1-27 Epigenetics

Question 1

Epigenetics

Answer 1

Defined as study of heritable changes in gene expression without a change in the actual DNA sequence

Question 2

Nucleosomes

Answer 2

made of 8 histones (H2A, H2B, H3, H4), 146 bp of DNA + 1 linker dna

can be tightly or loosely packed based on histone modifications (methylation, acetylation, phospho, deimination, UBquitination)

Question 3

Histone Acetylation

Answer 3

Increases negative charge -> reduces interaction with DNA (since it is also negative charged), therefore permits gene expression

Histone deacetylation (HDACs) reverse this

Question 4

DNA methylation

Answer 4

Cytosine -> 5’ methyl cytosine

methylation associated with closed chromatin confirmation and lack of gene transcription

Question 5

Topologically associated domains (TADS)

Answer 5

co-regulation of genes in these TAD “neighborhoods” within the nucleus,

TADs separated by CTCF

these TADs are turned on/off for transcription in different cell types = chromatin states confer cell specificity

cycles of high to low DNA methylation to guide cell type specificity, this is how we go from zygote to make all specialized cells of the body

Question 6

Epigenetics and diseases overview of potential mechanisms (5)

Answer 6

1. imprinting
2. pathogenic variants in genes that regulate epigenetic machinery
3. pathogenic variants that alter chromatin state
4. cancer
5. transgenerational inheritance

Question 7

Kabuki syndrome

Answer 7

Rare neurodev disorder: characteristic facial features, mild to severe dev delay intell dis, minor skeletal anomalies, heart defect, seizures, poor growth

one of first success stories of exome sequencing: looked for rare variants in exomes that impact protein function

30-50% are inherited, autosomal dominant, MLL2 or KMT2D mutations found in 35/53 families with kabuki

MLL2: histone 3 lysine 4 methyltransferase, when methylated there is an open chromatin, in kabuki there is reduced methylation at this site resulting in closed chromatin and reduced expression of important genes for development

KDM6A: histone 3 lysine 27 demethylase: normally unmethylated and there is open chromatin, in kabuki there is increased methylation at this site and now closed chromatin and reduced expression

Question 8

Developmental and epileptic encephalopathy

Answer 8

epilepsy, most severe of all pediatric epilepsies, refractory seizures, poor outcomes, cognitive arrest or regression, photosensitivity, drop attack, atonic-myoclonic-absence seizure

Exome sequencing: de novo variants, neither parent effected, all people have 0-2 de novo mutations/individual, when we sequence many individuals we can line up the same exome mutation which supports its role in this novel epilepsy syndrome

CHD2: chromatin remodeler, majority pathogenic variants are truncating suggesting haploinsufficiency, results in more closed chromatin confirmation and results in change in gene expression important for brain development (many of these dysregulated genes are implicated in epilepsy)

CHD7: associated with CHARGE syndrome
CHD8: autism spectrum disorder
*phenotypes are different therefore the CHDs target different chromatin spots in the genome

Question 9

Fragile X Syndrome

Answer 9

most common cause of intellectual disability in males, characteristic facial features, joint laxity, behavioral problems

healthy: promoter-CGG 6-44 repeats-FMR1 expressed
fragile X: promoter-CGG 200+ repeats get methylated-FMR1 not expressed

Question 10

Congenital limb malformations

Answer 10

1:500-1:1000 live births, some genes implicated but normally only as part of larger syndrome

isolated cause unknown so did exome sequencing and found deltions, duplications, inversions all within the same region

EPHA4: deleted in brachydactyly, but when delete that gene in mouse there is no phenotype, if you delete the larger sequence around EPHA4 perfect model of human disease based on increasing PAX3 expression

WNT6: expression increased for F-syndrome hand problem
IHH: expression increased in polydactyly

these are all related to disruption the TAD boundary structures in this same gene area

Question 11

Epigenetics in cancer

Answer 11

cancer hijacks: DNA methylation, histone modifications and microRNA silencings

Question 12

Transgenerational inheritance

Answer 12

some epigenetic marks can be passed generationally

Question 13

Epigenetic therapies

Answer 13

HDAC inhibitors: Kabuki, used and reversed phenotype in Kabuki syndrome, on its way to human trial

HDAC inhibitor: epilepsy, valproate: increases GABA levels although mech largely unknown

Cancer: many different ones in progress!