Lecture 27. Chromatin and epigenetic effects

Question 1

When are prokaryotic RNAs translated into proteins ?

Answer 1

Co-transcriptionally - as soon as they are made

Question 2

Why are prokaryotic RNAs translated as soon as they are made ?

Answer 2

Due to the absence of the nuclear envelope

Question 3

When are eukaryotic RNAs translated ?

Answer 3

They are first modified and then transported from the nucleus to cytoplasm

Question 4

Why is eukaryotic RNA transported into the cytoplasm for translation?

Answer 4

Eukaryotic DNA is compartmentalized within the nucleus

Question 5

What needs to happen to eukaryotic RNA to be transported into the cytoplasm ?

Answer 5

Addition of sequences to the 5’ end of the RNA (5’cap) as well as the 3’ end (the polyA tail)

Question 6

What is the function of adding sequences to the 5’end and the 3’end of eukaryotic RNA ?

Answer 6

1. Regulates stability of mRNA molecules

2. Exert a level of control over gene expression that prokaryotes don’t have

Question 7

What do eukaryotic RNA undergo that prokaryotic RNA do not ?

Answer 7

Splicing

Question 8

Where does splicing occur ?

Answer 8

In the nucleus

Question 9

What is the purpose of splicing ?

Answer 9

Remove introns

Question 10

What is an advantage of splicing to eukaryotes ?

Answer 10

Adds another layer of control and complexity over eukaryotic gene expression

Question 11

What is the function of eukaryotic mRNA modification ?

Answer 11

1. Stabilizes mRNA

2. Facilitate mRNA export from the nucleus

Question 12

What does mRNA from higher eukaryotes undergo ?

Answer 12

Splicing by small nuclear RNAs

Question 13

What function does splicing by small nuclear RNAs in mRNA in higher eukaryotes have ?

Answer 13

1. Removes introns

2. Generate splice variants of genes

Question 14

What do eukaryotic RNA polymerase require ?

Answer 14

Transcription factors

Question 15

What is eukaryotic RNA polymerase’s transcription factors access to DNA regulated by ?

Answer 15

1. Histones

2. DNA binding proteins

Question 16

Why is gene expression in eukaryotes constitutively off at most promoters ?

Answer 16

1. The requirement for specific and general transcription factors
2. The physical inaccessibility of gene promoters

Question 17

What do specific and general transcription factors regulate ?

Answer 17

The binding of the RNA polymerase complex to the promoter

Question 18

What makes gene promoters physically inaccessible ?

Answer 18

Histones

Question 19

What do histones form ?

Answer 19

Particles called nucleosomes

Question 20

What do nucleosomes bind tightly to ?

Answer 20

DNA

Question 21

What is the structure of a nucleosome ?

Answer 21

Has 200 base pairs of DNA wound around it and other DNA binding proteins

Question 22

How do DNA binding promoters regulate the binding of RNA polymerase to the promoter region ?

Answer 22

Compacts DNA into a closed state that blocks access of the RNA polymerase complex to the promoter

Question 23

What do eukaryotic RNA polymerases require that prokaryotic polymerases do not to initiate transcription ?

Answer 23

Transcription factors to be bound to the promoter region

Question 24

What is RNA polymerase 1 responsible for ?

Answer 24

Generating rRNA precursor molecules

Question 25

What is RNA polymerase 2 responsible for ?

Answer 25

Generating mRNA and RNA

Question 26

What is RNA polymerase 3 responsible for generating ?

Answer 26

Small RNAs such as tRNA and 5S rRNA

Question 27

What do RNA polymerase 2 promoters regulate ?

Answer 27

mRNA synthesis

Question 28

Where are RNA polymerase 2 promoters located ?

Answer 28

-30 to the transcription start site at a TATA box

Question 29

What is the actual sequence of of the TATA box in RNA polymerase 2 promoters ?

Answer 29

TATAAAA

Question 30

Do all polymerase 2 promoters have TATA boxes ?

Answer 30

No

Question 31

Where is the CCAAT box found ?

Answer 31

-75 region

Question 32

What is the upstream elements of polymerase 2 promoters ?

Answer 32

GGCCCAATCT element or CCAAT box

Question 33

What is the general rules about promotes recognized by RNA pol II ?

Answer 33

Typically contain a TATA box and at least one other upstream element

Question 34

What is the purpose of transcription factors for eukaryotic polymerases ?

Answer 34

need transcription factors to assist in eukaryotic RNA polymerases are recognizing the promoter regions of genes on their own

Question 35

What are the two types of transcription factors ?

Answer 35

1. General | 2. Gene specific

Question 36

What are the 7 general transcription factors that collaborate with RNA Pol II ?

Answer 36

1. TFIIA 2. TFIIB 3. TFIID 4. TFIIE 5. TFIIF 6. TFIIH 7. TFIIJ

Question 37

What does TFIID contain ?

Answer 37

Many subunits including the TATA box binding protein

Question 38

Where does the TATA box binding protein (TBP) bind to ?

Answer 38

The TATA box bringing TFIID

Question 39

What does the DNA binding domain of the TBP consist of ?

Answer 39

A large B-sheet that forms a saddle shaped structure that sits astride the DNA in the region of the TATA box

Question 40

What does the binding of TBP to the TATA induce ?

Answer 40

A dramatic distortion

Question 41

What does TBP binding cause structurally ?

Answer 41

A large kink in the DNA helix causing the DNA duplex to unwind over an 8 base pair span

Question 42

What does TBP binding allow access of ?

Answer 42

Allows access of the RNA polymerase to the template

Question 43

What does TFIID serve as ?

Answer 43

A platform for organisation of other transcription factors which then bind in the following order; D, A, B, F+ Pol II, E, H and J

Question 44

What order to transcription factors bind ?

