Epigenetics

Question 1

What are different kinds of histone modifications?

Answer 1

Acetylation, phosphorylation, methylation

Question 2

What is the significance of methylation in gene promoter regions?

Answer 2

Regions in the 5’ UTR that can be hypermethylated and that results in gene silencing
(hypomethylation –> gene activation)

Question 3

What is the significance of non-coding RNAs?

Answer 3

They bind to mRNAs to target them for degradation (this is an example of post-transcriptional gene silencing)

Question 4

What is the difference between euchromatin and heterochromatin?

Answer 4

Euchromatin: gene is switched on, meaning that the chromatin is open, cytosines are unmethylated, and histones are acetylated
Heterochromatin: gene is switched off, meaning the chromatin is condensed, cytosines are methylated, and histones are deacetylated

Question 5

Through what steps does X inactivation occur?

Answer 5

1. RNA is silenced via Xist
2. positive histone modifications are removed
3. negative protein complexes are recruited
4. Negative histone modifications are added when they recognize non-coding RNA bound to X chromosomes
5. widespread DNA methylation

Question 6

What is the parental pattern of gene expression on chromosome 15?

Answer 6

paternal chromosome: SNURF-SNRPN is ON; UBE3A is OFF

maternal chromosome: SNURF-SNRPN is OFF, UBE3A is ON

Question 7

What are the functions of SNURF-SNRPN and UBE3A?

Answer 7

UBE3A is responsible for protein degradation

SNURF-SNRPN contains imprinting control center

Question 8

What is the parental pattern of gene expression on chromosome 11?

Answer 8

Maternal allele: H19 is on which inhibits IGF2; KCNQ1 is on and CDKN1C is on
Paternal allele: IGF2 is on so H19 must be off; KCNQ1OT1 is on so CDKN1C is off

Question 9

What are the significance of H19, IGF2, CDKN1C, and KCNQ1OT1 on chromosome 11?

Answer 9

H19: lncrNA; tumor suppression
IGF2: growth and development
CDKN1C: negative regulator of growth
KCNQ1OT1: lncRNA; inhibits CDKN1C

Question 10

What is the epigenetic significance in Fragile X?

Answer 10

A trinucleotide repeat expansion in FMR1 signals for hypermethylation which ultimately leads to gene silencing

Question 11

What is the significance of mosaicism in Fragile X?

Answer 11

The phenotype that results may be affected by repeat size and methylation

Question 12

What are the clinical features of Fragile X?

Answer 12

Facial appearance (long, narrow face; macrocephaly; broad forehead; prominent ears; pointed chin; high-arched palate; long palpebral fissures; facial hypotonia)
Developmental delay/intellectual disability
Autism
Behavioral concerns (ADHD, anxiety, aggression)

Question 13

How do Prader-Willi and Angelman syndrome come about?

Answer 13

Prader-Willi is the loss of the paternal allele (too much UBE3A and no SNURF-SNRPN)
Angelman is the loss of the maternal allele (so no UBE3A)

Question 14

What are the clinical features of Prader-Willi?

Answer 14

Poor muscle tone
obesity
short stature
intellectual disability
hypogonadism
behavioral concerns

Question 15

What are the clinical features of Angelman syndrome?

Answer 15

Severe intellectual disability, absent speech, ataxia/weak gait, happy demeanor, macrocephaly

Question 16

What is the gene pattern associated with Silver-Rsussell syndrome?

Answer 16

IGF2 is silenced
CDKN1C is active

Loss of paternal allele!

Question 17

What is the gene pattern associated with Beckwith-Wiedemann syndrome?

Answer 17

IGF2 is active
CDKN1C is silenced
H19 is silenced

loss of maternal allele!

Question 18

What is the importance of the bisulfite conversion of DNA?

Answer 18

Differentiates methylated and unmethylated CpG sites

converts unmethylated cytosines to uracil and then you can look to see where the Ts are

Question 19

What is MLPA used for?

Answer 19

To determine whether DNA is hypo- or hypermethylated through the use of restriction enzymes (if it’s hypermethylated, the DNA can’t be cut)

Question 20

What is pyrosequencing?

Answer 20

an alternative method of sequencing based on release of light

Question 21

What is the etiology of Sotos syndrome? Inheritance? Phenotype?

Answer 21

Caused by haploinsufficiency of NSD1 which is an epigenetic writer
AD inheritance
facies (broad, prominent forehead; dolichocephaly; sparse frontotemporal hair; downslanting palpebral fissures; long, narrow face; long chin; malar flushing)
learning disability
overgrowth

Question 22

What is the etiology of CHARGE? Associated phenotype?

Answer 22

mutations in CHD7 which is a chromatin remodeler (bulldozer)
Coloboma
Heart defect
Choanal atresia
Retarded growth/development
Genital hypoplasia
Ear anomalies

Question 23

What is the etiology of Rett syndrome? Inheritance pattern?Phenotype?

Answer 23

Mutations in MECP2 which is a reader
X-linked dominant inheritance
phenotype includes regression around 6-18 mo; deceleration of head growth; stereotyping hand movements; absent or abnormal gait; laughing/screaming fits; seizures

Question 24

What does the episignature hypothesis refer to?

Answer 24

idea that certain disorders caused by gene mutations in epigenetic machinery have their own epigenetic signature

Question 25

What are the four types of epigenetic machinery?

Answer 25

Writer
Reader
Eraser
Bulldozer/remodeler

Question 26

What are the current indications for episignature testing?

Answer 26

There’s a clinical suspicion for syndrome with epigenetic signature
Extensive genetic work-up previously negative
VUS in gene/CNV with validated epigenetic signature
To resolve uncertain or discrepant testing results