Epigenetics

methylated cytosine can easily turn into —

T (thymine)

why are CpG island less common in DNA?

• because CpG islands are the target for methylation

• But, methylated C’s easily mutate

• so there’s a tradeoff, if you want to silence a gene, the base might mutate

what happens with epigenetics during cell division?

• it is Hemi-methylated

• parent strand retains methylation

• new strand NOT methylated

• hemi-methylated state acts as SIGNAL

• enzymes come and methylate using parent as a template

what does chip seq tell you?

the LOCATION in the genome where a protein bound

does chip seq tell you exactly what protein bound?

not exactly, but kind of because you use antibodies to bind to YOUR specific gene of interest soo yes

if a gene is imprinted, does this mean it is off or on?

Off , urgh

what deos the insulator region block or not block?

the enhancer

is IGF2 maternally or paternally expressed?

paternal

The maternal allele is silenced by — at the —-

CTCF binding

imprinting control region (ICR).

the paternal allele has —- which prevents —- from binding, this means that the gene can be trasncribed

dna methylation

CTCF

Most epigenetic marks get wiped during gametogenesis, but imprinted ones —

escape the erasure

are histones wrapped around double starnded dna?

yes

how do histone epigenetic modifications get conserveed through cell division?

• the histone need to be removed for replication but they don’t go very far

• the histones are distributed between 2 new ds dna pieces

• more gets added on after

once a nucleosome is put in place, its not there forever, it can move during

• replication

• transcription

• chromatin remodelling

• histone remodelling (replacing the histones)

why is methylation conserved at CpG islands on both strands?

• because the direction of dna is antiparralel, so even tho it looks like

CG

GC

when you read them both in the right direction, they’re both actually CG, CG, so they both are islands that should be replicated so thats why the hemi methylated thing works and serves as a template

t or f

without transcription factors, it is sometimes possible to have gene expression

true, you can have some leaky expression

regions that are consistently nucleosome-depleted across many cells

enhancer

promoters

not genes***

why would nucleosome occupancy be a helpful thing to study?

if you see areas where the digest enzymes are doing a lot of work, this means the dna was open, this means it was probably an enhancer or promoter

doesnt tell u about genes locations bc rna polymerase unwinds  and takes off nucelsoomes locally I think?

with chip seq, you can look at the density of acetlation vs methyaltion in areas,

so for studies, if u wanted to see if a epigeneteic modification was involved in activating something in liver vs brain, what could you do?

compare the markings between 2 cells, look at

• bisulphite seq and see if one has more methylation at gene

• chip seq, see if one has more activating/repressive marks around enhancer, promoter, gene

• look at nucleosome occupancy to see if the enhancer in one cell type is used for another cell type, see if its loosely packed

can histone marks survive mitosis?

yes

how do the histone marks get presevred?

• randomly distributed between daughter cells

• still need half the histones

• they get added

• they get modified because they’re near modified ones (in the cool club)

why are X chromosome aneuploidys not lethal?

because the cell defaults to shutting down any X chromosomes more than 1, whether its 1 or 2, it doesnt care

why are X-linked diseases like hemophilia rare in females but common and severe in males?

because the cell did X inactivation after a few rounds of cell division, so about 50% should be paternal X and 50% maternal X, mosaic

if XIC occured at the one cell stage, the whole body would have the same X being expressed, not mosaic

if females have a mutation in one of the X’s, their body is still producing 50% of the good protein, which can sometimes be enough

whats a Par region stand for

(pseudoautosomal region)

what are PAR regions?

• sections on X and Y chromosomes that have the SAME GENES

• this means they pair and do reocmbination there during meiosis

do PAR regions usually escape X inactivation?

yes

if X chromosome has acquired a gene from an autosome recently, that gene tends to —

escape X inactivation

what does it mean to say that the x chromosome inactiavtioon cnetre works in cis?

it means its the own chrosmome shutting istelf down, not the other one shutting it down

what is lamarckian evoltuion?

Organisms can inherit traits that their parents acquired during their lifetime.