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BI2132: Applications of Genetics > Gene Silencing > Flashcards

Gene Silencing Flashcards

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1
Q

Define epigenetics.

A

The study of changes in gene function that are heritable and that are not attributed to alterations of the DNA sequence.

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2
Q

Define gene silencing.

A

Any mechanism that switches a gene off without altering/mutating the DNA code. Not necessarily inherited.

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3
Q

What occurs during DNA methylation?

A

Cytosine is methylated at 5C.

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4
Q

What are the components of chromatin?

A

Histones + DNA.

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5
Q

What is euchromatin?

A

Chromatin that is loosely packaged (OPEN).

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6
Q

What is heterochromatin?

A

Chromatin that is condensed (CLOSED).

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7
Q

What is the function of N-terminal histone tails?

A

To modulate nucleosome structure and function.

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8
Q

What is a histone octamer?

A

The eight protein complex found at the centre of a nucleosome.

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9
Q

What is the histone code?

A

The theory that the transcription of genetic information encoded in DNA is partly regulated by chemical modifications to histone proteins, primarily on their unstructured ends. Part of the epigenetic code.

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10
Q

Is methylation or acetylation arguably more important?

A

Chemically, methylation is more stable than acetylation and is known to be less dynamic in cells.

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11
Q

What are transposons?

A

Fragments of repeating DNA that can insert into new chromosomal locations.

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12
Q

What % of the human genome is derived from transposons?

A

44%

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13
Q

What may have been the driver of the evolution of epigenetic mechanisms?

A

The need to silence foreign DNA such as transposons and viruses.

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14
Q

What is the restriction-modification system?

A

A system in prokaryotes that provides defence against foreign DNA such as DNA from bacteriophages.

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15
Q

How do siRNAs silence repetitive elements and transposons?

A

They recruit DNA methylases and histone-modifying enzymes to targets.

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16
Q

Where does methylation occur in mammals?

A

Almost exclusively at CpG dinucleotides.

17
Q

What are CpG islands?

A

Regions of the genome that contain a large number of CpG dinucleotide repeats over 200bp long.

18
Q

What are DNMTs?

A

A family of enzymes that catalyse the transfer of a methyl group to the 5C of cytosine.

19
Q

What is the function of Dnmt1?

A

Maintenance of methylation, preference for hemi-methylated DNA.

20
Q

What is Dnmt1o?

A

The oocyte specific isoform of Dnmt1.

21
Q

What is the function of Dnmt2?

A

Non-CpG methylation in Drosophila, no known function in mammals.

22
Q

What is the function of Dnmt3a and Dnmt3b?

A

de novo methylation, establishment of methylation. Dnmt3a methylates non-CpG cytosine.

23
Q

What is the function of Dnmt3L?

A

No catalytic activity, co-localises with 3a and 3b.

24
Q

When does DNA methylation first dip in mammals?

A

When sperm/eggs are being produced.

25
Q

When does DNA methylation dip a second time in mammals?

A

When the egg cell must get rid of the methylation silencing genes to allow the cells to differentiate.

26
Q

What is genetic imprinting?

A

Where a gene is only expressed from the maternal or paternal allele, not from both.

27
Q

What are some examples of imprinting genes?

A

IFG2 (insulin growth factor 2) and H19.

28
Q

Why is animal cloning unsuccessful (usually)?

A

Methylation does not reach as low levels as in fertilisation.

29
Q

What are some side effects of cloning/incomplete demethylation?

A

Shorter life expectancy and predisposed to age related disorders.

30
Q

Why are we more susceptible to cancer over time?

A

Hypermethylation of TSGs (tumour suppressor genes).

31
Q

What is the function of stress resistance genes?

A

To protect us against reactive oxygen species and other things like that.

32
Q

What are the 2 forms of chemotherapy?

A

5’-azacytidine - a DNMT inhibitor.

Trichostatin A - HDAC inhibitor.

33
Q

How does 5’-azacytidine work?

A

It causes the cells to die as daughter cells become cytotoxic as a result of demethylation. It passively demethylates the genome by preventing Dnmt1 binding. Affects all rapidly dividing cells.

34
Q

How does the sodium bisulfate reaction work?

A

Bisulfite deaminates C to U. Methylated C will not be deaminated, creating SNPs. PCR bisulfite modified genome. U shows up as T in a sequencing reaction so where C turns to T it was unmethylated.

BI2132: Applications of Genetics (20 decks)

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