Lecture 32 - Developmental genetics II

Question 1

Why mRNAs don’t diffuse freely like proteins, in the syncytium ?

Answer 1

Are bound to specific proteins that target them to a specific place

Question 2

What’s the point of having enhancers and silencers sequences near to each other (like in eve gene for example)

Answer 2

When repressor concentration is high, it will block the enhancer effect

Question 3

Segment polarity genes: 2 functions

Answer 3

1. Encode components of two cell-cell signaling pathways (Hedgehog and Wingless)
2. Define A and P within each segment

Question 4

Segment polarity genes: What kind of protein

Answer 4

TFs, secreted proteins, membrane receptors, kinases, …

Question 5

Segment polarity genes: What regulates their transcription

Answer 5

Pair-rule genes

Question 6

What happens in segment polarity genes mutants

Answer 6

Segments have mirroring of one half of the segment

Question 7

Cascade of TFs to regulate early drosophila embryogenesis. 5 types of genes and function

Answer 7

Egg-polarity genes (maternal-effect): A-P axis
Gap genes: Broad subdomains
Pair-rule genes: Individual segments identified
Segment polarity genes: Define polarity of individual segments
Segment identity genes (homeotic genes): Define identity of individual segments

Question 8

(notes) what genes are responsible for forming 14 equivalent segments + what we mean by serially reiterated segments

Answer 8

Segment polarity genes. Serially reiterated = have equal capacity of becoming different parts of the body

Question 9

Homeotic mutations meaning and name of gene category identified

Answer 9

Mutations in segment identity genes. Hox genes

Question 10

What happens in homeotic mutants (name the phenomenon)

Answer 10

A particular structure is replaced by another one normally found somewhere else (homeotic transformation)

Question 11

2 examples of homeotic mutations

Answer 11

Ultrabithorax (Ubx, a TF) : second thorax and set of wings replace halteres
Antennapedia (Antp): leg in place of antenna

Question 12

Number of homeotic genes (hox genes) identified in drosophila + type of protein and common characteristic

Answer 12

8. all encode homeodomain family transcription factors

Question 13

What’s a homeodomain

Answer 13

A DNA binding domain with a helix-helix structure

Question 14

Where the hox genes are found in the drosophila genome and particular characteristic

Answer 14

In 2 gene complexes (antennapedia complex and bithorax complex) on third chromosome. Colinearity: Aligned in chromosome in same order as body parts when their function is needed

Question 15

What genes activate/repress hox (or selector) genes

Answer 15

Gap genes and pair-rule genes

Question 16

Pattern of expression of hox genes

Answer 16

Each is expressed in specific segments and some overlap

Question 17

How is hox genes transcription regulated once they are commited

Answer 17

Through epigenetic regulation (their faith is maintained during development) methylation or acetylation depending on segment

Question 18

What will ultimately determine the structure that a segment develops

Answer 18

The specific hox genes that are expressed in this segment

Question 19

Developing wing and developing haltere: where is Ubx expressed

Answer 19

Not expressed in wing. Expressed in haltere

Question 20

What happens at the level of the Ubx gene in the ultrabithorax mutant

Answer 20

Ubx is mutant so halteres develop into a second pair of wings and thorax

Question 21

How was the Ubx gene linked to the ultrabithorax mutant phenotype (how was its function uncovered ?)

Answer 21

Forced expression of Ubx in wings and it converted them to halteres

Question 22

Name of portions of body structure that stick out of the body and hox gene that controls that

Answer 22

appendages (antennae, legs, wings, halteres). Gene distal-less (Dll)

Question 23

When is dll expressed in appendages and in abdominal segments

Answer 23

Expressed in earliest stage in appendage development (about 20 cells)
Not expressed in abdominal segments

Question 24

What repressed Dll expression in the abdomen and type of protein

Answer 24

Ubx and Abd-A (abdominal A) Hox genes. ARE TRANSCRIPTION FACTORS

Question 25

In double mutants (Ubx - and Abd-A -) what happens to Dll expression in the abdominal segments

Answer 25

Dll is derepressed and expressed in abdominal segments

Question 26

In Ubx mutants, what happens to Dll expression

Answer 26

Dll is derepressed in abdominal segment A1 and is expressed there

Question 27

Regulatory sequences in the Dll gene

Answer 27

Has binding sites for several TFs, including 2 for Hox genes

Question 28

What happens when the Dll gene's regulatory sequences that are binding sites for Hox genes are mutated

Answer 28

Dll is not repressed and is expressed in abdominal segments

Question 29

What are the Dll gene regulatory sequences other than the binding sites for Ubx and Abd-A

Answer 29

Binding sites for segment polarity genes: sloppy-paired (slp) - anterior (halves of) segments. engrailed (en) posterior (halves of) segments

Question 30

What is minimally required to repress dll expression in abdominal segments

Answer 30

- Ubx OR Abd-A | - Slp OR En

Question 31

How do Ubx, Abd-A, Slp and En TFs work to repress Dll

Answer 31

Cooperative regulation

Question 32

What happens when Slp is mutated

Answer 32

Dll is derepressed in segments aA1 to aA7 (a meaning the anterior half of these segments)

Question 33

What happens when En is mutated

Answer 33

Dll is derepressed in segments pA1 to pA7 (p meaning the posterior half of these segments)

Question 34

What happens when Slp and En are mutated

Answer 34

Dll is derepressed in segments A1 to A7

Question 35

Which genes function to define A and P within each segment (2 examples of these) and effect of mutations in these.

