20.1.10 Functional Noncoding RNAs

Question 1

Give 4 examples of functional non coding RNAs

Answer 1

• Ribosomal RNA (rRNA)
• Small nuclear (snRNA)
• Small nucleolar RNA (SnoRNAs)
• Transfer RNA (tRNA)

Question 2

How many rRNA molcules are there

Answer 2

• 5 molcules

- 5S, 28S, 5.8S, 16S, 23S

Question 3

What are cytoplasmic ribsosomes composed of

Answer 3

• Large 60S ribosomal unit associated with 28S, 5.8S and 5S rRNA
• Small 40S subunit associated with 18S rRNA.

Question 4

What are mitochondrial ribsosomes composed of

Answer 4

• 16S rRNA associated with small mitochondrial ribosomal subunit and
• 23S rRNA associated with the large mitochondrial subunit.

Question 5

Where is rRNA synthesised and where does biogenesis of ribosomes take place

Answer 5

Nucleolus

Question 6

Which rRNAs are encoded by a 13kb multigenic transcription unit

Answer 6

-18S, 5.8S, 28S

Question 7

Where is the 13kb multigenic transcription unit encoding 18S, 5.8S and 28S found

Answer 7

-On the short arms of acrocentric chromosomes (13, 14, 15, 21, 22)

Question 8

Which rRNAs are cleaved from H strand of mtDNA?

Answer 8

23S and 16S

Question 9

What are ribosomopathies

Answer 9

-Heterogeneous group of disorders that result from ribosome dysfunction.

Question 10

What is the disease mechanism in ribosomopathies

Answer 10

• Disrupted ribosome biogenesis leads to accumulation of free ribosomal proteins that bind the p53 suppressor MDM2, leading to activation of p53. This then causes increased apoptosis and cell death.
• or. Ribosomes from different tissues may have different compositions, which is critical to the translation of specific mRNAs.

Question 11

Examples of mutations in ribosomal proteins

Answer 11

• 5q minus syndrome (myelodysplastic syndrome) is due to haploinsufficiency of the RP514 gene.
• Diamond Blackfan anemia is an inheited bone marrow failure syndrome. Cuased by haploinsufficiency of the gene encoding RPS19.

Question 12

Examples of defects in ribosome biogenesis

Answer 12

• Treacher Collins syndrome is caused by AD mutations in TCOF1 or POLR1D or AR mutations in POLR1C/D. All expressed in neural crest cells and encode proteins involved in ribogenesis
• Shwachman Diamond syndrome is characterised by bone marrow failure, risk of MDS, AML. Caused by AR mutations in SBDS gene Leads to impaired maturation of large ribosomal subunit.

Question 13

What are spliceosomal small nuclear RNAs (snRNA)

Answer 13

• 106-186 nucleotides long and required for functioning of the two spliceosomes
• 9 human snRNAs
• Uradine rich

Question 14

What else is a spliceosome composed of

Answer 14

• snRNAs
• snRNPs (small nuclear ribonucleo proteins)
• non-snRNPs

Question 15

What are the two types of spliceosome

Answer 15

• Major U2- dependent

- Minor u12-dependent

Question 16

What is the major spliceosome composed of

Answer 16

snRNAs U1, U2, U4, U5, U6.

Question 17

What does the major spliceosome target

Answer 17

CU-AG introns in pre-mRNA splicing

Question 18

What is the minor spliceosome composed of

Answer 18

U4atac, U6atac, U11, U12

Question 19

What does the minor spliceosome target

Answer 19

Rare AU-AC introns.

Question 20

What are the two subclasses of spliceosomal snRNAs

Answer 20

• Sm-class

- Lsm-class

Question 21

What do sm class of snRNAs have

Answer 21

• They have a consensus Sm site, directs the assembly of a ring of 7 Sm core proteins.
• e.g. U1, U2, U4, U4atac, U5, U7, U11, U12

Question 22

What do Lsm-class of snRNAs have

Answer 22

Terminating stretch of uradines (Lsm site) that form the binding site for a ring of 7 Lsm core proteins.

Question 23

Examples of non-spliceosomal snRNAs

Answer 23

U1 and U2

Question 24

What function does U1 have

Answer 24

-Stimulates transcription by RNA Pol II

Question 25

What function does U2 have

Answer 25

-Stimulates transcription elongation by RNA Pol II

Question 26

Spliceosomes and disease. What autosomal recessive disorder is caused by mutations in RNU4ATAC

Answer 26

- Microcepahlic osteodysplastic primordial dwarfism type 1 (MOPD1). - Mutations alter secondary structure of snRNA

Question 27

How is spinal muscular atrophy linked to snRNAs

Answer 27

- SMN2 is needed for paturation of snRNPs. - SMN2 mutations lead to haploinsufficiency, causing a decifit in snRNP assembly capacity. - Consequently leads to spinal motor neuron death

Question 28

How is retinitis pigmentosa linked to snRNAs

Answer 28

- Autosomal dominant - 5% cases due to mutations in genes encoding protein components of snRNP complexes (PRPF31, PRPF8, HPRP3, PAP1, SNRNP200). - Mutations lead to death of retinal photoreceptor cells.

Question 29

What are small nucleolar RNA (snoRNA)

Answer 29

RNAs (60-300nt long) that have a function in RNA modification and processing

Question 30

What two classes of snoRNAs are there

Answer 30

- C/D box - H/ACA box - Based on their conserved secondary structures and associated modification reactions.

Question 31

What do C/D box snoRNAs do

Answer 31

-Sequence specific 2'-O-methylation fo rRNAs, snRNAs and tRNAs

Question 32

What do H/ACA box snoRNAs do

Answer 32

Pseudouridylation of rRNA to generate a mature product.

Question 33

What transcribes snoRNAS

Answer 33

RNA Pol II

Question 34

Are snoRNAs ubiquitously expressed

Answer 34

Yes (mostly, some are tissue specific)

Question 35

How is Prader-Willi syndrome linked to snoRNAs.

Answer 35

PWS is caused by loss of expression of C/D box snoRNAs encoded within paternally expressed SNRPN locus

Question 36

What are transfer RNAs (tRNAs)

Answer 36

- 75-95 nts. | - Transfer the correct amino acid to the ribosome during protein synthesis

Question 37

Where are tRNAs encoded

Answer 37

Nuclear and mitocondrial DNA

Question 38

What structure do tRNAs have

Answer 38

- Clover leaf - 3 hairpin loops: anticodon loop (3 nucleotides that base pair with mRNA), D-loop and T-loop - Mitochondrial tRNAs have a non-classical structure and a decreased melting temperature

Question 39

What chemical modifications do tRNAs get after synthesis

Answer 39

pseudouridine and dihydrouridine

Question 40

What synthesises tRNAs

Answer 40

RNA Pol III

Question 41

What is wobble base pairing (tRNAs)

Answer 41

-Third base of tRNA anticodon can form a hydrogen bond with more than one type of base at the 3' position of a codon

Question 42

Name two diseases caused by mutations in mitochondrial tRNAs

Answer 42

- MELAS (mitochondrial encephalopathy, lactic acidosis, stroke-like episodes) - MERRF (myoclonic epilepsy with raged red fibers). - Both conditions are associated with the failure to modify tRNAs with taurine.

Question 43

What causes MELAs

Answer 43

- MELAS (mitochondrial encephalopathy, lactic acidosis, stroke-like episodes) - MTTL1 gene mutations (mt-tRNALeu gene). - Causes a complex 1 deficiency

Question 44

What causes MERRF

Answer 44

- MERRF (myoclonic epilepsy with raged red fibers). | - m.8344A>G mutation in mt-tRNALys gene