Epigenetic Phenomena

Question 1

Epigenetics

Answer 1

Study of heritable changes that do not involve changes in DNA sequence that either silence or activate chromosomal regions by changing DNA methylation and histone acetylation patterns

Question 2

CpG dinucleotide repeat

Answer 2

Where DNA is methylated on cytosine residue (about 70% silenced this way, including repetitive DNA, telomeres, and centromeres)

Question 3

Retrotransposons in human genome

Answer 3

Thought to be the origin of of 45% of the human genome (from viruses); transposable elements are able to move around in the genome

Question 4

CpG islands

Answer 4

Clusters of CpG dinucleotide repeats close to 5’ region of genes that are generally unmethylated – methylation will shut down expression of neighboring genes

Question 5

Effect of hypermethylation on genome stability

Answer 5

Shuts down expression of genes close to CpG islands (TOO MUCH methylation)

Question 6

Effect of hypomethylation on genome stability

Answer 6

Initiates expression of genes in normally silent regions and reactivates transposable elements in normally genomic region (TOO LITTLE methylation)

Question 7

De-novo methylation

Answer 7

Introduced into unmethylated strand of DNA by DNA methyltransferases DNMT3a and b (primary methylation) – may be triggered by histone modification

Question 8

Maintenance methylation

Answer 8

Maintains the primary methylation pattern through mitosis by the use of DNA methyltransferase DNMT1

Question 9

How does DNMT1 function?

Answer 9

1. During DNA replication (S-phase), DA polymerase synthesizes non-methylated strand on methylated template strand
2. New double strand consists of methylated and non-methylated single strand
3. Non-methylated strand methylated by DNMT1 using template of precious methylation pattern

Question 10

How do methylcytosine binding proteins (MBPs) function?

Answer 10

MBPs repress transcription by interacting with repressors of transcription (block transcription) and HDACs (remove acetyl groups from histones) – leads to chromosome condensation

Question 11

Rett syndrome

Answer 11

Mode of inheritance: XD
Pathology: mutations in methyl-cytosine binding protein MECP2 leading to loss of transcriptional silencing
Symptoms: autism-like, teeth-grinding/hand-wringing, motor problems, characteristic gait
Other: onset is 6-18 mo.

Question 12

Histone acetyltransferases (HATs)

Answer 12

Acetylate histones to decrease their binding affinity to DNA and facilitate transcription

Question 13

Histone deacetylase (HDAC)

Answer 13

Deacetylate histones to increase their binding affinity to DNA and silence transcription

Question 14

HP1 proteins

Answer 14

After de-acetylated histones beome methylated, bind the methylated histones and histone methylases and cause methylation to spread along chromosomes until boundary elements are reached

Question 15

Histone methylases

Answer 15

Bound to HP1 proteins along with methylated histones and help spread methylation

Question 16

What modifications do we find on histones?

Answer 16

1. Acetylation
2. Methylation
3. Phosphorylation
4. Ubiquitination
   - -Constitute “histone code”

Question 17

Histone acetylation

Answer 17

Occurs on tail region, decreases affinity to DNA due to tighter binding

Question 18

Histone exchange

Answer 18

Cells can exchange standard histones with specific variants – often observed in activation of stress response genes (ex. H2A exchanged with variant H2Az to facilitate transcription of adjacent genes)

Question 19

Boundary elements (chromatin barriers)

Answer 19

Important for separating active and inactive genomic regions by terminating methylation;

Question 20

Example of mutant phenotype due to boundary element problems

Answer 20

If inactivated region of X-chromosome is translocated to autosome, it can silence autosomal region and lead to dominant mutant phenotype

Question 21

2 biological processes imprinting is important for

Answer 21

1. Development (cell-type specific)
2. Maturation of gametes (parent-of-origin specific)
   - -Both maintained through mitosis

Question 22

What is imprinting?

Answer 22

Form of DNA silencing that marks a chromosome as coming from father or mother due to differing repression of specific genes; done using DNA methylation and histone deacetylation

Question 23

When does imprinting take place?

