B: The Human Genome

Question 1

-Where does DNA methylation occur in mammalian DNA?

Answer 1

At carbon 5 of cytosine to generate 5-methyl cytosine at CG sequences

Question 2

—Explain the relationship between DNA methylation at cytosines in human DNA and the frequency of SNPs in the genome.

Answer 2

• Cytosine tends to be methylated at the 5th carbon atom, creating 5-methylcytosine.
• The deamination of 5-methylcytosine (loss of amino group) generates a thymine.
• Thymine DNA glycolase (TDG) usually removes thymine, and the base excision repair pathway (BER) repairs the DNA.
• TDG is not very efficient, so C to T mutations are replicated frequently.
• This is why the T:G pairing (instead of C:G) is the most comment SNP (single nucleotide polymorphomism).

Question 3

—Describe deamination of cytosine and its relationship to mutation.

Answer 3

• The deamination of cytosine (loss of amino group) generates a uracil.
• Uracil DNA glycolase (UDG) usually removes uracil, and base excision repair (BER) pathway repairs the DNA by reinserting cytosine.
• UDG is very efficient, so no frequent U:G mutations

Question 4

—Describe deamination of 5-methyl cytosine and its relationship to mutation.

Answer 4

• The deamination of 5-methylcytosine (loss of amino group) generates a thymine.
• Thymine DNA glycolase (TDG) usually removes thymine, and base excision repair pathway (BER) repairs the DNA.
• TDG is not very efficient, so C to T mutations are replicated frequently.
• This is why the T:G pairing (instead of C:G) is the most comment SNP (single nucleotide polymorphomism).

Question 5

-Name the enzymes that methylate and demethylate 5-methylcytosine in DNA.

Answer 5

DNA methyltransferase (DNMT) and demethylation enzymes

Question 6

—What is the difference between the genome, transcriptome, proteome, methylome and epigenome?

Answer 6

• Genome = DNA sequence (same in all somatic cells)
• Transcriptome = RNA that is transcribed from genes in a tissue (different in cells from different tissues)
• Proteome = full complement of proteins expressed in a cell or tissue (different in cells from different tissues)
• Methylome = methylation pattern of the DNA in a cell (different in cells from different tissues)
• Epigenome = nucleosome + DNA + pattern of all methylated cytosines + pattern of all modifications to cytosine + TFs bound to chromatin + remodelling complexes bound to chromatin

Question 7

—Are the different –omes the same in different tissues?

Answer 7

• Genome are the same in different tissues
• The rest aren’t the same in different tissues

Question 8

Features of cancer cells:

Answer 8

Global hypomethylation –> contributes to genome instability.
Silence of tumour suppressant genes by methylation.