Epigenetics, DNA, Methylation, Imprinted Genes

Question 1

What is epigenetics?

Answer 1

study of heritable changes in genome function that occur without alterations to the DNA sequence

Question 2

How can epigenetics occur?

Answer 2

changes in gene expression occur by DNA methylation (hallmark of epigenetic), histone modifications and chromatin remodeling

very difficult to reverse/are irreversible

note: upregulating and downregulating gene effect is the same as a mutation

Question 3

How are epigenetic factors inherited?

Answer 3

mitotically (somatic cells) or meiotically (transgenerationally)

typically, it is the grandparent’s change that is shown in the grandkids

Question 4

what are the three most important effects of epigenetics?

Answer 4

1. developmental plasticity: environmental exposures produces a broad range of adult phenotypes from a single genotype
2. fetal basis or developmental origins of adult-onset of disease
3. potential targets for new therapies: stem cells (developmental reporgramming of somatic nucleus) and cancer

Question 5

Describe the ways in which a variety of phenotypes can be expressed given the same genotype from an embryo standpoint.

Answer 5

prenatal and postnatal environmental factors; nutritional supplements, xenobiotics chemicals, behavioral cues, reproductive factors and low-dose radiation can result in altered epigenetic programming and subsequent changes in the risk of developing disease

Question 6

what are the four major mechanisms of epigenetic changes?

Answer 6

1. dna methylation: subset of C residues can be modified by methylation
2. histone modifications: acetylated, replaced/substituted
3. non-coding RNAs: miRNAs and long non-coding RNAs
4. chromatin remodeling: heterochromatin vs euchromatin

Question 7

how do these epigenetic mechanisms affect each other?

Answer 7

may be additive

a change in one may influence whether another change will occur

Question 8

what is the difference between constitutive or faculative heterochromatin?

Answer 8

faculative: less condensed, less stable, and much less polymorphic; can change from euchromatin to heterochromatin
constitutive: composed mainly of high copy number tandem repeats known as satellite repeats, minisatellite and microsatellite repeats, and transposon repeats

Question 9

what is the difference between euchromatin and heterochromatin? specifically the methylation

Answer 9

euchromatin: high histone acetylation, low DNA methylation, H3-K4 methylation
heterochromatin: low histone acetylation, dense DNA methylation, H3-K9 methylation

Question 10

what nt is methylationed, where and how?

Answer 10

cytosine, on C5, and by DNMts

the CpG islands that are 1/100bp are mostly methylated
the CpG islands that are 1/10bp are mostly unmethylated (near promoters)

Question 11

what type of modification occurs on histone tails?

Answer 11

covalent modifications - determine the formation of euchromatin and heterochromatin

Question 12

describe how histone aceylation occurs and where?

Answer 12

lysine is acetylated by HATs and deacetylated by HDACs; occurs at N terminus and acetylation removes positive charge, which reduces the affinity between histones and DNA -> makes RNA polymerase and TF easier to access the promoter region

Question 13

what are the two types of non-coding RNAs? How do they affect cancer?

Answer 13

miRNAs: amplification, deletion, methylation, gene expression

long ncRNAs: gene expression, translocation

Question 14

What are the mechanism of actions of miRNAs?

Answer 14

endonucleolytic cleavage, deadenylation and degradation, inhibition of translation initiation, inhibition after translation initiation, stimulation of translation

Question 15

what are the mechanism of actions of lncRNA?

Answer 15

flexible scaffold for chromatin-modifying complexes, enhancer RNAs, tumor suppressor signaling, RNA processing, RNA-RNA interactions, miRNA squestration

Question 16

How does chromatin remodeling influence level of gene expression? three main types?

Answer 16

mediated by ATP dependent nucleosome - remodeling complexes that use the E of ATP hydrolysis to noncovalently reposition histone octamers and generate nucleosome free or dense chromatin

writing, editing and reading

Question 17

what is the mechanism of X-inactivation? How does the cell know which x chromosome to inactivate?

Answer 17

1. initiated at X inactivation center (XIC)
2. at XIC there is a gene for Xist RNA (X inactive specific transcript) - signals that this X chromosome is to not be activated
3. Xist RNA binds in cis (independent of DNA sequence) then spreads up and down chromosome
4. once established, the pattern of inactivation is maintained through mitosis

histones are under acetylated and DNA is heavily methylated on cytosines of CpG sequences

**expression of XIST on the active X chromosome is blocked by an antisense RNA called TSIX

Question 18

How does transcription occur on the x chromosome?

Answer 18

ICE - chromatin boundary element that binds CTCF (barrier to transcription) in unmethylated state; TSIX makes the x chromosome active and on this chromosome, ICE is methylated - CTCF cannot bind to ICE when ICE is methylated

Question 19

what is genomic imprinting?

Answer 19

mechanism of epigenetic gene regulation through which the activity of a gene is reversibly modified depending on the sex of the parent that transmits it; results in the unequal expression of the maternal and paternal alleles of a gene

challenges the assumption that the maternal allele = paternal allele

Question 20

what are some characteristics of genomic imprinting?

Answer 20

located in clusters, noncoding RNAs and antisense transcripts, differential methylation, histone modifications, and heritable

Question 21

what is Beckwith-Wiedemann syndrome?

Answer 21

on chromosome 11…must have a mutation in the gene and epigenetic changes

in females: H19 (promotes embryoic growth - from dad) is expressed (DMD/ICR is blocked by CTCF)
in males: Igf2 (tumor suppressor RNA - from mom) is expressed (DMD/ICR, H19 is methylated)

fetal overgrowth disorder: gigantism, macroglossia, viceromegaly, and embryonic Wilms tumors

Question 22

how can epigenetics affect cancer? (generally, histone acetylation, miRNA, lncRNAs

Answer 22

may not have a mutation, but have hypermethylation of CpG islands that turn off tumor suppressor genes; can also have hypomethylation to turn on oncogenes

histone acetylation: H4K16 can be acetylated (normal transcription) or deacetylated (tumorigenesis)

miRNA: normally have let-7; in many cancers can have a down regualtion of let-7, which results in activation of oncogenes….can also have miRNA-10b which is upregulated in cancer

lncRNAs - angiogenesis, viability, proliferation, growth suppression, motility, immortality