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Foundations 1 > Epigenetics > Flashcards

Epigenetics Flashcards

1
Q

Epigenetics

A
  • 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
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2
Q

Levels of DNA packaging

A
  • double helix
  • nucleosomes
  • chromatin fiber of packed nucleosomes
  • chromosome
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3
Q

What are the components of a nucleosome?

A
  • 8 histone molecules: 2x H2A, H2B, H3, and H4
  • Wrapped with 146 bp DNA
  • Nucleosomes connected by linker DNA (H1)
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4
Q

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

A
  • acetylation
  • methylaiton
  • phosphorylation
  • deimination
  • ubiquitination
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5
Q

How does histone acetylation impact chromatin structure and transcription?

A
  • Acetylation opens chromatin: acetyl groups are negatively charged and do not want to interact with negatively charged DNA
  • This increases gene expression
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6
Q

What enzymes are involved in histone acetylation?

A
  • Histone acetyltransferases (HATs)

- Histone deacetylases (HDACs)

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7
Q

What nucleic acids are methylated?

A

Cytosine => 5’ methyl-cytosine

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8
Q

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

A
  • Hypermethylation = condensed chromatin = less expression

- Hypomethylation = open chromatin = more expression

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9
Q

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

A
  • found near chromosome ends or centromeres where there are few genes
  • methylated cytosines; deacetylated histone tails
  • transcriptional repression
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10
Q

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

A
  • Acetylated histone tails; hypomethylation

- transcriptional activation

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11
Q

What are TADs?

A
  • Topolocigally associated domains are genetic neighborhoods
  • Genes in a TAD are co-regulated
  • TADs are consistent across cell types but their regulations vary
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12
Q

How many chromatin states are there?

A

15 (more than just open/closed!)

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13
Q

What confers cell-type-specific transcription?

A

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

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14
Q

What is role of methylation in development?

A
  • Increasing methylation in prospematognoia and oocyte growth
  • Decreasing methylation from fertilization to blastocyst formation
  • Increasing methylation throughout embryogenesis as cells begin to differentiate
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15
Q

What are ways in which epigenetics can cause disease?

A
  • Imprinting
  • Pathogenic variation in genes that regulate epigenetic machinery
  • Pathogenic variation that affects chromatin state
  • Cancer
  • Transgenerational inheritance
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16
Q

What is Kabuki syndrome?

A
  • Rare neurodevelopmental disorder
  • Symptoms include: characteristic facial features, developmental delay, intellectual disability, growth deficiency, skeletal anomalies, congenital heart defects, genitourinary anomalies, seizures
17
Q

What are the mechanisms of Kabuki syndrome inheritance/occurence?

A
  • Autosomal dominant

- De novo

18
Q

What are the genetic causes of Kabuki syndrome?

A

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
19
Q

What is CHD2 associated epilepsy?

A
  • most severe pediatric epilepsy
  • first few day - years of life
  • drop attacks and atonic-myoclonic-absence seizures
  • no response to medication
20
Q

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

A

De novo mutation

21
Q

What is the genetic cause of CHD2-associated epilepsy?

A
  • 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)
22
Q

What are the symptoms of Fragile X syndrome>

A
  • Intellectual disability in males
  • Characteristic facial featuers
  • Joint laxity
  • Behavioral problems: social anxiety and autism spectrum disorder
23
Q

What is the genetic cause of Fragile X?

A

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
24
Q

What is the occurrence of congenital limb malformations?

A

1/500-1/1000 live births

25
Q

What is a genetic cause of isolated congenital limb malformation?

A
  • Deletion of a region including a TAD boundary => changed regulation of a gene in a neighboring TAD
26
Q

How can epigenetic marks contribute to cancer?

A
  • Hypermethylation of a tumor suppressor gene promoter => decreased expression
  • Hypermethylation and deacetylation of a tumor suppressor gene => decreased expression
27
Q

Can epigenetic modifications be inherited?

A

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

28
Q

What can epigenetic therapies be used to treat?

A
  • Kabuki (HDAC inhibitors)
  • Epilepsy (HDAC inhibitors)
  • Cancer (many targets)

Foundations 1 (26 decks)

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