epigentics - x inactivation

Question 1

define epigenetics

Answer 1

heritable changes in gene function that DO NOT affect the dna sequence itself (not a mutation). Changes to DNA are chemically modified
> way that genes can be regulated as it can control how and when a gene is transcribed!
> underpins cell differentiation!

Question 2

how can epigenetic modifications be inherited?

Answer 2

inherited when cells divide
via mitosis - within generations
via meoisis - transgenerational

epigenetic marks are maintained by DNA methyltransferases (DNMTs)

Question 3

name some general epigenetic mechanisms

Answer 3

methylation - of histones
methylation - of DNA (CG dinucleotides)

these are covalent modifications to the DNA

Question 4

describe how DNA and histones can become methylated?

Answer 4

methylation generally works to down-regulate gene expression.
DNA methyltransferases catalyse the transfer of a methyl group to a CG dinucleotide.
similarly histone methyltranferases (HMTs) add a methyl group to histones (particularly to lysine residues)

Question 5

How does Xist downregulate gene expression?

Answer 5

Xist will coat the chromosome to be inactivated and recruit primary and secondary silencing factors:

• loss in acetlyation = removes negative charge
• ubiquination of H2aK119
• inactive chromosome expresses macro H2A variant instead of normal H2A protein which can promote X inactivation
• loss in H3K4 trimethylation and a gain in H3K9,K27 dimethylation (silencing histone marks)`

Question 6

describe the roles of various DNA methyltransferases (DNMTs) in maintaining epigentic modification

Answer 6

> > DNMT1 has a preference for hemimethylated DNA and methylates the newly synthesised strand
DNMT 3a,b,l involved in denovo methylation/ gene silencing processes
(seen in paternal and maternal genomes)

Question 7

where are CPG islands found?

Answer 7

CpG islands are areas of CG dinuleotides at a high frequency (60% observed or above) and associated with housekeeping genes
over 200bp long
often overlap with the promoter and first exon of gene and near TSS
this is because these CG are unmethylated so protected from the effects of spontaneous deamination
» associated with actively transcribed genes

Question 8

how does a CPG island avoid being methylated

Answer 8

has boundary elements which can exclude DNMTs from dna via barrier action, preventing enzyme progression

Question 9

what is the difference between euchromatin and heterochromatin

Answer 9

euchromatin is loosely structured (EWW) so associated with actively transcribed genes

hetrochromatin is tightly structured so associated with silenced/repressed genes

Question 10

what is a BArr body? where can they be found in the cell?

Answer 10

the final result of X- inactivation allowing for dosage compensation in females.
Very condensed and highly methylated heterochromatin

found right on the edges of the nucleus
(nuclear periphery)

Question 11

is X-inactivation reversible?

Answer 11

once the CPG islands acquire methylation, heterochromatin confirmation will form and condense forming the Barr body now irreversible
> and Xist will then be degraded and all the daughter cells will inactivate that same X-chromosome (clonal x inactivation)

but in vitro we can do reverse this e.g to make iPSC
> downregulating Xist to remove DNA methylation

Question 12

explain the term genetic imprinting

Answer 12

describes an epigenetic phenomenon/gene silencing where imprinting marks are added to DNA during oogenisis/spermatogenies

so instead of biallelically expressed gewn is maternally or paternally expressed

genomic imprinting disorders depend on the parent of origin
» explains why we cant reproduce assexually as we need most genes to be biallelically expressed

Question 13

can we use epigenetic drugs to remove epigentic marks?

Answer 13

epidrugs can be use to activate or repress gene expression
we can use HDACs to remove acetyl to silence a gene
we can use DNMT inhibitors to remove methylation marks to activate genes
> such as Azacitidine which is used to treat myelodysplastic syndrome

Question 14

aging and epigentics

Answer 14

age - increase in global demethylation and increased in methylation in Cpg islands
Could increase risk of cancer

in cancer - hypermethylation of tumour suppressor genes at their promoters like p16 and VHL will silence those genes and promote tumourgenesis
also mice with mutations in DNMT1 have been shown to be at more risk of developing cancer as it can contribute to genomic instability

Question 15

the thrifty phenotype

Answer 15

Alteration of gene expression in reososne to the environment

the dutch famine 1944-1945
malnourished mothers gave birth to children who has a higher risk of noncommunicable disease and general poorer health in later life

diet high in methyl donors in mice can increase dna methylation on offspring

Question 16

how can we REMOVE methyl groups?

