Epigenetics

Question 1

Epigenetics

Answer 1

• Study of heritable changes in gene expression without a change in the actual DNA sequence
• AKA the reason different cell types/tissues look different despite having the exact same DNA

Question 2

Levels of DNA packaging

Answer 2

• double helix
• nucleosomes
• chromatin fiber of packed nucleosomes
• chromosome

Question 3

What are the components of a nucleosome?

Answer 3

• 8 histone molecules: 2x H2A, H2B, H3, and H4
• Wrapped with 146 bp DNA
• Nucleosomes connected by linker DNA (H1)

Question 4

What are the possible modifications that can be made to histones?

Answer 4

• acetylation
• methylaiton
• phosphorylation
• deimination
• ubiquitination

Question 5

How does histone acetylation impact chromatin structure and transcription?

Answer 5

• Acetylation opens chromatin: acetyl groups are negatively charged and do not want to interact with negatively charged DNA
• This increases gene expression

Question 6

What enzymes are involved in histone acetylation?

Answer 6

• Histone acetyltransferases (HATs)

- Histone deacetylases (HDACs)

Question 7

What nucleic acids are methylated?

Answer 7

Cytosine => 5’ methyl-cytosine

Question 8

What is the effect of methylation on chromatin structure and transcription?

Answer 8

• Hypermethylation = condensed chromatin = less expression

- Hypomethylation = open chromatin = more expression

Question 9

Where is heterochromatin found, what modifications are present, and how is it transcribed?

Answer 9

• found near chromosome ends or centromeres where there are few genes
• methylated cytosines; deacetylated histone tails
• transcriptional repression

Question 10

What modifications are present on euchromatin and how is it transcribed?

Answer 10

• Acetylated histone tails; hypomethylation

- transcriptional activation

Question 11

What are TADs?

Answer 11

• Topolocigally associated domains are genetic neighborhoods
• Genes in a TAD are co-regulated
• TADs are consistent across cell types but their regulations vary

Question 12

How many chromatin states are there?

Answer 12

15 (more than just open/closed!)

Question 13

What confers cell-type-specific transcription?

Answer 13

Chromatin state: heterochromatin vs. enhancers vs. TSS’s vs. enhancers

Question 14

What is role of methylation in development?

Answer 14

• Increasing methylation in prospematognoia and oocyte growth
• Decreasing methylation from fertilization to blastocyst formation
• Increasing methylation throughout embryogenesis as cells begin to differentiate

Question 15

What are ways in which epigenetics can cause disease?

Answer 15

• Imprinting
• Pathogenic variation in genes that regulate epigenetic machinery
• Pathogenic variation that affects chromatin state
• Cancer
• Transgenerational inheritance

Question 16

What is Kabuki syndrome?

Answer 16

• Rare neurodevelopmental disorder
• Symptoms include: characteristic facial features, developmental delay, intellectual disability, growth deficiency, skeletal anomalies, congenital heart defects, genitourinary anomalies, seizures

Question 17

What are the mechanisms of Kabuki syndrome inheritance/occurence?

Answer 17

• Autosomal dominant

- De novo

Question 18

What are the genetic causes of Kabuki syndrome?

Answer 18

MLL2 (H3 lys 4 methyltransferase):

• normal = methylates = open chromatin and gene expression
• mutated copy = less methylation = closed chromatin and less expression of genes important to development

KDM6A (H3 lys 27 demethylase)

• normal = demethylation = open chromatin and gene expression
• mutated copy = more methylation = closed chromatin and less gene expression

Question 19

What is CHD2 associated epilepsy?

Answer 19

• most severe pediatric epilepsy
• first few day - years of life
• drop attacks and atonic-myoclonic-absence seizures
• no response to medication

Question 20

What is the mechanism of CHD2-associated epilepsy inheritance/occurence?

Answer 20

De novo mutation

Question 21

What is the genetic cause of CHD2-associated epilepsy?

Answer 21

• CHD2: chromatin remodeler important in opening chromatin so enzymes can access promoter
• Truncationsto CHD2 => less gene expression of genes that depend on CHD2 remodeling (haploinsufficiency)

Question 22

What are the symptoms of Fragile X syndrome>

Answer 22

• Intellectual disability in males
• Characteristic facial featuers
• Joint laxity
• Behavioral problems: social anxiety and autism spectrum disorder

Question 23

What is the genetic cause of Fragile X?

Answer 23

FMR1 = exon 1 of FMRP protein

• normal structure: promoter => 6-44 CGG repeats => FMR1
• fragile x structure: promoter => 200 CGG repeats => FMR1
• additional C’s = more methylation in promoter region = inhibition of transcription

Question 24

What is the occurrence of congenital limb malformations?

Answer 24

1/500-1/1000 live births

Question 25

What is a genetic cause of isolated congenital limb malformation?

Answer 25

- Deletion of a region including a TAD boundary => changed regulation of a gene in a neighboring TAD

Question 26

How can epigenetic marks contribute to cancer?

Answer 26

- Hypermethylation of a tumor suppressor gene promoter => decreased expression - Hypermethylation and deacetylation of a tumor suppressor gene => decreased expression

Question 27

Can epigenetic modifications be inherited?

Answer 27

There is evidence traits can be inherited (Dutch Hunger Winter)

Question 28

What can epigenetic therapies be used to treat?

Answer 28

- Kabuki (HDAC inhibitors) - Epilepsy (HDAC inhibitors) - Cancer (many targets)