Epigenetic Phenomena

Question 1

Epigenetic Changes in gene expression consist of?

Answer 1

• -methylation and demethylation of DNA regions

- -modification of histones

Question 2

Definition of Epigenetics

Answer 2

–study of stable, heritable changes in gene expression that DO NOT involve changes in DNA sequence

Question 3

Regulation of Gene expression by epigenetic mechanism is important for (3 things)?

Answer 3

• -imprinting during development and gametogenesis
• -inactivation of X-chromosome
• -progression of cancer

Question 4

Stability of Epigenetic Changes

Answer 4

• -permanently silence or activate large chromosomal regions
• -conserved through mitosis and persist through the life of individual
• -others are stable even through meiosis/gametogenesis and can be passed on through germline

Question 5

Epigenetic Writers

Answer 5

• -enzymes that are able to methylate cytosine bases in response to cellular signaling events (de novo DNA methyltransferases
• -highly regulated
• -done by more specific DNA methyltransferases

Question 6

Epigenetic Copiers

Answer 6

• -enzymes that copy a methylation pattern from an old DNA strand over to a freshly synthesized new one
• -accomplished by more general DNA methyltransferases

Question 7

Epigenetic Readers–

Answer 7

• -enzymes that recognize methylated stretches of DNA and initiate silencing of the affected chromosomal region (methylcytosine binding proteins)
• -recognition of methylated DNA puts into motion a process of chromatin modification that induces covalent modification of histones

Question 8

DNA methylation occurs where?

Answer 8

• -CpG dinucleotide repeats
• -70% of these repeats are silenced in human genome by methylation (includes highly repetitive DNA, telomeres, centromeres)
• -45% of genome is thought to be derived from retrotransposons of viral origin and DNA methylation helps keep these silenced

Question 9

Hypo- vs. Hypermethylation

Answer 9

• -need a balance between the two
• -hypomethylation will give expression of normally silenced genes (retrotransposons = somatic recombination and genomic instability
• -hypermethylation will shut down expression of genes close to CpG islands

Question 10

CpG Islands

Answer 10

• -clusters of CpG dinucleotide repeats
• -found close to 5’ region of genes
• -generally unmethylated

Question 11

2 types of DNA methyltransferases

Answer 11

• -more specific used as a writer enzyme

- -more general = copier enzyme since all it needs to do is copy methylation pattern

Question 12

Steps of DNA methylation

Answer 12

• -writers (DNMT) methylate the DNA that is to be silenced
• -DNA is replicated and only the template strand contains methylated bases (new strand is unmethylated–helpful for DNA repair since machinery can tell which was original template strand)
• -Copiers copy methylation pattern according to template strand (more general DNMT1)

Question 13

After DNA has been methylated….(methylcytosine binding proteins)

Answer 13

• -repression of transcription is brought about by binding of methylcytosine binding proteins (MBP’s)
• -MBP’s interact w/ repressors of transcription and histone deacetylases (HDAC’s)

Question 14

Rhett Syndrome

Answer 14

• -defects in methylcytosine binding protein MECP2
• -loss of transcriptional silencing
• -X-linked dominant (only seen in girls since it is perinatal lethal in boys)
• -onset at 6-8 months
• -autism-like symptoms, teeth grinding, motor problems, characteristic gait

Question 15

Spread of Deacetylated Histones

Answer 15

• -deacetylated histones become methylated
• -methylated histones bind HP1 protein
• -HP1 proteins bind histone methylases and methylation of histones spreads along the chromosomes until a boundary element is reached

Question 16

Boundary Element

Answer 16

• -aka chromatin barriers

- -essential for separating active and inactive genomic regions

Question 17

Self propagating nature of DNA activation and possible problems

Answer 17

• -DNA methylation spreads when histone methylase binds to HP1
• -fragment of inactive X chromosome translocates to autosome where the inactive fragment will propagate across DNA that is not supposed to be inactivated

Question 18

Imprinting is an important part of what two biological processes?

Answer 18

• -development (to permanently change the gene expression pattern of a cell line)
• -maturation of gametes (to mark parental origin of a chromo)

Question 19

Imprinting

Answer 19

• -silences chormosomal regions by DNA methylation and histone deacetylation
• -can be reversed (in theory) by in general is stable though somatic cell divisions (mitosis)
• -during gametogenesis, both females and males reprogram their maternally and paternally inherited chromosomes to make them both look like maternal and paternal chromosomes, respectively

Question 20

Inactivation of X-Chromosome

Answer 20

• -occurs by imprinting
• -X inactivating center (XIC) has unusual gene called XIST which must be transcribed for X-chromosome to be inactivated
• -XIST RNA associates w/ X chromosome

Question 21

Uniparental Disomy

Answer 21

–instead of having one maternal chromo and one paternal chromo to make a pair of homologs you either have both maternal or both paternal pairs

Question 22

Rescue of Aneuploid Zygote

Answer 22

• -trisomy zygote will most likely spontaneously abort

- -however, loss of a chromosome can result in mosaicism or uniparental disomy w/ viable life

Question 23

Prader-Willi Syndrome

Answer 23

• -deletion on paternal copy of chromo 15 or maternal uniparental disomy
• -1/10,000-50,000
• -excessive food seeking behavior, hypogonadism, mental retardation, hypotonia

Question 24

Angelman Syndrome

Answer 24

• -deletion on maternal copy of chromo 15 or paternal uniparental disomy
• -1/15,000
• -unusual facial features, excessive laughter, movement disorders, seizures, severe mental retardation

Question 25

Beckwith-Wiedemann Syndrome

Answer 25

• -paternal uniparental disomy of chromo 11
• -1/13,000
• -microcephaly, macroglossia, umbilical hernia
• -overabundance of insulin-like growth factor 2 causes multiple organ problems (hypoglycemia)
• -susceptibility to childhood cancer

Question 26

Global Hypomethylation of DNA outside of CpG islands

Answer 26

• -found in most cancers
• -causes genomic instability (elevated transposon activity, chromosomal abnormalities)
• -genomic instability in turn causes cancer

Question 27

Global Hypermethylation of DNA

Answer 27

• -can silence much needed tumor supressor genes
• -other genes that are very much needed
• -10-15% of non-familial breast cancers due to hypermethylation of BRCA1

Question 28

Systemic Lupus Erythematosus

Answer 28

• -caused by epigenetic changes in T-cells
• -autoimmune disease (1/2,000) affecting females 8-10x more frequently
• -antibodies against nuclear components are produced
• -SLE Pts. have global hypomethylation of T-cell genome
• -treating T-cells w/ DNMT inhibitors causes SLE-like phenotypes

Question 29

Two Classes of Drugs available to influence DNA methylation and histone deacetylation

Answer 29

• -Histone deacetylase (HDAC) inhibitors: promotes histone hyperacetylation and gene re-expression in chronic lymphocytic leukemia
• -DNA methyltransferase (DNMT) inhibitors: (5-azacytidine) causes hypomethylation of genome, potential to counteract malignancies associated w/ hypermethylation and has been approved for therapy of acute myeloid leukemia