genomic imprinting Flashcards by Tahmin Ahmed

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!

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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)

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name some general epigenetic mechanisms

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

these are covalent modifications to the DNA

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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)

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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

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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

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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

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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

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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

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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!

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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?

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discrete areas of genome where DNA methlylation occurs and differentially methylated on maternal and paternal allele

what is an imprinting centre?

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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?)

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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?

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11p15 region of human chromosome which contains 2 DMRs

what is CDKN1c? what is its function?

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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

genomic imprinting Flashcards

(42 cards)