L16: Gene Regulation in Development

Question 1

explain differential gene expression in eukaryotic development

Answer 1

• diverse cell types produced from a constant genome
• genes are expressed at different times in different cells/tissues

Question 2

what are the postulates of differential gene expression

Answer 2

1. every cell nucleus contains the complete genome established in the fertilized zygote
2. only a small percentage of the genome is expressed in each cell
3. unused genes in differentiated cells are not destroyed or mutated but retain the potential for expression - implies genomic equivalence

Question 3

what is genomic equivalence

Answer 3

• all somatic cells are mitotic descendants of a single cell: the zygote
• therefore, all somatic cells contain the same genes

Question 4

genomic equivalence - evidence

Answer 4

• cloning of Dolly (1996)
• researchers performed a nuclear transfer using a mammary cell from an adult sheep as a nucleus donor and an enucleate ovum as recipient

Question 5

cloning of Dolly - how is this proof of genomic equivalence

Answer 5

the nuclei of differentiated somatic cells (from the original sheep) still contain all the genes necessary to generate an adult organism

Question 6

what are two mechanisms of initiation of differential gene expression

Answer 6

1. mRNA localization
2. cell signaling

Question 7

initiation of differential gene expression - mRNA localization

Answer 7

mRNA can be asymmetrically localized in the cell so that only one daughter cell inherits the genetic determinant following division

Question 8

initiation of differential gene expression: mRNA localization - example

Answer 8

• Macho-1
• determinant for programming cells towards muscle differentiation in the sea squirt
• only B4 blastomeres (early embryonic cells) inherit Macho-1

Question 9

initiation of differential gene expression - cell signaling

Answer 9

• gives positional information: influence of location on development
• creates secreted signaling molecule gradients (morphogen gradients)

Question 10

initiation of differential gene expression: cell signaling - morphogen gradients

Answer 10

• cells near the source receive high concentrations of the signal
• different concentrations specify different cell fates
• fates conferred by differential gene expression

Question 11

initiation of differential gene expression: cell signaling - example

Answer 11

• neural tube development in vertebrates
• the ventral floorplate of the neural tube secrets a morphogen signal called Sonic hedgehog (Shh)
• the fate of neurons in the neural tube is dictated by the concentration of Shh

Question 12

what is a common theme in eukaryotic gene regulation

Answer 12

• complex enhancers are used for combinatorial control
• this results in a sharp on/off pattern of gene expression
• many transcription factors bind DNA as monomers with low affinity
• binding of multiple proteins is often required to control gene expression

Question 13

sea squirt - what is MesP?

Answer 13

• determinant of cardiac mesoderm in the sea squirt
• activated only in specific blastomeres

Question 14

sea squirt: MesP - what is it activated by?

Answer 14

• activated by two transcription factors
• neither factor alone is sufficient to induce MesP which is expressed only where there is overlap between the two regulators
• induces MesP via direct interaction

Question 15

Drosophila dorsoventral patterning - what is the dorsal protein?

Answer 15

• it is expressed only in the ventral-most cells
• it forms a gradient that directs the cell fate of the dorsal-ventral axis in a concentration dependent fashion (morphogen)
• the cell fate is regulated by three target genes of Dorsal: (1) sog, (2) rhomboid, (3) twist

Question 16

Drosophila dorsoventral patterning - explain how the target genes behave

Answer 16

• they display different expression thresholds
• this is based on varying affinities for Dorsal binding

Question 17

Drosophila dorsoventral patterning - snail

Answer 17

• a repressor that binds sog and rhomboid and antagonizes Doral
• prevents gene activation even in the presence of Dorsal
• via competition or inhibition

Question 18

Drosophila dorsoventral patterning - where will rhomboid and sog be expressed?

Answer 18

• rhomboid: in the ventral NE
• sog: throughout NE

Question 19

Drosophila dorsoventral patterning - gene expression patterns are controlled by what?

Answer 19

1. binding affinities to Dorsal concentration gradient
2. presence of Snail repressor

Question 20

Drosophila anterior-posterior patterning - what are segmentation genes?