Answer 44

D, A, B, F + Pol II, E, H, J

Question 45

What happens upon assembly of the RNA Pol II preinitiation complex ?

Answer 45

The C-terminal domain of the largest subunit of RNA polymerase II becomes heavily phosphorylated

Question 46

What is most likely the largest subunit of RNA polymerase II that becomes heavily phosphorylated ?

Answer 46

TFIIH

Question 47

What is TFIIH ?

Answer 47

A kinase

Question 48

What does the phosphorylation of the largest subunit of RNA polymerase II do ?

Answer 48

A trigger that uncouples the polymerase from transcription factors allowing the polymerase to move along the DNA template

Question 49

What are general transcription sufficient to enable ?

Answer 49

A basal level of transcription

Question 50

What are some gene-specific transcription factors ?

Answer 50

1. Myc 2. Max 3. Fos 4. Jun 5. NfkB 6. NFAT

Question 51

What are the 4 classes that contain motifs that allow interaction between the transcription factors and the major grooves of DNA ?

Answer 51

1. Zinc finger motif 2. Helix-loop-helix motif 3. Leucine zipper motif 4. High mobility group box motif

Question 52

What is the purpose of the four motifs ?

Answer 52

Allow recognition of specific DNA sequences by the transcription factors

Question 53

What do most motifs contain ?

Answer 53

A segment (often alpha helix) that is inserted into the major groove of DNA

Question 54

What do motifs that contain a segment recognise and form ?

Answer 54

1. Recognise the side chains of the bases lining the groove | 2. Forms non-covalent interactions with the side chains

Question 55

What makes the otherwise weak strength of the contact between the transcription factor and the DNA very high ?

Answer 55

1. The number of contacts | 2. The overall strength and specificity of the transcription factor DNA interaction

Question 56

Where are enhancer sequences often found ?

Answer 56

Thousands of base pairs away from a promoter region that the enhancer controls

Question 57

What is chromatin looping facilitated by ?

Answer 57

Specific transcription factors and mediators (associated proteins)

Question 58

What is the function of chromatin looping ?

Answer 58

Brings the promoter region in close proximity to the TATA box and the associated RNA pol II complex

Question 59

What an histones be modified by ?

Answer 59

1. Acetylation 2. Methylation 3. Phosphorylation

Question 60

What do modifications that neutralize the positive charged on histones do ?

Answer 60

Reduce their affinity for DNA

Question 61

What is a histone code ?

Answer 61

The number of possible patterns of histone modifications

Question 62

What is another name for the modification of the histone c-terminal tail

Answer 62

Acetylation

Question 63

What is the enzyme involved in acetylation ?

Answer 63

Histone acetyltransferases

Question 64

What is the enzyme responsible for the reverse modification of acetylation ?

Answer 64

Histone deacetyltransferases

Question 65

What does acetylation lead to ?

Answer 65

A more open chromatin state due to neutralization of the negative charges on histones thereby loosening the histones contact with DNA

Question 66

What do histones associated with more active genes tend to be rich in ?

Answer 66

Acetyl modifications

Question 67

What can some histone modifications also recruit ?

Answer 67

Proteins for example polycomb proteins

Question 68

What is epigenetic control ?

Answer 68

Inherited modifications that are not present in a DNA sequence

Question 69

What is gene expression regulated by ?

Answer 69

DNA binding proteins called transcriptional regulators as well as the accessibility of the stretch of DNA harbouring the gene (chromatin state)

Question 70

What are nucleosomes ?

Answer 70

Histone octamers

Question 71

What causes nucleosomes to be moved off promoters to facilitate the initiation of transcription ?

Answer 71

Switch/Sniff complex or SWI/SNF complex

Question 72

What do all eukaryotic cells contain and what its function ?

Answer 72

A large multi subunit complex that can disrupt histone-DNA interactions in an ATP dependent manner and allow binding of transcription factors to gene regulatory regions

Question 73

How was the SWI/SNF complex discovered ?

Answer 73

Screen genes involved in growth on sucrose and screens the genes involved in the ability to switch mating type. One of the genes was found in common

Question 74

What is the function of SWI/SNF complex ?

Answer 74

Bulldoze histones off promoters and facilitate access of the RNA Pol complex to the promoter

Question 75

How many proteins is the yeast SWI/SNF complex comprised of ?

Answer 75

11

Question 76

What does the yeast SWI/SNF complex act as ?

Answer 76

An ATP driven nucleosome plough to facilitate transcription

Question 77

How do certain transcription factors function ?

Answer 77

By attracting the SWI/SNF complex to the promoter to facilitate transcription

Question 78

Where are 1% of nucleotides methylated at ?

Answer 78

Cytosine residues

Question 79

What does the methylated nucleotides produce ?

Answer 79

5-methylcytosine

Question 80

What does the 5-methylcytosine modification act as ?

Answer 80

A molecular tag that allows certain regions of DNA to be regulated differently than others

Question 81

Where are almost all methylated cytosines found ?

Answer 81

CG dinucleotides within symmetrical sequences

Question 82

Where do symmetrical sequences occur (methylated) ?

Answer 82

Tend to be clustered in G rich regions called CpG islands close to gene regulatory regions

Question 83

Where are unmethylated CpG islands found ?

Answer 83

Near active gene promoters

Question 84

What is methylation likely involved in ?

Answer 84

Silencing gene expression

Question 85

What is methylation in vertebrates ?

Answer 85

Dynamic

Question 86

What does DNA methylation correlate with ?

Answer 86

Gene expression patterns

Question 87

How does methylation inhibit transcription ?

Answer 87

1. By interfering with the recognition of DNA binding sites by transcription factors 2. By attracting transcriptional repressors to certain sites