Answer 23

During gametogenesis

Question 24

Parent-of-origin specific imprint in gametogenesis

Answer 24

Needs to be erased and rewritten
Female: reprograms both paternal and maternal to make them look maternal
Male: reprograms both to make them look like paternal

Question 25

X-chromosome inactivating center (XIC)

Answer 25

Section of the chromosome with XIST gene that initiates X-chromosome inactivation

Question 26

XIST (inactive X-specific transcript)

Answer 26

Gene in XIC region that is transcribed on X-chromosome that will be inactivated; has RNA that associates closely with X-chromosome to mediate inactivation of chromosome

Question 27

Uniparental disomy

Answer 27

Abnormality in which an individual only has maternally or paternally imprinted homologues of a chromosomes, normally due to a correction of a trisomy; leads to problems with gene dosage (ex. Beckwith-Wiedemann syndrome)

Question 28

Beckwith-Wiedemann syndrome (BWS)

Answer 28

Prevalence: 1/13,000
Pathology: child inherits both homologues of portion of chromosome 11 from father leading to overabundance of insulin-like growth factor 2
Symptoms: kidney, adrenal, and liver problems, severe hypoglycemia

Question 29

Effects of imprinting on BWS

Answer 29

Uniparental disomy leads to overabundance of region A from paternal chromosome and lack of B (which would normally come from region of maternal chromosome that is not silenced)

Question 30

Parent-of-origin effect is best studied in which two syndromes?

Answer 30

1. Prader-Willi syndrome (PWS)

2. Angelman syndrome (AS)

Question 31

Prader-Willi syndrome

Answer 31

Prevalence: 1/10,000-50,000
Pathology: deletion on paternal copy of chromosome 15 or maternal uniparental disomy
Symptoms: excessive food-seeking behavior, hypogonadism, mental retardation, hypotonia, small hands, specific facial features

Question 32

Parent-of-origin effect in Prader-Willi syndrome

Answer 32

Deletion in paternal chromosome leads to lack of A (since A would have come from the area on paternal chromosome that was deleted)

Question 33

Angelman syndrome

Answer 33

Prevalence: 1/15,000
Pathology: deletion on maternal copy of chromosome 15 or paternal uniparental disomy
Symptoms: unusual facial features, excessive laughter, seizures, severe mental retardation and absence of speech

Question 34

Parent-of-origin effect in Angelman syndrome

Answer 34

Deletion in maternal chromosome leads to lack of B (since B would have come from that area on paternal chromosome that was deleted)

Question 35

How do epigenetic changes play a role in development of cancer?

Answer 35

Hypermethylation: silencing genes – functions like loss-of-gene mutation and often affects tumor suppressor genes
Hypomethylation: activation of silent chromatin – leads to genomic instability and can cause tumor cells to form

Question 36

Genome instability

Answer 36

Results from hypomethylation; either initiates or facilitates transformation of a cell into a tumor cell

Question 37

How does genome instability lead to formation of tumor cell?

Answer 37

• -Somatic recombination (breakage and re-sealing with non-homologous recombination) can change expression/function of oncogenes and tumor suppressor genes
• -Leads to drastic increase in mutations after tumor is established, causing rapid evolution

Question 38

Systemic lupus erythrematosus (SLE)

Answer 38

Autoimmune disorder with diverse clinical manifestations that leads to production of antibodies against nuclear components; thought to be caused by abnormal T-cell function due to hypomethylation that reduces activity of DNMT1 and causes expression of normally silenced genes

Question 39

HDAC inhibitors

Answer 39

A drug used to counteract malignancy by promoting histone hyperacetylation and gene re-expression

Question 40

What illness do HDAC inhibitors help with?

Answer 40

Chronic lymphocytic leukemia

Question 41

DNA methyltransferase (DNMT) inhibitors

Answer 41

Cause hypomethylation of genome to counteract hypermethylation

Question 42

5-azacytidine

Answer 42

DNMT inhibitor that has potential to counteract malignancies associated with hypermethylation using hypomethylation

Question 43

What illness do DNMT inhibitors help with?

Answer 43

Acute myeloid leukemia

Question 44

Heterochromatin in terms of histone composition/DNA methylation

Answer 44

Tightly packed; in contact with histones and highly methylated

Question 45

Euchromatin in terms of histone composition/DNA methylation

Answer 45

Not condensed; not in contact with histones and not methylated