genomic imprinting Flashcards
define epigenetics
heritable changes in gene function that DO NOT affect the DNA sequence itself (not a mutation), instead DNA is chemically modified
> way that genes can be regulated as it can control how and when a gene is transcribed!
> underpins cell differentiation!
how can epigenetic modifications be inherited?
inherited when cells divide
via mitosis - within generations
via meoisis - transgenerational
epigenetic marks are maintained by DNA methyltransferases (DNMTs)
name some general epigenetic mechanisms
methylation - of histones
methylation - of DNA (CG dinucleotides)
these are covalent modifications to the DNA
describe the roles of various DNA methyltransferases (DNMTs) in maintaining epigentic modification
> 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)
what is the difference between euchromatin and heterochromatin?
euchromatin is loosely structured (EWW) so associated with actively transcribed genes
hetrochromatin is tightly structured so associated with silenced/repressed genes
explain the term genetic imprinting
describes an epigenetic phenomenon where imprinting marks are added to DNA during oogenisis/spermatogenies
so instead of biallelically expressed, the gene is maternally or paternally expressed
can we use epigenetic drugs to remove epigentic marks?
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
how can we REMOVE methyl groups?
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
the 11p15 chromosome is implicated in many genomic imprinting disorders. describe the structure of the gene.
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
why are TF and hormones not considered epigenetic modifications?
epigenetics = heritable changes
so if we remove the hormone or TF there gene function is restored so that isn’t a heritable change!
which gene encodes maintenence DNA methylase
A DNMT3L
B DMNT1
C DNMT3A
D DNMT3B
OPTION B
1 has a preference for hemi-methylated DNA so able to maitain the methylation marks onto daughter strand of DNA
IGF2 is
A maternally expressed
B maternally imprinted
C paternally expressed
D paternally imprinted
Option C
paternally expressed gene
'’saying its imprinted is ambigious as unclear if its silenced
CDKN1c is
A maternally expressed
B maternally imprinted
C paternally expressed
D paternally imprinted
maternally expressed imprinted gene
'’saying its imprinted is ambigious as unclear if its silenced
H19DMR is…?
A paternally methylated imprinting centre for CDKn1c
B paternally methylated imprinting centre for IGF2
C maternally methylated imprinting centre for CDKn1c
D maternally methylated imprinting centre for IGF2
igf2 impriitng centre
so paternally methylated
so option B
KvDMR is…?
A paternally methylated imprinting centre for CDKn1c
B paternally methylated imprinting centre for IGF2
C maternally methylated imprinting centre for CDKn1c
D maternally methylated imprinting centre for IGF2
impriting for CDKn1c
materal methlyated
so option C1
Lit1 is a long ncRNA which…?
A activates CDKN1c in trans
B silences CDKN1c in trans
C activates CDKn1C in cis
D silences CDkN1c in cis
OPTION D
on same chromosome
Lit1 silences CDKN1c on paternal allele via many theorised mechanisms
LOF of IGF2 in mice leads to
A large placenta and heavy pup
B small placenta and small pup
C small placenta and normal weight
D large placenta and normal birth weight
lower expression of IGF2
which normally promotes growth
option B
LOF of CDKn1C in mice leads to…?
A large placenta and heavy pup
B small placenta and small pup
C small placenta and normal weight
D large placenta and normal birth weight
Option D
CDKN1C normally inhibit cell proliferation so LOF we see overgrowth
but placenta is non-functional, so overgrowth cannot be supported and pups are birth weight
this is different in humans where high birth weight is seen
from mouse studies, BWS most likely caused by?
