Gerber L4 Non coding RNAs

Question 1

what was the first non coding RNA to be characterised

Answer 1

tRNA-Phe

tRNAsdecode the mRNA sequence during protein synthesis at the ribosome

Question 2

what is the most abundant RNA in cells

Answer 2

rRNA
80%
- transcribed by RNA Pol I (except 5S by Pol III)
- rRNA is processed in the nucleolus

Question 3

ribosome subunits size/

and which rRNA

Answer 3

40Ssubunit > 18S rRNA 60Ssubunit > 5S, 5.8S, 28S

Question 4

what is the full form and function of snRNAs

Answer 4

small nuclear RNAs

• important in splicing pf pre-mRNA (U1,2,4,5,6)
• base pairing with and pre mRNAs defines splice-sites
• Additional regulatory functions: telomer maintenance, transcription factors
• evolutionarily conserved
• highly expressed (1m)

Question 5

what is the full form and function of snoRNAs

Answer 5

small nucleolar RNAs

• 200 different species in mammals
• 2 types: C/D box:
  1) directs 2’-O-ribose methylation by recruiting a methyl transferase enzyme
  2) H/ACA box: recruits an enzyme that converts uridine to pseudouridine
• help to process and chemically modify rRNAs in NUCLEOLUS

Question 6

what %of the genome is transcribed

Answer 6

80%

Question 7

what is the role of miRNAs and siRNAs

Answer 7

miRNAs: regukate gene transcription by blocking translation of specific mRNAS, causes their degradation

siRNAs: small interfering RNAs, turn off gene expression by directing spexific mRNA degradation

they both bind to COMPLEMENTARY 3’-UTR seq in mRNA forming (RNA INDUCED SILENCING COMPLEX)

Question 8

how do miRNAs repress translation

Answer 8

by imperfect hybridisation with target mRNAs in cytoplasm

- nt 2-7 form the “SEED” seq that is important for targetting 3’ UTRs

Question 9

what is the difference between siRNAs and miRNAs

Answer 9

miRNAs use iimperfect hybridisation

Question 10

how do siRNAs repress translation

Answer 10

cleave mRNAs upon PERFECT hybridisation

• defense mech against invading dsRNA viruses and transposons/ repetitive elements expressed from the genome
• invading dsRNA is processed into siRNAs that then targets the invader mRNAs for degradation
• siRNA defense mechanism are crucial in plants, worms and insects, less in mammals where a proteinbased system to fight viruses

Question 11

how are miRNAs and siRNAs generated in cells

Answer 11

1) RNA Pol II makes primary miRNA transcripts, primary miRNA
2) DROSHA (endonuclease) cleaves pri-mRNA generating ~70nt long precursor miRNA (precursor miRNA)
3) pre miRNA EXPORTED via EXPORTIN-5 to cytoplasm
4) DICER processed pre miRNA to double starnded miRNA
5) RISC complex binds one of the 2 strands and assembles with mRNA target (with argonauteproteins). The other strand is degraded

Question 12

what does Dicer gene knock out cause

what does conditional dicer knock out cause

Answer 12

eliminates miRNA generation in mammals, is lethal to embryos
- “conditional” Dicerknockout in limb primordia leads to defects in tissue morphogenesis/ developmen

Question 13

what genes do miRNAs control

Answer 13

cell prolif
development
inflammation
ageing

Question 14

what diseases have miRNAs been linked to

Answer 14

cancer
drug target?
as we can see miRNA expression signatures, O can establish cancer markers

Question 15

what is a lncRNA

Answer 15

long non coding RNA

Question 16

what is the function of lncRNA

Answer 16

• serve as scaffolds
• regulate diverse cell processes inc X-chromosome inactivation
• transcribed by Pol II mainly
• most cont 5’ cap and poly A tail at 3’
• not translated
• Tissue/cell-type specific expression; many of them of very low abundance (1-2 copies/ cell)
• Involved in many cellular processes, such as gene imprinting, cell differentiation and development, antiviral response

Question 17

where do lncRNAs work

Answer 17

nucleus and cytoplasm

Question 18

what do nuclear lncRNAs control

Answer 18

-chromatin structure/transcription in cis or trans

Question 19

how many lncRNAs are there

Answer 19

16,000

Question 20

what is cis lncRNA

trans

Answer 20

cis:
works on the same area (chromosome) that it is produced (XIST)
trans: have long range interactions on other chromosomes (HOTAIR)

Question 21

XIST

Answer 21

one of the first lncRNA discovered

• controls mammalian dosage compensation (one of the X chromosomes is silenced in women)
• binds to the X chromosome
• initiates histone modification: methylation and deacetylation, that results in HETEROCHROMATIN being formed
• DELETION of XIST abolishes X inactivation

Question 22

HOTAIR

Answer 22

• 2.2kb INTERGENIC RNA (lincRNA)
• capped and polyadenylated
• highly overexpressed on metastatic breast cancer
• associates with POLYCOMB complex 2 which is req for transcriptional silencing

Question 23

how do lncRNAs regulate mRNA stability

Answer 23

• the lncRNA TINCR (terminal differentiation-induced ncRNA > epidermal differentiation )interacts with STAU1 and targets mRNAcontaining TINCR box motif
• promotes STABILITY of the mRNA

Question 24

how do lncRNAs regulate and translation

Answer 24

Under stress conditions, the lncRNA antisense to Uchl1 moves from the nucleus to the cytoplasm and binds the end of the Uchl1 mRNA to promote translationunder stress conditions

Question 25

give an example of lncRNAs acting as a decoy

Answer 25

NORAD= noncoding RNA activated by DNA damage

• 5.3 kb polyadenylated transcript predominantly localised in the cytoplasm
• NORAD sequesters PUMILIO RNA binding proteins, O acts as NEGATIVE REGULATOR by limiting their availability to interact with mRNA targets
• control of CELL MITOSIS

Question 26

how can circRNAs act as decoys for

Answer 26

act as decoys for miRNAs/RBPs

• eg CDR1as
• generated by: BACK SPLICING, joining of 5’ and 3’ end of linear RNA molecules ORIGINATING FROM PROTEIN CODING GENES
• lack cap & poly A tail
• highly abundant
• fairly stable
• orginally thought to be non coding, but recently shown to be translated in Drosophila