNA = Ribozyme

  • cleavage or joining of phosphodiester bonds
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3
Q

What does regulatory RNA do?

A

interacts with target through basepairing

  • long ncRNAs. xist
  • small: miRNA, esiRNAs, piRNA
  • short bacterial
  • riboswitches
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4
Q

rRNA

A

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
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5
Q

snRNA

A

Small nuclear RNA (splicing)

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6
Q

snoRNA

A

small nucleolar RNA (modification)

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7
Q

tRNA

A

transfer RNA (translation)

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8
Q

miRNA

A

micro RNA (regulation)

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9
Q

siRNA

A

small interfering RNA (regulation)

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10
Q

esiRNA

A

endogenous siRNA (regulation)

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11
Q

piRNA

A

piwi interacting RNA (regulation)

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12
Q

sNRA

A

small RNA (bacteria, regulation)

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13
Q

What are ribozymes and what reactions are they involved in?

A

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
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14
Q

hammerhead ribozymes

A

Catalytic RNA that perform self cleavage

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15
Q

What is RNA editing? What types of reactions are involved?

A
  • 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
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16
Q

Give som examples of RNA editing.

A

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
17
Q

RNA modification

A
  • common
  • post transcriptional
  • more than one hundred different types described
  • different enzymes are involved, som use guide RNAs
18
Q

What are guide RNAs? In which processes are they involved?

A
  • 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
19
Q

List the 4 different types of regulatory RNA

A
  • Riboswitches
  • Log, non-coding RNA
  • Short bacterial RNA
  • short eukaryotic RNA (esiRNAs, miRNAs, piRNAs)
20
Q

How does regulatory RNA interact with it’s targets?

A

Through base pairing

21
Q

What are riboswitches?

A
  • 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
22
Q

Give an example of a riboswitch.

A

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.

23
Q

How big is long ncRNA?

A

> 200 nt

24
Q

Give some examples of how genes can be regulated by long ncRNA in eukaryotes.

A

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

25
Q

Differences between sRNA and short eukaryotic RNA

A

Prokaryots: RNA-RNA interactions, bigger 50-200 nt
Eukaryotes: RNA-protein interactions, smaller 30-30 nt

26
Q

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.

A
  • miRNA, piRNA, esiRNA

- associate with argonaute family proteins

27
Q

What are argonaute proteins? Which two subfamilies exist? How do AGO proteins exert their function?

A
  • 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)

28
Q

Which domains exist in AGO proteins?

A

Three domains: PAZ, MID, PIWI

29
Q

Biogenesis miRNA

A
  • 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
30
Q

Biogenesis piRNA

A
  • 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!
31
Q

Biogenesis esiRNA

A
  • 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
32
Q

what is the function of snoRNA and where is it found?

A

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

33
Q

Altman and Czechs discovery

A

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

Eukaryotic Genes and Genomes (9 decks)

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