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MCD Nucleic Acids And Gene Expression > 5 Small RNAs In The Regulation Of Biological Processes > Flashcards

5 Small RNAs In The Regulation Of Biological Processes Flashcards

1
Q

Q: Define C-value. What is the C-value paradox? Does C-value relate to the complexity of an organism?

A

A: genome size

There is a constant amount of genetic material in cells from the same species

no, not necessarily

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2
Q

Q: What are ncRNAs? What does it not include? What does it include?

A

A: non-coding RNAs = Any RNA molecule that is NOT TRANSLATED into a protein. (i.e. does not include mRNA)

This category includes house keeping ncRNAs

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3
Q

Q: Give examples of housekeeping ncRNAs? (7)

A 
A: rRNA ribsomal
tRNA transfer
snRNA small nuclear
miRNA micro
siRNA small interfering
piRNA piwi-interacting
Long ncRNA long non coding
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4
Q

Q: What is miRNA? (5) found? (3) Functions in? (2) What does miRNA control?

A

A: small non-coding double stranded RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression

control the translation of most genes

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5
Q

Q: What is siRNA and RNAi? (3) Similar to? Role?

A

A: double-stranded RNA molecules, 20-25 base pairs in length, similar to miRNA, and operating within the RNA interference pathway (RNAi= process)

act as defence against virii, experimental tool

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6
Q

Q: What is piRNA important for?

A

A: germ cell production (endo-siRNAs)

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7
Q

Q: What is an example of long ncRNA being important?

A

A: X chromosome inactivation

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8
Q

Q: What is antisense RNA a tool for? How? (4)

A

A: tool to block mRNA function

If there is a gene you want to block, you can transcribe a reverse of the gene to make an ANTISENSE RNA STRAND

The antisense and sense RNA strands will hydrogen bond to form a double strand.

Therefore, sense RNA cannot be translated.

This forms Double Stranded RNA (dsRNA)

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9
Q

Q: What is RNA silencing used by? How?

A

A: plants as a defence mechanism against viral infection- Plants make siRNA from virus RNA -> cause these to degrade

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10
Q

Q: What is the experimental support for small non-coding RNAs in gene regulation?

A

A: dsRNA is the silencing trigger in C. elegans. It switches off genes

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11
Q

Q: RNA interferance (RNAi) Overview.

A

A: Double stranded RNA is used to produce siRNA which inhibits RNA that the dsRNA is derived from

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12
Q

Q: What is dsDNA derived from?

A

A: virus

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13
Q

Q: Explain RNA interference RNAi. (3)

A

A: RNA interference

  1. dsRNA derived from virus is broken up into 21-25bp fragments by ‘dicer’
  2. endonuclease activity acts to remove one of the siRNA strand known as the passenger strand. Requires ARGONAUTE-PIWI PROTEINS (AGO). The strand that is retained is antisense to the target strand
  3. Multiprotein, RNA-induced silencing complexes or RISC complexes are formed. They recognise and cleave target mRNA molecules which have complementary sequences to the incorporated single-stranded guide siRNA

sliced mRNA = silenced

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14
Q

Q: What is ‘dicer’? (2) What would happen without? why? (2)

A

A: Dicer is an Rnase III like endonuclease activity

Dicer is an essential gene.

Without dicer, there would be lethality in early embryonic stages because embryonic stem cells are unable to differentiate leading to a depletion of multipotent stem cells

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15
Q

Q: What are Genomically Encoded shRNAs: Micro RNAs? use?

How can shRNA be expressed? (3)

A

A: small hairpin RNA is an artificial RNA molecule with a tight hairpin turn that can be used to silence target gene expression via RNA interference (RNAi).

Expression of shRNA in cells is typically accomplished by delivery of plasmids or through viral or bacterial vectors

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16
Q

Q: How are miRNAs made? (4) What do they go on to do?

A

A: miRNAs are not made as very small RNAs. They are made as much bigger RNAs called pri-miRNAs and pre-miRNAs.

Pri-miRNA is processed and chopped up a little and is exported into the cytoplasm as pre-miRNA.

become mature miRNAs by Dicer an RNase III type protein

and loaded onto the Argonaute (ago) protein to produce the effector RNA-induced silencing complex (RISC)

Once the pre-miRNAs become miRNAs they can target genes at an RNA level and silence genes (control other genes)

17
Q

Q: Where can alteration in ncRNA or miRNA expression be seen?

A

A: in many diseases e.g. leukemia, carcinoma,heart disease

18
Q

Q: What’s the difference between miRNA and siRNA?

A

A: siRNA can inhibit the expression of one specific target mRNA

miRNA regulates the expression of multiple mRNAs

19
Q

Q: What did Ambros and Ruvkun discover when they were working with C. elegans? (6) (What were they looking into?) Main point? (2)

A

A: Lin-14 is a protein that they were looking into. They found that:

  • RNA production for Lin-14 persists throughout development
  • Protein production for Lin-14 disappears pretty early in development.
  • They made more mutants which give the same phenotype but not lin-14 mutants.
  • They found a separate set of genes which also controls the loss of protein and called them Lin-4.
  • They looked closely at Lin-4 but they couldn’t find any genes.
  • They found that Lin-4 was a microRNA which can bind to Lin-14 mRNA and stop it from making proteins.

MAIN POINT: There are miRNAs in the genome that are involved in regulating other genes. It’s another level of gene regulation

20
Q

Q: What is gene knockdown?

A

A: = decreasing the amount of protein you get from a gene

21
Q

Q: How do you know where miRNA genes are in a genome? What can they be turned into?

miRNA bioinformatics

A

A: It’s relatively easy to see where miRNA genes are. You usually have two matching areas separated by a bulge.

Classically miRNAs are arranged as a sequence-mismatched sequence-sequence or MATCH-BULGE-MATCH.

It can fold over to form the shRNA.

Mismatches, usually in the centre form a bulge, often followed by a less stringent degree of complementarity in the 3’ region

22
Q

Q: What is the ‘seed region’ in terms of miRNA? Where?

A

A: most important region of the miRNA for targeting. Lies between nucleotide positions 2 to 8 from 5’ end and is often flanked by adenosines

23
Q

Q: Where do the vast majority of known miRNA target sites lie?

A

A: The within 3’ UTRs (untranslated region)

24
Q

Q: What does deletion of part of gene on chromosome 14 leads to? How was it used to illustrated the power of miRNA as a therapeutic?

A

A: loss of miRNA and promotes CLL = Chronic Lymphoid Leukoemia (CLL)
By supplementing the miRNA to nude mice who have CLL, you can get rid of the cancer

25
Q

Q: What are the 3 modes of action of miRNAs?

A

A: miRNA degradation
translational regulation
transcriptional regulation

MCD Nucleic Acids And Gene Expression (8 decks)

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