A loss of imprinting at IGF2 and CDKN1c
B LOF of IGF2 and CDKN1c
C LOF of IGF2 and loss of imprintin of CDKN1c
D Loss of imprinting of IGF2 and LOF of CDKN1c
option D
loss of imprinting of IGF2 as it is now biallelically expressed
and/or loss of function of CDKN1c as it is continuously repressed
Lots of growth
Cell cycle not regulated = megly
what is an imprinting centre?
discrete areas of genome where DNA methlylation occurs and differentially methylated on maternal and paternal allele
what is an imprinting centre?
region of DNA which can regulate expression of neighbouring imprinted genes on the same allele and characterisd by differentially methylated regions
what is a unique feature of genomic imprinting disorders (compared to mendelian inheritance?)
the have sex specific transmission but not sex specific inheritance
so can appear both dominant or recessive depending on the parent of origin
which chromosome area is affected by BWS?
11p15 region of human chromosome which contains 2 DMRs
what is CDKN1c? what is its function?
encodes a cyclin-dependent kinase inhibitor
also known as p57 so its a cell cycle inhibitor
prevents cell proliferation
what is h19?
h19 is a lncRNA expressed on the maternal allele of the H19DMR
expressed in similar tissues as IGF2
may function as a tumour supressor
what is IGF2? what is its function?
encodes for insulin-like growth factor 2 , a peptide hormone
regulates cell proliferaton, survival and growth
what is CTCF? How does it function in 11p15 locus?
its a insulator protein and able to bind to UNMETHYLATED DNA and alter chromatin interactions
so can regulate imprinting of IGF2 and H19 by creating interchromosomal loop, preventing igf2 enhancer-promoter interaction
what is Lit1?
lncRNA expressed from paternal allele
in imprinting seems to silence the paternal allele (acts in cis) by coating the allele and recruting silencing factors
this allows for monoallelic expression of CDKN1c on maternal allele
why is hypermethylation of h19DMR a possible molecular cause of BWS?
if methylated, CTCF the insulator protein is unable to bind to h19DMR
so cannot alter chromatin and repress IGF2 expression by preventing interaction with promoter
so instead IGF2 is able to be Over-expressed as nothing is repressing it = biallelic expression
how can IGF2 become overexpressed in 11p15 locus?
if h19DMR is deleted on the maternal allele
then IGF2 is free to interact with enhancer on maternal allele and not repressed so can be biallelically expressed
this leads to overgrowth symptoms of BWS
why does CDKN1c KO result in normal birthweight pups?
despite placentamegly occuring in the embryo, the placenta itself is abormal and dysfuntional and cannot support foetal overgrowth
the mice embryos are heavy but the pups are not
what features of BWS does IGF2 contribute to?
GAIN of IGF2 (OE) leads to overgrowth symptoms
> high birthweight at 95%
> macroglossia (large tongue
what features of BWS does CDKN1c contribute to?
A LOF of CDKN1C (from SNP, deletion) means there is uncontrolled cell growth, proliferation, differetiaiton
> placentamegly
> renal hyperplasia->wilms
> cleft palate
what would hypomethlyation of the kvDMR result in?
(in relation to the genes CDKNC1c and Lit1 ncRNA)
no silencing of lit1 and instead remains active
lit1 able to silence CDKN1c in cis on both alleles resulting in LOF of CDKN1c
why are translocation events also a cause for BWS?
translocation of CDKN1c moves the gene body away from its very distal enhancers
so overall loss of impriting of CDKN1c = classical features of BWS
does genetic testing always happen to diagnose BWS?
not always!
if clinical score/phenotypes is above 4 no need for testing
But molecular diagnosis would be useful to guide treatment
what is the process of BWS diagnosis?
first identify any cardinal symptoms = 2 point
then identify any suggestive features = 1 point
name some cardinal features
macroglossia
wilms tumour
family history
hemi-hyperplasia
name some suggestive features of BWS
high birthweight
ear creases
kidney abnormalities
when would genetic testing be deemed appropiate for BWS diganosis?
when the clincial score is above 2 but below 4
what is the aim of the various genetic testing tools for BWS?
they been developed to detect for abberant methylation or chromosomal abnormalities at the 11p15 region
what is a multi-locus imprinting disorder?
where a patient presents with symptoms from 2+ impriting disorders
due to dysfunction of epigenetic regulators in early embro development affecting impriting on multiple loci
