Homeobox Genes

Question 1

The important question of “how do we develop our body plan” has been extensively studied in which two model organisms?

Answer 1

Drosophila Melanogaster (fruit fly) and Mus musculus (house moue)

Question 2

One advantage of using the fruit fly is that they have a short generation time. How long does it take for the fruit fly to go from egg to adult?

Answer 2

14 days

Question 3

One advantage of using the mouse is that they are very amenable to genetic manipulations such as

Answer 3

Gen knockouts and knock ins, and transgenics

Question 4

Deleting a gene via embryonic stem (ES) cells

Answer 4

Gene knockout

Question 5

Replacing one version of a gene with another via embryonic stem cells

Answer 5

Gene knockin

Question 6

Adding extra copis of any gene

Answer 6

Transgenics

Question 7

In early mouse development, the group of cells in the center of the blastocyst is called the

Answer 7

Inner cell mass (ICM)

Question 8

Pluripotent for the embryo

Answer 8

ICM cells

Question 9

Cells in the outer epithelium are committed to generate part of the

Answer 9

Placenta

Question 10

Can be isolated and grown in cultures

Answer 10

ICM cells

Question 11

These mice ICM cells retain their pluripotency in vitro and are called

Answer 11

Embryonic stem (ES) cells

Question 12

Enable a mouse to be generated that has a specific DNA change that we want to study

Answer 12

The pluripotent ES cells

Question 13

If you delete a gene in the ES cells then a mouse can be generated that contains all the genes in the genome except the specific one that was deleted. These mice are called

Answer 13

Kock-outs

Question 14

If you introduce more subtle specific changes into the DNA such as replacing a wild type sequence with a specific mutation, then you get mice called

Answer 14

Knock-ins

Question 15

The insertion of DNA into the genome. DNA is not deleted, rather, extra copies of a gene are added. Mice that undergo this process are called

Answer 15

Transgenics

Question 16

How are transgenics made?

Answer 16

DNA injected into nuclei of fertilized egg

Question 17

Mutations where one structure is replaced with another or is duplicated

Answer 17

Homeotic Mutations

Question 18

Homeotic mutations were known to exist since the 1930’s, but the genes responsible for these defects were not known until the development of

Answer 18

DNA recombinant technology (1980’s)

Question 19

Cloning of genes responsible for homeotic mutations was first achieved in

Answer 19

Drosophila

Question 20

Sequence homology was observed between genes responsible for different homeotic mutations. This DNA sequence was termed the

Answer 20

Homeobox

Question 21

The homeobox is 180 bp in length and encodes a protein called a homeobox transcription factor. The part of the protein that binds DNA is called the

Answer 21

Homeodomain

Question 22

Encode transcription factors that typically initiate a cascade of gene expression necessary for the development of a body structure or cell type

Answer 22

Homeobox genes

Question 23

Homeobox proteins are transcription factors that bind DNA in a sequence specific manner. All homeobox proteins bind

Answer 23

AT rich elements in promoters and enhancers

Question 24

The homeodomain amino acid sequence is responsible for binding and recognizing the AT rich binding site found in many

Answer 24

Promoters and Enhancers

Question 25

The homeodomain protein sequence is comprised of 3 alpha helices. Which helix makes direct contact with the DNA?

Answer 25

The 3rd helix

Question 26

All homeobox transcription factors bind

Answer 26

AT rich DNA sequences

Question 27

In vitro, homeobox proteins demonstrate little or no specificity. However, in vivo, homeodomain transcription factors form protein complexes to determine

Answer 27

Specificity (very important in vivo or legs would be arms)

Question 28

Only makes up a small portion of the homeobox transcription factor

Answer 28

Homeodomian

Question 29

Other proteins bind to different parts of homeobox transcription factors to modify function and help determine

Answer 29

Specificity

Question 30

There are many genes that contain homeobox sequences. These genes are broken into which two classes?

Answer 30

1. ) Hox genes | 2. ) Genes that when mutated, do not result in structural change

Question 31

Genes that when mutated result in homeotic transformations

Answer 31

Hox Genes

Question 32

The second class of homeobox sequences are not physically

Answer 32

Clustered together

Question 33

Control the patterning of cell types, and mutations in these genes often result in the loss or gain of parts of cell types

Answer 33

Second class genes

Question 34

Clustered into 4 physically linked groups in humans

Answer 34

Hox genes

Question 35

In the evolution from drosophilia to mouse to human, there is a consistent increase in the number of

Answer 35

Homeobox genes (i.e. from 1 to 4)

Question 36

Function in patterning the body axis

Answer 36

Hox genes

Question 37

Expressed in specific embryonic domains and function in the generation of that particular body part

Answer 37

Hox genes

Question 38

Hox genes are positioned on the chromosome in the same order in which they are expressed. Where are the following genes expressed? 1. ) Genes positioned 5' in the Hox cluster 2. ) Genes positioned 3' in the Hox cluster

Answer 38

1. ) Posterior domain | 2. ) Anterior domain

Question 39

How many Hox clusters are present in mice and humans?

