Gregg

Question 1

Anatomy of a gene

Answer 1

5’ end - promoter
5’-UTR
Start codon (ATG) (encodes M)
next exon has an accepter site
introns are regions that don’t make it into protein
stop codon
3’-UTR
poly-A site

Question 2

role of epigenetic mechanisms

Answer 2

maintain cellular
identity

Question 3

Protocadherin Gene Clusters (PCDHG) are responsible for what in mammalian neurons?

Answer 3

Self-Recognition

Question 4

BRAIN DERIVED NEUROTROPHIC FACTOR

Answer 4

*Regulates cell differentiation, survival, migration, dendritic arborization, synaptogenesis, and
activity-dependent plasticity
*Expression is induced by neuronal activity

long 3’UTR targets transcript to dendrites

*BDNF val66met polymorphism is associated with altered hippocampal volume and anxiety
behavior (Chen et al. Science 2006; Egan et al., Cell 2003)
impaired episodic memory and hippocampal function

Question 5

Olfactory monoallelic

Answer 5

Question 6

Imprinted Genes

Answer 6

Question 7

lncRNAs - long non-coding RNAs

Answer 7

*thousands of lncRNAs in the human
genome (Guttman et al. 2009)
*can be megabases in length, but defined as non-coding RNA > 200 bps
low sequence conversion
involved in regulating gene expresison

Question 8

How do lncRNAs regulate gene expression

Answer 8

lncRNAs Regulate Expression of Neighboring Protein Coding
Genes By Forming Scaffolds to Regulate Chromatin

Question 9

micro RNAs

Answer 9

defined as 21-24 nucleotides in length
*Discovered by Victor Ambros, Gary
Ruvkan and David Baulcombe (Lasker Prize
2008)
*one miRNA can influence many genes

miRNAs regulate the translation of target RNAs by triggering transcript translation-interference or
degradation depending on the degree of matching.
1. Complete complementation = RNA degradation by Ago2
2. Incomplete complementation = translation-interference by Ago1

Question 10

miRNA biogenesis

Answer 10

1. Primary miRNA transcribed by Pol II
2. Pasha + Drosha RNase III form
   microprocessor
3. Microprocessor cleaves pri-RNA to
   form precursor mirRNA (60-70 nt)
4. Exportin 5 transports pre-miRNA to
   cytoplasm
5. Dicer + Loquacious (co-factor) cleaves
   pre-miRNA to form miRNA:miRNA
   duplex (22-23 nt)
6. miRNA duplex is sorted into
   Argonaute proteins to form RISC

Question 11

miRNAs = ?
siRNAs = ?

Answer 11

miRNAs = imperfect duplexes => AGO1
siRNAs = perfect duplexes => AGO2

Question 12

Epigenetics (MODERN meaning)

Answer 12

an epigenetic trait is a stably
inherited phenotype resulting from changes in a chromosome without
alterations in the DNA sequence

Question 13

Epigenetics studies:

Answer 13

Reversible heritable changes in gene function
that occur without a change in the sequence of
nuclear DNA
How environmental factors and signals result
in long-term gene expression changes
How cellular identity is maintained

Question 14

Epigenetic mechanisms maintain ______

Answer 14

cellular
identity

Question 15

Heritability = ?

Answer 15

Heritability = 2 x (MZ - DZ)

Question 16

Non-DNA parts of genome (w/ image)

Answer 16

Chromatin
Solenoid
Nuclesome
Histone Ocamer
Histones

Question 17

Chromatin

Answer 17

mass of DNA and protein that composes a chromosome

Question 18

Solenoid

Answer 18

packing of nucleosomes + DNA as a 30 nm fiber of chromatin resulting from helical winding of at least 5 nucleosome strands

Question 19

Nucleosome

Answer 19

146 bp of DNA wrapped 1.76 times around a histone octamer

Question 20

Histone Octamer

Answer 20

two H2A-H2B dimers and a H3-H4 tetramer

Question 21

Histones

Answer 21

5 major families - H2A, H2B, H3, H4 (core histones); H1/H5 (linker histones). Amino termini tails project out of the nucleosome core and can be epigenetially modified (acetylation, methylation, phosphorylation)

Question 22

2 types of chromatin

Answer 22

euchromatin

heterochromatin

Question 23

euchromatin

Answer 23

Less condensed
@ chromsome arms
contains unique sequences
gene-rich
replicated throughout S phase
Recombination during meiosis

Question 24

Heterochromatin

Answer 24

highly condensed
at centromeres/telomers
contains repetitious sequences
gene-poor
replicated in late S phase
no meiotic recombination

Question 25

Answer 25

Question 26

Epigenetic processes can be divided into:

Answer 26

1. Signals that trigger the establishment of an epigenetic mark 2. Epigenetic initiator factors that define the location of the mark in the genome. 3. Maintenance signals that sustain the epigenetic mark

Question 27

Where does DNA methylation occur?

Answer 27

DNA methylation occurs on the 5th carbon of cytosine = 5mC 1. 5mC consitutes ~1% of all bases and is found almost exclusively as symmetrical methylation of the dinucleotide CpG

Question 28

What is CpG island?

Answer 28

a sequence of >200bp with a greater number of CpG sites than expected for its GC content. ~60% of human genes have CpG islands at their promoters.

Question 29

Answer 29

DNA methyl transferase (DNMT) 3A and DNMT3B = de novo methylation DNMT1 = maintenance methylation (affinity for hemi-methylated DNA)

Question 30

Effects of methylination on DNA

Answer 30

*DNA methylation at CpG islands in promoters leads to chromatin structure changes that inhibit gene expression *Methylated DNA promotes DNA binding by some proteins: Methyl CpC-binding domain proteins (MBD 1, 2, 3 and 4) Methyl CpG-binding protein 2 (MeCP2) *Methylated DNA inhibits DNA binding by some proteins: CCCTC-binding factor (CTCF) - an insulator protein ETS1 - a transcription factor

Question 31

Which proteins are responsible for active DNA-demethylation

Answer 31

ten-eleven translocation (Tet) dependent demthylation (tet1,2,3)

Question 32

5hmc

Answer 32

Formed by adding methyl group to cytosine and then an hydroxyl group

Question 33

Tet mechanism

Answer 33

Role for TET enzymes in 5mC conversion to 5hmC was discovered by Tahiliani et al. 2009 *Trypanosomes contain base J - a modified thymine produced by the JBP1 and JBP2 enzymes *Mammalian JBP paralogous proteins were identified TET1, TET2, TET3

Question 34

Answer 34

Question 35

4 major post translational histone modifications

Answer 35

1. acetylation 2. methylation 3. ubiquitylation 4. phsphorylation

Question 36

Expressed Gene

Answer 36

Question 37

Repressed Gene

Answer 37