Answer 20

• these define the repeating units of the body plan
• includes even-skipped (eve)

Question 21

Drosophila anterior-posterior patterning - what is even-skipped (eve)

Answer 21

• pair-rule gene
• a type of segmentation gene that is expressed in 7 stripes across the embryo

Question 22

Drosophila anterior-posterior patterning: even-skipped (eve) - Stripe Modules

Answer 22

• the eve gene has multiple regulatory regions called stripe modules
• Each controls expression of a specific stripe
• the are cis-regulatory elements that respond to different combinations of transcription factors in the embryo

Question 23

Drosophila anterior-posterior patterning: even-skipped (eve) - stripe 2 module

Answer 23

• contains binding sites for 2 repressors and 2 activators
• repressors: Kruppel (K), Giant (G1-G3)
• activators: Bicoid (B1-B5) and Hunchback (H)

Question 24

Drosophila anterior-posterior patterning: even-skipped (eve) - when is eve stripe 2 expressed

Answer 24

only in the region where activators (Bcd & Hb) are present, but repressors (Gt & Kr) are not

Question 25

*Drosophila* anterior-posterior patterning: *even-skipped (eve)* - what defines *eve* stripe 2 expression

Answer 25

**Kruppel** and **Giant** act to define the posterior and anterior boundaries of this expression

Question 26

*Drosophilla* patterning - what are homeotic gene?

Answer 26

- they specify the characteristic structures of each segment - they are regulated by segmentation genes - they are found on the **Homeotic Complex (Hom-C)**

Question 27

*Drosophilla* patterning - William Bateson (1894)

Answer 27

coined the term **homeosis** for mutants with one structure replaced by another

Question 28

*Drosophilla* patterning: homeotic genes - Homeotic complex (Hom-C)

Answer 28

- contains two regions in the genome: 1. **Antennapedia complex** 2. **bithorax complex**

Question 29

*Drosophilla* patterning: Hom-C - what does the gene order reflect?

Answer 29

- the gene order in the genome reflects the spatial distribution of each gene's activity in specifying the segment plane - each gene is repressed by the homeotic genes expressed posterior (behind) it

Question 30

*Drosophilla* patterning and homeotic genes - *Antennapedia (Antp)*

Answer 30

- specifies fate of thoracic segment T2 - the misexpression in the head is significant to convert antennae into T2-like legs

Question 31

*Drosophilla* patterning and homeotic genes - *Ultrabithorax (Ubx)*

Answer 31

- it specifies the fate of T3 segment - produces balancing organs called **halteres**

Question 32

*Drosophilla* patterning and homeotic genes: *Ultrabithorax (Ubx)* - loss-of-function mutations

Answer 32

- loss-of-function *Ubx* mutations allow the spread of *Antp* into T3 - T3 is converted into T2 fate - it produces an extra set of wings

Question 33

*Drosophilla* patterning and homeotic genes: *Ultrabithorax (Ubx)* - missexpression

Answer 33

- converts T2 to T3 identity - 2 sets of halteres

Question 34

arthropod diversity

Answer 34

diversity is affected by changes in homeotic gene function

Question 35

arthropod diversity - arthropod limb identity

Answer 35

- **maxilliped**: appendage on the 1st thoracic segment modified for feeding - its present in **isopods** - but absent in **branchiopods**

Question 36

arthropod diversity: maxilliped - what is the identity controlled by?

Answer 36

- the expression patterns of two homeotic genes: 1. ***Sex combs reduced (Scr)*** 2. ***Ultabithorax (Ubx)***

Question 37

arthropod diversity: maxilliped - *Sex combs reduced (scr)*

Answer 37

- expressed in the head - specifies feeding appendage fate - *Scr* spreads into T1 and specific maxilliped identity

Question 38

arthropod diversity: maxilliped - *Ultrabithorax (Ubx)*

Answer 38

- repressed *Scr* expression in thoracic segments - isopod *Ubx* is not expressed in T1

Question 39

arthropod diversity - insects vs crustaceans limb number

Answer 39

- **insects**: six legs (found as pairs on three thoracic segments) - **crustaceans**: can have limbs on every segment of thorax and abdomen

Question 40

arthropod diversity - what causes the differences in arthropod limb number

Answer 40

- its due to *functional* differences in *Ultrabithorax (Ubx) protein product*

Question 41

arthropod diversity - insects vs crustaceans limb number mechanism

Answer 41

- **insects**: Ubx represses ***Distal-less*** - **crustaceans**: Ubx does not repress ***Distal-less*** - *Distal-less* is the gene required for limb formation

Question 42

arthropod diversity: insects vs crustaceans limb number mechanism - why are Ubx different?

Answer 42

- Ubx protein sequences from different organisms vary outside of the homeodomain - this is bc a mutation replaced the C-terminus of the **insect** Ubx with a poly-alanine string that acts to repress Distal-less

Question 43

arthropod diversity - the developmental diversity from homeotic genes results in what?

Answer 43

- diversity can result from changes in: 1. gene expression patterns (*Scr* and *Ubx* in Branchiopod and Isopod ) 2. protein product function (*Ubx* expression in Insects and Crustaceans)