Epigenetics I: DNA methylation Flashcards
What is epigenetics for developmental biologists?
Stable propagation of phenotype without a change of genotype
Epigenetics help maintain cellular __________ during development
Memory
What is involved in epigenetic effects?
Chromatin
High transcription or open chromatin indicate (heterochromatin/euchromatin) and low transcription or closed chromatin indicate (heterochromatin/euchromatin)
Euchromatin; heterochromatin
What are components of constitutive heterochromatin?
Centromeres, telomeres, retrotransposons
What are components of facultative heterochromatin?
Developmental genes, imprinting, inactive X chromosome
What are some cellular mechanisms for altering chromatin structure?
Nucleosome movement, assembly and disassembly, large-scale movement of chromatin in the nucleus, covalent modification of chromatin components
True or false: 5-methylcytosine is present in the DNA of all vertebrates and flowering plants, some invertebrates, protists and bacteria
True
5-mC is a critical component of the _______ state (heterochromatin)
Off
Where is DNA methylation in the genome?
CpGs
Most CpGs in the mammalian genome are (methylated/unmethylated)
Methylated
Where do a large proportion (40%) of methylated CpGs reside?
Retrotransposons
Transcription of retrotransposons by RNA polymerase II leads to what events?
Aberrant recombination, insertional mutagenesis, antisense transcription, mobilization
What percentage of promoters of human genes contain CpG islands?
70%
CpGs in CGIs are almost always (methylated/unmethylated), at both active and inactive promoters
Unmethylated
Rare CGI methylation is strongly correlated with what event?
Repression of transcription
What type of CGI is commonly methylated?
ICRs that control imprinted genes
What is methylation at shores associated with?
Whether gene is on or off
High methylation at shores means (high/low) expression and low methylation at shores means (high/low) expression
Low; high
What are the regulatory DNA elements that can act at large genomic distances and that are the binding sites for transcription factors?
Enhancers
High methylation is _____________ with transcription factor binding and enhancer activity
Anti-correlated
What is the mechanism of repression by DNA methylation?
Methyl-DNA binding proteins function in combination with histone modifications to repress transcription and block factor access to DNA
What is a technique used to detect CpG methylation?
Bisulfite treatment
What does bisulfite treatment involve?
Treatment of DNA with sodium bisulfite converts unmethylated cytosine to uracil through deamination
Methyl-cytosine is not affected
What is the use of bisulfite sequencing?
Uracil is converted to thymidine
Able to distinguish methylated and unmethylated cytosines in the genome
Which DNA methyltransferase is used for the following
a. Maintenance (inheritance)
b. De novo (establishment of methylation)
c. Germline-specific, targeting function
a. DNMT1
b. DNMT3A/B
c. DNMT3L
Where does DNMT1 localize?
Sites of DNA replication in S phase
Where is DNMT3B the major de novo methyltransferase?
Embryo
What is the role of DNMT3A?
Germline development and somatic tissues
Which domains of DNMT3A/B bind to chromatin?
ADD, PWWP
Identify the DNMT mutant phenotype
a. Chromosome stability
b. Loss of imprinting
c. Reanimation of retrotransposons
b and c
If progenitor cells do not self-renew, what happens to DNMT1?
Loss of DNMT1
What experiment was done to observe the role of DNMT1 in the renewal of progenitors?
WT progenitors and DNMT1 KO progenitors are introduced into an in vivo skin regeneration assay
WT progenitors restore graft, but KO DNMT1 do not
DNMT1 KO progenitors show increased expression of differentiation genes
Genes associated with skin cell differentiation are (methylated/unmethylated) in progenitors but (methylated/unmethylated) in differentiated cells
Methylated; unmethylated
How is DNA de-methylated?
Oxidation of 5-mC by TET enzymes
Oxidized 5-mC removed passively by replication or actively removed by DNA repair enzymes