Answer 35

Segment polarity genes. Mutation = mirror effect in segments. Examples = gooseberry and patched genes

Question 36

Summary of effects of Ubx mutant (2)

Answer 36

Halteres develop into second thorax and wing pair | Dll is derepressed in segment A1 (Abd-A still present to repress Dll in segments A2 to A7. Ubx represses in 1 to 7)

Question 37

Hox genes conservation on other species

Answer 37

Conserved in mammals. All duplicated twice. 4 Hox gene clusters in mammals.

Question 38

Hox genes characteristic in mammals that is similar to to flies'

Answer 38

Colinearity. The order of hox genes on the chromosome parallels the order of body parts in which they are expressed

Question 39

Example of serially repeated structure in vertebrates

Answer 39

Vertebraes

Question 40

Normal number of lumbar and sacral vertebrae in vertebrates

Answer 40

6 lumbar and 4 sacral

Question 41

2 types of mutants causing changes in vertebraes identity in vertebrates

Answer 41

Mutant in Hoxd11 (hox gene) has an additional (7) lumbar vertebra Double mutant in Hoxd11 and Hoxa11 (hox genes) has 2 additional (8) lumbar vertebrae

Question 42

Summary of 5 types of genes (involved in EG) effect

Answer 42

``` Maternal-effect genes (specify A and P) Gap genes (divide A-P axis into broad subdomains) Pair-rule genes (divide A-P axis into 7 stripes - expression/non-expression) Segment polarity gene (define + organize the 14 segments, and define A and P halves of each segment) Homeotic genes (define structures produced by each segment) ```

Question 43

Classify Bicoid, Nanos, Even-skipped, Engrailed and Ultrabithorax genes (in the 5 categories) and find the odd one out of the group

Answer 43

Bicoid: maternal-effect. Nanos: maternal-effect. Even-skipped: Pair-rule. Engrailed: Segment polarity. Ubx: Homeotic. Odd one = Nanos (bc not a TF)

Question 44

One technique of developmental timing in C.elegans

Answer 44

Use of miRNAs

Question 45

C.elegans total number of cells and pattern of cell divisions

Answer 45

959 (somatic) cells total. Cell divisions follow a stereotyped pattern (lineages). Number of muscle cells, gonad cells, neuron cells is well known.

Question 46

What the screen for heterochronic mutants in C.elegans led to

Answer 46

Found that mutants in gene let-7 repeat the L4 division at the adult stage

Question 47

Consequence of mutations that affect V1-4 vulval cell division pattern in C.elegans (2)

Answer 47

Gives rise to hypodermal cells and let-7 mutants die of vulval rupture

Question 48

let-7 function

Answer 48

encodes short (22 nt) miRNAs derived from double stranded RNA precursors. Are incorporated in the RISC complex and bind complementary mRNA's 3' UTR

Question 49

General consequence of mutations in genes like let-7

Answer 49

The target protein(s) is not repressed

Question 50

Proteins targeted by let-7 and give one example and where it is targeted

Answer 50

let-7 targets several protein-coding mRNAs. (ex. lin-41) | Recognize two sequences in lin-41's 3' UTR

Question 51

Mutation in lin-41 consequence

Answer 51

Too little Lin-41 protein -> L4 is not performed in the V1-4 vulval cell division pattern

Question 52

Mutation in let-7 vs mutation in lin-41

Answer 52

let 7 mutations -> too much lin-41 -> L4 repeated | lin-41 mutation -> too little lin-41 -> L4 not performed

Question 53

2 constructs used to show that let-7 targets lin-41 3' UTR

Answer 53

1. Insert GFP in lin-41 protein to make a fusion protein (lin-41 promoter, GFP, lin-41 sequence, lin-41 3'UTR) 2. col-10 (an exogenous promoter), lacZ, lin-41 3'UTR

Question 54

How they proved that let-7 targets lin-41 3' UTR using the 2 constructs

Answer 54

Followed percentage of animals that expressed GFP and LacZ in hypodermial cells during L1 to L4 and adult stage and percentages of animals for both constructs at each phase were similar

Question 55

Segments over which Abd-A, Abd-B and Ubx repress Dll

Answer 55

Abd-A : From A2 to A7 Abd-B: From A4 to A7 Ubx: From A1 to A7