Answer 39

4 (Hox a, b, c, and d)

Question 40

Homologous genes between species

Answer 40

Orthologs

Question 41

Homologous genes within a species

Answer 41

Paralogs

Question 42

Expressed in the developing neural tube as well as the flanking somites

Answer 42

Mouse Hox genes

Question 43

Body segments containing the same internal structures -seen in embryonic mouse

Answer 43

Somites

Question 44

Somite expression is always shifted

Answer 44

Posteriorly

Question 45

Hox genes further 3' have more anterior expression boundaries. This is called

Answer 45

Spacial co-linearity

Question 46

3' Hox genes are also expressed earlier in development than 5' genes. This is called

Answer 46

Temporal co-linearity

Question 47

Different groups of cells express distinct patterns of Hox genes depending on their position along the anterior-posterior (A-P) axis. This is called the

Answer 47

Hox code

Question 48

Dictates the development of different structures along the A-P axis

Answer 48

Hox code

Question 49

Hox genes are transcription factors, so they will determine which downstream genes get turned

Answer 49

On

Question 50

These downstream genes will in turn determine the developmental structures that will be

Answer 50

Derived

Question 51

Loss of function Hox mutations (knock-outs) lead to

Answer 51

Anterior transformations

Question 52

Gain of function Hox mutations lead to

Answer 52

Posterior transformations

Question 53

Have less severe phenotype than double or triple mutants -an example of redundancy or overlapping function

Answer 53

Single mutants

Question 54

Function as transcription factors so they either initiate or repress downstream gene expression

Answer 54

Hox genes

Question 55

One function of Hoxa2 and Hoxb2 is to initiate gene expression responsible for the generation of

Answer 55

Cervical vertebrae C2

Question 56

Hoxa3, Hoxb3 and Hoxd3 are expressed in a more posterior compartment and one of their functions is to initiate gene expression responsible for the generation of

Answer 56

Cervical vertebrae C3

Question 57

Hoxa2, Hoxb2, Hoxa3, Hoxb3 and Hoxd3 are all co-expressed in the same set of cells along the A-P axis. What would happen if a deletion knocked out Hoxa3, b3, and d3?

Answer 57

A second C2 vertebrea would form instead of a C3

Question 58

Initiates the expression of genes responsible for the generation of C4 vertebrae

Answer 58

Hoxd4

Question 59

Every Hox gene works together with the Hox genes located

Answer 59

Downstream in the cluster

Question 60

In a transgenic mouse with misexpression of Hoxd in a more anterior structure, we would see

Answer 60

2 C4 vertebrae and no C3

Question 61

Hox gene expression extends as far anterior as the

Answer 61

Hindbrain

Question 62

Formation of Drosophila head structures is controlled by a homeobox transcription factor called -NOT part of the Hox cluster

Answer 62

Orthodenticle (Otd)

Question 63

No hox genes are expressed in the

Answer 63

Anterior head structures

Question 64

Mice and humans have 2 Otd analogs called

Answer 64

Otx1 and Otx2

Question 65

Drosophila Otd is expressed in anterior blastocyst in a region of the embryo that will give rise to

Answer 65

Anterior brain structures

Question 66

Drosophila null mutants for Otd result in embryos without

Answer 66

Head and brain structures

Question 67

Mice with Otx1 knockouts survive embryogenesis, but have

Answer 67

Smaller brains

Question 68

Results in lethality and the deletion of forebrain structures during early mouse development, which is similar to the Otd Drosophila phenotype

Answer 68

Otx2 knockout

Question 69

These studies demonstrate that Otx or Otd transcription factors are essential for regulating gene expression necessary to generate

Answer 69

Anterior (head/forebrain) brain structures

Question 70

Turn on a series of downstream genes, which then function together to generate head/forebrain structures

Answer 70

Otc and Otx1/2

Question 71

Situated at the top of a transcriptional cascade and NO other transcription factor in the genome is capable of performing this function

Answer 71

Otd and Otx1/2

Question 72

Overexpression of Otd or Otx results in a

Answer 72

Larger brain

Question 73

When mouse Otx1 was expressed in drosophila in place of Otd, the result was

Answer 73

Larger brains (shows functional redundancy)

Question 74

What hapened when fly Otd was inserted into a mouse in place of Otx1?

Answer 74

The brain size was equal to wild type

Question 75

Fly Otd is functionally equivalent to

Answer 75

Mouse Otx1

Question 76

Caused by diseases such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy, progressive muscular atrophy or by injury to the spinal cord

Answer 76

Motor neuron damage

Question 77

Can generate mature cell types in vitro

Answer 77

ES cells

Question 78

Basic science has identified a cascade of transcription factors required for

Answer 78

Motor neuron generation

Question 79

Researchers have used this knowledge to generate motor neurons in culture from

Answer 79

ES cells

Question 80

A transcription factor code has been identified for generating embryonic stem cells. These genes can convert other cell types into ES cells. What are the genes?

Answer 80

OCT4 and NANOG (homeobox TF's), SOX2, C-MYC, and KLF4

Question 81

The forced expression of these genes in skin fibroblasts converts them to

Answer 81

Induced pluripotent stem cells (iPS cells)

Question 82

Have been implicated in human disease

Answer 82

Homeobox genes

Question 83

Important for patterning the vertebrate limbs

Answer 83

Hox genes

Question 84

Mutations in HOXD13 in both humans and mice result in digit malformations known as

Answer 84

Synpolydactyly

Question 85

Observed in individuals with hand malformations

Answer 85

Missense mutations in HOX13D (3rd alpha-helix)

Question 86

Protein modeling studies indicated that these amino acid changes affect the 3-D configuration of the

Answer 86

Hox gene

Question 87

Protein-DNA binding assays demonstrate that the the missense mutations affect

Answer 87

DNA binding