Chapter 13

Question 1

Mechanisms of gene regulation in eukaryotes before transcription

Answer 1

• Regulatory proteins
• Regulatory sequences (enhancers, silencers)
• Chromatin structure
• Alternative promoters
• Methylation

Question 2

Mechanism of gene regulation in eukaryotes after transcription

Answer 2

• Alternative 5’ capping
• 3’ polyadenylation
• splicing

Question 3

Mechanisms of gene regulation in eukaryotes after splicing

Answer 3

• Small RNAs that influence mRNA stability
• Other factors that influence mRNA transport and stability and the initiation of translation

Question 4

Mechanisms of gene regulation in eukaryotes in the cytoplasm, after export of the mature mRNA

Answer 4

• Factors that influence the initiation of translation

Question 5

Mechanisms of gene regulation in eukaryotes in the cytoplasm, after translation

Answer 5

• Posttranslational modifications
• Binding of regulatory molecules
• Regulation of protein stability

Question 6

Variation in cis-element regulator elements

Answer 6

• In single celled eukaryotes, cis regulatory elements are usually upstream and near the start of transcription
• In multicellular eukaryotes, cis regulatory elements may be upstream, downstream; near or far

Question 7

Sonic Hedgehog in mammals

Answer 7

• Two enhancers: one for brain cells and one for limb cells
• the one for brain cells is near the start of transcription
• the one for limb cells in 1 million bp upstream in the intron of another gene
• Regulation of SHH is modular and depends on what transcription factors are expressed in each cell

Question 8

Conservation of enhancer sequences

Answer 8

• Enhancer sequences can be highly conserved among diverse organisms
• Natural selection

Question 9

What is a nucleosome

Answer 9

• a segment of DNA wound 2x around 8 histone proteins
• Not static - can dissociate from DNA, move, translocate to different sections of DNA

Question 10

Euchromatin

Answer 10

region that is more accessible

Question 11

Heterochromatin

Answer 11

region that is less accessible

Question 12

Facultative heterochromatin

Answer 12

Accessible to transcription when there are reversible changes in nucleosomes

Question 13

What causes variation in accessibility of chromatin

Answer 13

• Cell type
• Developmental stage
• Environmental conditions

Question 14

What influences accessibility of chromatin

Answer 14

• Chemical changes in DNA
• protein

Question 15

Important features of epigenetic modification

Answer 15

• chromatin structure change
• Transmissible during mitosis
• Reversible
• Affects transcription
• Does not alter nucleotide sequence of DNA

Question 16

Positive effect variegation

Answer 16

Change in expression due to change in location of heterochromatic region that partially prevent expression
- no change in sequence

Question 17

Varigated eye

Answer 17

• su(var) - Mutations that reduce heterochromatin partially restore the wildtype phenotype
• E(var) - Mutations that increase heterochromatin make the mutant phenotype more extreme

Question 18

How are genes made available for transcription in eukaryotes

Answer 18

• Gene may be inside euchromatin where chromatin is open and expression is largely continuous
• Proteins called chromatin remodelers may change the distribution or composition of histones to make transcription temporarily possible
• Proteins called chromatin modifiers may add or remove acetyl or methyl groups to make transcription temporarily possible

Question 19

Chemical modification of chromatin

Answer 19

• Proteins that add chemical groups to histones are called writers; those that remove them are called erasers
• Proteins that bind to these groups are called readers

Question 20

Histone Acetyltransferase

Answer 20

chromatin writers that add acetyl groups; addition of acetyl groups makes protein less positive charged and less strongly attracted to DNA

Question 21

Histone deacetylase

Answer 21

Erasers that removed acetyl groups

Question 22

Histone methyltransferase

Answer 22

Chromatin writers that add methyl groups; methylation can open or close chromatin

Question 23

Histone demethylases

Answer 23

Erasers that remove methyl groups

Question 24

DNA methyltransferase

Answer 24

Add methyl groups to DNA nucleotides; repressed expression

Question 25

Epigenetic heritability

Answer 25

• Chromatin structure is broken down during DNA replication
• During mitosis, some histones are repackaged after replication; these influence the epigenetic state of newly translated histones
• During meiosis, most epigenetic marks are lost - some passed to the next generation

Question 26

Insulator sequence

Answer 26

cis-acting sequences that influence the ability of enhancers to initiate transcription

Question 27

Open promoters

Answer 27

promoters not bond by histones - nucleosome depleted region
- no TATA box

Question 28

Covered promoters

Answer 28

• Genes with tissue specific, developmental-specific, environmentally induced expression
• blocked transcription until nucleosome is removed
• contian TATA boc and other transcription-factor binding sequences
  -active competition between nucleosomes and transcription factors for binding

Question 29

Pioneer factors

Answer 29

initiate and recruit activators and repressors to enhancer and silencer respectively

Question 30

Chromatin remodeling

Answer 30

• Genes within facultative heterochromatin are expressed when trans-acting factors cause changes in nucleosome structure, chemistry and composition