HC10 DNA methylation and genome regulation

Question 1

genomic regions and modifications associated with absence of 5mC

Answer 1

• H3K4me: prevents binding of DNMT3
• TSS
• active enhancers: associated with low methylated regions.
• CpG islands at promotors

Question 2

Targets of DNA methylation

Answer 2

• TEs
• gene bodies
• nucleosomal DNA

Question 3

CpG protected from 5mC by:

Answer 3

• H3K4me: inhibits 5mC and increases H3ac
• binding of TFs
• H3K4 methyltransferases
• TET
• absence of nucleosomes

Question 4

CTCF
- function?
- presence of 5mC

Answer 4

• binds to insulator sequences needed for insulator function.
• presence of 5mC blocks CTCF binding.

Question 5

H3K36me

Answer 5

stimulates 5mC

Question 6

roles of 5mC

Answer 6

• genome stability
• gene regulation

Question 7

TEs threaten genomic stability by:

Answer 7

• insertional mutagenesis
• spreading of 5mC in cis
• promotor inactivation
• gene repression
• homologous recombination
• transcription interference.

Therefore 5mC represses TE activity.

Question 8

genomic imprinting + in germ cells

Answer 8

parent-of-origen manner
monoallelic expression
5mC is the imprint.

in germ cells: imprints need to be reset. and is restablished: female germ line gets female imprints, male germline get male imprints.

Question 9

5mC and Igf2-H19 locus

Answer 9

in female: DMD (differentialy methylated domain) and H19 are unmethylated –> CTCF can bind to DMD –> insulator active –> only H19 activation

male: DMD and H19 are methylated –> CTCF cannot bind to DMD –> insulator is inactive –> ehancer activates Igf2.

Question 10

Cancer and 5mC link:

Answer 10

general loss of 5mC –> TE jumping and selective hypermethylation of regulatory sequences –> of tumor suppressor genes for instance.

for instance: hypermethylation of SEPT9 –> colorectal cancer.

Question 11

Demethylation of DNA

Answer 11

Removal of 5mC leads to 5-hydroxymethylcytosine (5hmC)

• TET removes 5mC at promotors and regulatory sequences –> gene expression
• 5hmC prevents MeCP2 binding
• TET prevents access of DNMTs

Question 12

de novo DNA methylation

Answer 12

DNMT3A/B. Newly added methylation on unmethylated DNA.
primarly methylate CG
also CA»CT>CC

Question 13

maintenance DNA methylation

Answer 13

maintain DNA methylation during replication.
DNMT1
DNMT1 –> recognises CG in animals and CG/CHG in plants.
Recognises hemimethylated sites.

Question 14

two methods of DNA demethylation

Answer 14

• active: TET enzymes
  mostly in males
• passive: methylation gets lost during replication in the absence of DNMTs.
  mostly in females