Exam 2

Question 1

Mechanisms of epigenetics

Answer 1

DNA methylation - transcriptional
Histone modification - transcriptional
miRNA - post-transcriptional
siRNA - post transcriptional
Prions

Question 2

Heritability

Answer 2

Epigenetic changes ARE heritable

• non-mutational changes that are transmitted from one cell to its daughter cell
• transmitted between generations

Question 3

Epigenetics defintion

Answer 3

structural adaptation of chromosomes so as to register, signal, or perpetuate altered activity states

Question 4

Factors that affect the epigenome

Answer 4

Diet (higher effect in utero, eg. methyl deficiency prevents necessary methylation marks from occurring)
Toxins/chemicals (bisphenol A - aberrant imprinting)
Environment (maternal behavior)
Aging (histone acetylation and deacetylation)
Drugs/pharmaceuticals

Question 5

Epigenetic defects

Answer 5

Imprinting disorders (Angelman, Prader-Willi, Beckwith-Wiedemann)
Cancer
Multifactorial disorders (autism, bipolar disorder)

Question 6

DNA methylation and histone modification

Answer 6

Control availability of chromatin to transcriptional machinery

Question 7

Types of chromatin

Answer 7

Euchromatin - decondensed, may be silent or active
Heterochromatin - highly compacted and silenced
Constitutive heterochromatin - Always silenced (centromeres and telomeres)
Facultative heterochromatin - repressed but may be active for specific parts of the cell cycle or development

Question 8

Chromatin organization

Answer 8

• Nature of DNA sequence is important
• Quality of RNA produced determines whether it is a fully functional mRNA or if it will be earmarked for use in RNA interference to target heterchromatin

Question 9

Histones

Answer 9

• Very small, highly basic, make up the nucleosome
• Highly conserved - serve critical functions
• Histone tails are subject to post-translational modification
• Majority of modifications occur at N-terminal tail of histones (many lysines and arginines here) - typically methylation but can also see acetylation, phosphorylation, and ubiquitination
• H1 histone is the “bar” that holds the nucleosome together

Question 10

Histone modifications

Answer 10

• Cis effects - Changes in physical properties of modified tails (acetylation and phosphorylation)
• Trans effects - Recruitment of modification-binding partners to chromatin (bromo and chromo domains)
• Modifications can be activating or repressive
• May lead to decrease or increase in contacts between nucleosome leading to increased of decreased access to chromatin respectively

Question 11

DNA Methylation

Answer 11

• Typically occurs in CpG islands
• Catalyzed by methyltransferases (DNMT1, DNMT3a, DNMT3b)
• Inverse relationship between CpG methylation and transcriptional activity
• Serves mainly as a host defense mechanism to silence much of the genome of foreign origin
• Silencing
• Some can be reversed
• Hypermethylation can lead to changes in structure and silencing of tumor supressor genes
• Important in X inactivation
• Bivalent domains mark CpG-rich promoters of developmental genes in embryonic stem cells
• Trithorax group methylates histone H3K4
• Polycomb complexes methylate histone H3K27

Question 12

RNA interference

Answer 12

A conserved silencing mechanism whereby dsRNA induces specific down-regulation/silencing of homologous sequences

Question 13

RNAi mechanisms

Answer 13

miRNA or siRNA (in lower organisms)

• dsRNA cleaved into siRNA by DICER
• bind RNA-induced silencing complex (RISC)
• RISC-RNA complex binds mRNA of interest and argonaute protein cleaves the mRNA leading to degradation

Question 14

miRNA vs siRNA

Answer 14

siRNA - usually exogenous, come from viruses

miRNA - genomically encoded to help regulate gene expression, particularly during development

Question 15

Purpose of RNAi

Answer 15

-plays a role in immunity in lower organisms/plants
-maintenance of undifferentiated or incompletely differentiated types
-imprinting
-cell cycle
can be applied to medicine and biotechnology

Question 16

Enhancer

Answer 16

-set of short sequence elements which stimulate transcription and whose function is not critically dependent on their location

Question 17

Promoter

Answer 17

Combination of short sequence elements typically just upstream of a gene to which RNA polymerase binds to initiate transcription

Question 18

Locus control region

Answer 18

stretch of DNA containing regulatory elements which control the expression of genes in a cluster that may be far away

Question 19

Insulator/boundary element

Answer 19

DNA elements that act as barriers to the spread of chromatin changes or the influence of cis-acting effects

Question 20

Transcription factor

Answer 20

Upregulates or downregulates transcription

Question 21

ChIP

Answer 21

chromatin immuno-precipitation sequencing

-examines histone modifications and protein binding

Question 22

DNA footprinting

Answer 22

Use an enzyme with random cleavage activity to determine binding sites for specific proteins
-if protein binds, it produces a “footprint” on gel where protein protected sequence from cleavage

Question 23

Databases

Answer 23

ENCODE
ORegAnno - Open regulatory annotation
TRED - Transcriptional Regulatory Element Database
ReulomeDB

Question 24

What are the goals of identifying genetic risk factors for eye diseases?

Answer 24

Developing clinically useful gene-based screening tests and new therapeutic strategies with the final goal of reducing the global burden of visual impairment from these conditions.

Question 25

What are two loci with substantial effect on AMD risk?

Answer 25

• 1q32

- 10q26

Question 26

What are the 5 pathways involved in AMD?

Answer 26

• inflammation, specifically the innate immune system disregulation & enhanced complement activation
• lipid transport
• ECM remodeling
• angiogenesis
• cell survival, including DNA repair, apoptosis, and stress response

Question 27

Which immune system (innate or adaptive) is involved in SLE and AMD?

Answer 27

AMD - innate only!!!

SLE - both innate and immune

Question 28

Which region is important for several diseases including AMD and SLE? (The most important genetic factors influencing susceptibility to autoimmune diseases are located at the)

Answer 28

MHC (major histocompatibility complex) - 6p21

Question 29

Which member of the innate immune system involved in a number of pathways is involved in SLE and AMD?

Answer 29

Complement system/complement cascade

Question 30

Describe the signature that plays a central role in the initiation and progression of SLE

Answer 30

Interferon-alpha (IFN-alpha) levels have been consistently shown to be elevated in sera from SLE patients and the type-I IFN system-regulated genes (inducible by IFN-alpha) have been found to be upregulated in their peripheral blood mononuclear cells (so called ‘interferon signature’)