Answer 16

there is no demethylase enzyme // passively or actively

DNMTs can passively demethylate by forgetting to maintain methylation on newly synthesized DNA strands so following a few rounds of cell division these methylation marks are lost

or use TET enzymes (1,2,3) to actively demethylate 5Mc cytosine using oxidation and base excision repair
FIRST OXIDATION PRODUCT is 5hmC which can then deaminate and BER = cytosine

Question 17

the 11p15 chromosome is implicated in many genomic imprinting disorders. describe the structure of the gene.

Answer 17

has 2 differentially methylated regions
kwDMR - this is methylated in oocytes controlling CDKN1c expression

H19 DMR - this is methylated in sperm and controls IGF2 and H19 expression

Question 18

which 2 genes/molecules are affected by beckwith weidermann syndrome and silver russel syndrome?

Answer 18

examples of genetic imprinting disorders due to a duplication/disomy of gene or loss of methylation in DMR.

Insulin growth like factor 2 - promotes cell proliferation
Cyclin dependent kinase inhibitor 1c - inhibits cell cycle

BWS there is too much IGF2 due to paternal disomy so foetal overgrowth or there is a loss of methylation on the maternal KvDMR
SRS there is too much CDKN1c so there is foetal growth restriction and maternal disomy

Question 19

why are TF and hormones not considered epigenetic modifications?

Answer 19

epigenetics = heritable

so if we remove the hormone or TF there gene function is restored so that isn’t a heritable change!

Question 20

apart from in CpG islands, why are CG dinucleotides so infrequent?

Answer 20

in their methylated form they are unstable and can spontaneously deaminate to a thymine residue

Question 21

how does methylation of DNA or histones affect gene expression

Answer 21

> usually can repress genes by silencing promoter

MBDomain proteins attract HDAC to the area and remove acetylation marks
which remove the additional negative charges from DNA making it more positively charged

so histone and DNA will attract insteasd of repel so will switch to a heterochromatin structure
preventing access for transcription machinery/TF binding proteins thereby silencing the promoter

Question 22

which locus controls X inactivation
A HDAC
B kv DMR
C XIC
D h19 DMR

Answer 22

OPtion C
X- inactivation centre
> Xist noncodingRNA is transcribed from here and Tsix is expressed antisense

Question 23

what is x inactivation?

Answer 23

sequential epigentic mechanism that occurs in female mammals resulting in one X chromosome becoming inactivated in early embryonic development

this allows gene dosage compensation between male and female chromosomes
> random process, can occur on maternal or paternal genome

Question 24

when would demethylation occur?

Answer 24

maternal genome is passively demethylted fro zygote to morula stage

howver paternal genome is very rapidly (actively) demethylated so happens over a shorter time period so from ferilisation to zygote most epigenetic marks are removed

Question 25

what is an example of clonal x inactivation

Answer 25

a calico cat
each X chromosome encodes genes for coat colour -black or orange

so maybe the black x chromosome is inactivated or maybe the orange x chromosoe is inactivated

Question 26

why would a calico cat mother give birth to a normal CLONE kitten? they are genetically identical??

Answer 26

because to generate the clone, you will need to REACTIVATE the inactive X chromsome in the genome

and then it will undergo a new round of RANDOM x inactivation meaning the kitten may look different in appearnae

Question 27

Why are female patients of Hemophililia show no symptoms?

how could the process of X inactivation affect the phenotype of haemophillia?

Answer 27

hameophillia is X-recessive
so normally there intermittent phenotype as females are Heterozygous for disease so theres an averaging effect of normal and abnormal clotting factors in blood so no clinical phenotype seen

if the normal/WT allelle is inactivated then carriers of disease will show clinical manifestation
> a recessive disorder can appear dominant due to skewed x inactivation depending on if the mutant or normal allele is affected

Question 28

what is leptin and GLUt4 a good example of?

Answer 28

leptin has a cpg island overlapping with TSS. So if Cpg island is methylated gene regualtion is downregulated
but is normally active in white adipose tissue so unmethylated Cpg Acts as a promoter to keep it active

conversrly, GLUT 4 can be regualted through the methylation of 2 distinct CpGs rather than a CpG island. located at TF binding sites and if methylated can block the TF from biding so GLUT4 expression will fall