Regulation of Gene Expression I

Question 1

What are the 2 major modifications that dictate if a region of a chromosome is active vs inactive?

Answer 1

DNA methylation

Histone modification

Question 2

Where is DNA methylated?

Answer 2

5-methyl cystosine

Question 3

What is chromatin composed of?

Answer 3

DNA plus all the associated proteins stuck on it

Question 4

What is a histone?

Answer 4

Core of nucleosomes, with DNA wrapped around it

Question 5

in eukaryotes, most genes are ___.

Answer 5

Silenced

Question 6

What are the characteristics of the DNA and histones in heterchromatin?

Answer 6

DNA is hypermethylated at CpG dinucleotides

Histones are deacetylated

Question 7

What are the characteristics of the DNA and histones of euchromatin?

Answer 7

DNA is hypomethylated

Histones are acetylated

Question 8

Which is being actively transcribed, heterochromatin or euchromatin?

Answer 8

Euchromatin

Question 9

What do histone acetyl transferases (HATs) do?

Answer 9

Unwind DNA to promote transcription

Question 10

What do histone deacetylases (HDACs) do?

Answer 10

Reverse HATs and form nucleosomes

Question 11

When chromatin relaxes, what results?

Answer 11

Hypersensitivity to DNase treatment

Question 12

What does epigenetic mean?

Answer 12

Changes in phenotype without changes in genotype - Genes are the same, but only some are active in certain tissues

Question 13

What is the gene silencing mechanism?

Answer 13

DNA methylation

Question 14

What is the gene activation mechanism?

Answer 14

Histone acetylation

Question 15

What are the 2 epigenetic modification activating marks that we need to know?

Answer 15

Histone acetylation of H3 and H4

Unmethylated CpG

Question 16

What are the 2 epigenetic modification silencing marks that we need to know?

Answer 16

Histone deacetylation at H3 and H4

Methylated CpG

Question 17

DNA methylation = ?

Answer 17

Gene silencing

Question 18

CpG pairs have been lost from the genome over time except in ___.

Answer 18

Euchromatin

Question 19

What does spontaneous deamination of 5-methyl cytosine yield?

Answer 19

Thymine

Question 20

CpG sites are hotspots for what?

Answer 20

Genetic mutation

Question 21

What do methylcytosines do?

Answer 21

Attract/recruit repressor proteins - directly block transcription factor from binding; may recruit other proteins to block transcription of the gene

Question 22

Histone deacetylation is a marker for what?

Answer 22

Silencing

Question 23

What regulates X-inactivation?

Answer 23

The Xist gene transcript, transcribed from the inactivated X chromasome

Question 24

What are the classic examples of genomic imprinting?

Answer 24

Prader-Willi

Angelman

Question 25

If only paternal genes are expressed, which disease is present?

Answer 25

Angelman

Question 26

What is the mutant chromosome present in Angelman?

Answer 26

Mutant maternal chromosome 15

Question 27

If only maternal genes are expressed, which disease is present?

Answer 27

Prader-Willi

Question 28

What is the mutant chromosome in Prader-Willi?

Answer 28

Mutant paternal chromosome 15

Question 29

What are the symptoms of Prader-Willi?

Answer 29

``` Mental retardation Obesity Hypogonadism Small hands and feet Itchy skin Voracious appetite ```

Question 30

What are the symptoms of Angelman?

Answer 30

``` Mental retardation Hypotonia Absence of speech Large mandible Tongue thrusting Epilepsy ```

Question 31

DNA methyltransferases uses what as the methyl donor?

Answer 31

SAM

Question 32

Which enzyme is important in silencing genes?

Answer 32

THF

Question 33

Folate deficiency during development increases the risk of what?

Answer 33

Neural tube defects

Question 34

Hyperhomocysteinuria increases the risk for what?

Answer 34

Cardiovascular disease

Question 35

What 2 things does smoking cause in genes?

Answer 35

Hypomethylation of oncogenes (increases activity of proliferation genes) Hypermethylation of tumor suppressor genes (turns them off)

Question 36

What DNA-protein interactions are required in transcriptional regulation? (proteins)

Answer 36

DNA binding proteins | Chromatin modifiers

Question 37

What DNA-protein interactions are required in transcriptional regulation? (DNA)

Answer 37

Core promoter sequences | Enhancer/repressor DNA sequences

Question 38

What are the DNA binding proteins that regulate transcription initiation?

Answer 38

Transcription factors (TFs)

Question 39

TFs serve as recruiters for what?

Answer 39

The basal transcriptional machinery, like RNA polymerase

Question 40

Binding of TFs can increase the transcription rate of a gene by how much?

Answer 40

Many thousand fold

Question 41

What do basal factor TFs do?

Answer 41

Position RNA polymerase on the core promoter

Question 42

What do activators do? (TFs)

Answer 42

Bind to enhancer elements | Increase rate of assembly of transcriptional machinery (like NFkB, P53)

Question 43

What are the classes of TFs?

Answer 43

``` Basal factors Activators Co-activators Repressors Chromatin modifiers ```

Question 44

Co-activators are also known as what?

Answer 44

Mediators

Question 45

What do repressors bind to?

Answer 45

Silencer elements

Question 46

What are the chromatin modifiers?

Answer 46

HATs HDACs HMG