1
Q
What is epigenetics
A
- term coined by Waddington in 1942
- epi=above (above genetics)
- refers to changes in gene expression driven by alterations of chromatic structure or DNA structure
- not differences in DNA sequences
2
Q
Molecular processes leading to epigenetic changes
A
- Changes in patterns of DNA methylation
- Chemical modifications of histone proteins
- RNA molecules that affect chromatin structure and gene expression
- common attributes
- alters expression of genes
- stably transmitted through mitosis, sometimes through meiosis
- mostly related to changes in chromatin structure
3
Q
DNA methylation
A
- most common form is the conversion of cytosine to 5-methylcytosine
- typically targets CG positions
- referred to as CpG dinucleotides
- the C on opposite strands are both methylated, leading to diagonal methylation pairs
- in plants, methylation also occurs at CpNpG trinucleotides
- genome regions rich in CpG pairs are known as CpG islands
- often in or near gene promoter regions
- CpG islands not methylated when genes are actively transcribed
- methylation of CpG islands near a gene —> repression of transcription
4
Q
Maintenance of methylation through cycles of DNA replication
A
- methyltransferases turn C into 5-methylcytosine
- demethylases remove methyl groups
- DNA replication of fully methylated DNA leads to hemimethylated DNA
- only one strand is methylated
- then the methyl groups on one strand attract methytransferases, causing non-methylated daughter strand to be methylated
- results in fully methylated DNA
5
Q
DNA methylation and bees
A
- determines the difference between a queen bee and a worker bee
- bee larvae destined to be queens are fed royal jelly
- royal jelly silences Dnmt3, which is involved in methylation
- future Queen bees have less methylated DNA —> more active genes
- functional ovaries develop
-in worker bees, the Dnmt3 gene is active and genes are methylated
6
Q
Repression of transcription by DNA methylation
A
- methyl groups sit in major grooves of DNA
- inhibits binding of transcription factors and other proteins needed for tanscription
- also attracts proteins that directly repress transcription
- attracts histon deactylase enzymes that remove acetyl groups from tails of histone proteins, altering chromatin structure and further repressing transcription
7
Q
Histone modifications
A
- in eukaryotic cells DNA is complexed to histone proteins to form nucleosomes, basic repeating units of chromatin
- many chemical modifications of histones, often positively charged tails
- histone acetylation destabilizes chromatin, making it more open
- increased transcription
- histone methylation decrease or increase transcription
- mechanisms for maintenance of histone modification across cell division not as well understood as DNA methylation
8
Q
Epigenetics effects of RNA molecules
A
- X chromosome inactivation is best understood example
- involves long non-coding RNA called Xist
- siRNA that silence genes implicated in other examples
- also microRNAs
- how RNA-mediated epigenetic effects are maintained across cell generations not well understood
- small RNAs may be transmitted in cytoplasm
9
Q
X inactivation
A
- in all female mammals, 1 copy of X chromosome is inactivated in all cells
- inactivation occurs early in development, then inactive H remains so for all remaining cells divisions (=an epigenetic change)
- leads to a patchy distribution of active maternally and paternally derived X chromosomes
- RNA coded by Xist gene on X chromosome coats one X but not the other, leading to inactivation
- Xist RNA recruits PRC2 which produces histone modification
10
Q
Paramutation in Corn
A
- B1 locus influences pigmentation
- B1B1 homozygote = high expression = purple
- B’B’ homozygote = low expression = light pigment
- B1B’ heterozygote = light pigment…..
- B1 and B’ allele sequences are IDENTICAL
- B’ converts B1 allele to B’* allele
- paramutation of B1 locus requires presence of 7 tandem repeats 100kb upstream
- both alleles have the repeats, but different chromatin structures
- open chromatin stimulates expression of B1
- closed chromatin represses expression of B1
- siRNAs produced from tandem repeats converts B1 —> B’*
11
Q
Normal roles of epigenetic imprinting
A
- differentiation of cells during development, from pluripotent stem cells, to particular tissue types, involves epigenetic silencing
- genomic imprinting
- some genes are expressed differently depending on whether the allele comes from the mother or the father
12
Q
DNA methylation and Cancer
A
- altered DNA methylation patterns though to play important roles in cancer
- CpG islands in percentromeric heterochromatin are normally hypermethylated
- in tumour cells they become hypomethylated, leading to genomic instability, more recombination, and aneuploidy
- growth regulatory genes (tumour suppression genes) are normally hypomethylated
- in cancers they become hypermethylated
- this causes transcription to be silenced
13
Q
Methylation and aging
A
- studies have shown that genome-wide methylation increases as humans age
- strong correlation between chronological age and methylation age predicted by a model
- some individuals age relatively fast, some slow, in terms of methylation accumulation
- males accumulate methylation faster than females
14
Q
Monozygotic twins
A
- not completely identical because of epigenetics
- patterns of histone acetylation and methylation diverge over time
- likely in response to different life experiences
15
Q
Dutch Hunger Winter and epigenetic hardships
A
- sever famine in Netherlands in winter of 1945
- 20,000 people died of starvation
- children of women who were pregnant at the time suffered life long health effects
- heavier, higher triglycerides, LDL cholesterol, obesity, diabetes etc
- 10% higher mortality rate by 68 years
- study of methylation patterns in 2000s found difference linked to famine and health conditions later in life
- of 15loci linked to growth and metabolic disease, showed difference in methylation patterns compared to control groups born before and after famine
- May reflect an adaption to hardship
16
Q
Epigenetic effects from 1998 ice storm
A
- ice storm affected Ontario, Quebec, New England
- study recruited women pregnant at the time and assessed degree of hardship they experienced
- 13 years later found a distinctive methylation signature in T cells in kids of the pregnant women
- long term health consequences not known yet
17
Q
Detecting DNA methylation
A
- REs can be used to detect methylation
- some REs sensitive to methylation (ie. will not cut if DNA is methylated)
- isoschizomers (REs that are NOT sensitive to methylation) recognize the same sequence and will cut whether or not it is methylated
- can compare cut patterns from methylation sensitive and non-sensitive REs
- use is limited to examining methylation in RE cut sites
18
Q
Detecting DNA methylation 2
A
- bisulfite sequencing is more powerful than REs
- relies on conversion of unmethylated cytosines to uracil, which is read during DNA sequencing as thymine
- compare output of DNA sequencing from both
-treatment with sodium bisulfite converts C to U
