Dna Methylation

Front 1

Outline where in the genome DNA methylation occurs.

Back 1

- at CpG dinucleotides on cytosine
- at CpG islands (rarely)
- at intergentic intervals
- at repetetive elements

Front 2

Why are CpG dinucleotides 'stable' in the genome?

Back 2

- symmetrical
- so can be easily copied

Front 3

How is methylation laid down?

Back 3

- by DNMT3a and 3b in mammals
- by DNMT1 in replication

Front 4

The replication of a methylated CpG dinucleotide produces...

Back 4

1. 2x hemi-methylated DNA
2. 2x methylated DNA following treatment by DNMT1

Front 5

- Where are CpG islands often found?
- What is the role of this region?

Back 5

- promoter regions
- these are the starts of genes where transcription factors can bind and transcribe genes

Front 6

Methylation at CpG islands =>

Back 6

silencing of gene expression

Front 7

How does DNA methylation cause silencing?

Back 7

- CpG binding proteins MeCP1 and 2 bind to meCpG
- these contain transcription repression domain
- these also recruit other factors that condense chromatin
- so meCpG is associated with condensation of chromatin (this is repressive)
- meCpG itself also inhibits transcription factor binding

Front 8

Explain why there are fewer meCpG dinucleotides in the genome than expected.

Back 8

- DNA methylation is mutagenic:
- methylated cytosine is prone to deamination to thymine - so there are more T-G residues found than C-G residues

Front 9

Outline the function of DNA methylation at intergenic regions.
What evidence is there for this?

Back 9

- maintains genomic integrity
- cells without DNMT1 exhibit genomic instability (more indels, replicationof chromosomes, reciprocal transmission
- silences cryptic promoter sites/ cryptic splice sites
-prevents transcription of repetetive elements, and therefore transposition of these elements

Front 10

Outline how transcriptional interference occurs at cryptic promoter sites.

Back 10

- RNA polymerase binds at a promoter site (site A) at a gene and transcribes gene
- by chance there is a weak promoter in an intergenic region/ there is another promoter region associated with gene nearby
- this promoter region causes transcription in the opposite direction to site A and is positioned in such a way that RNA polymerase binding with transcribe and collide with RNA polymerase transcribing from site A.

Front 11

Where is transcriptional interference most disruptive?
What can prevent transcriptional interference?

Back 11

- when it occurs in the middle of a gene
- DNA methylation at CpG islands

Front 12

Why are repetetive elements mutagenic?

Back 12

- they copy or cut themseleves out from one locus and reposition themselves elsewhere in the genome.
- there is a risk of them transposing themselves in such a way that it disrupts another gene

Front 13

Outline the structure of a repetetive element.

Back 13

--LTR----promoter region-->--gag----pol----LTR----promoter region-->--

Front 14

Outline how methylation can prevent transposition.

Back 14

- methylation at gag and pol promoter sites silences transcription of genes for gag and pol proteins
- these are required for function of repetetive elements
mutation of methylated CpGs to thymine can prevent transcription and transposition over evolutionary time

Front 15

Other than transposition, how else can long terminal repeats cause genomic instability?

Back 15

- transcriptional interference with neighbouring genes

Front 16

How are CpGs in repetetive elements normally found?
Why is this?

Back 16

- methylated
- there is evolutionary benefit to this - methylation being used as a 'genomic defense' by preventing transcription of gag and pol proteins, and therefore transposition of repetetive elements

Front 17

What is notable about genome of cancer cells, regarding methylation?

Back 17

- intergenic regions and repetetive elements are hypomethylated
- sometimes CpG islands are hypermethylated

Front 18

How can demethylation occur?

Back 18

- due to a lack of DNMT1 (due to underexpression/ other reasons) during DNA replication
- TET proteins break C-CH3 bond, removing methyl group

Front 19

What evidence is there to suggest that DNA methylation is essential for life?

Back 19

- Mice without DNMT1 die in utero.