Homeobox Genes Flashcards
1
Q
Knockouts:
A
- delete any gene of the genome via embryonic stem (ES) cells
2
Q
Knock-ins:
A
- replacing one version of a gene with another (usually mutant gene) via embryonic stem (ES) cells
3
Q
Transgenics:
A
- add extra copies of any gene to a genome
4
Q
Inner Cell Mass (ICM):
A
- Group of cells in the center of blastocyst
- ICM cells are pluripotent for the embryo
- embryonic stem (ES) cells
5
Q
Inner cell mass cells are pluripotent for:
A
- all cell types in the embryos.
6
Q
Cells in the outer epithelium of the blastocyst are committed to generate:
A
- part of the placenta
7
Q
Embryonic Stem Cells:
A
- retain their pluripotency to generate all embryonic cell types
- if the DNA of these cells is altered then an organism can be generated that has this specific DNA change
8
Q
Homeotic mutations:
A
- mutations where one structure is replaced with another or is duplicated
- a transformation
9
Q
Homeobox:
A
- a DNA sequence, around 180 base pairs long, found within genes that are involved in the regulation of patterns of anatomical development (morphogenesis).
10
Q
About how many base pairs is the homeobox?
A
180bp
11
Q
What protein domain does the homeobox encode for?
A
- a protein domain called a homeodomain
12
Q
The function of homeobox genes is:
A
- to regulate the expression of other genes during development.
13
Q
Homeobox genes are:
A
- transcription factors and bind to DNA in a sequence-specific manner.
- All homeobox genes bind AT rich elements in promoters and enhancer of other genes to regulate expression.
14
Q
All homeobox genes bind what type of DNA sequences?
A
- AT rich elements in promoters and enhancer of other genes to regulate expression
15
Q
Structure of the homeodomain protein:
A
- 3 alpha helices
- amino acids in helix #3 make contact/bind with the DNA (AT rich sequences)
16
Q
The homeodomain sequence is what part of the homeodomain protein?
A
- the amino acids in helix #3 that make contact/bind with the DNA (AT rich sequences)
17
Q
The current model of how homeodomain transcription factors recognize and bind to specific DNA sequences states:
A
- Homeobox proteins form complexes with other proteins and together have DNA sequence specificity.
- These other proteins which bind the homeobox protein regulate its function and dictate binding to the correct sites in vivo.
18
Q
What regulates the DNA binding specificity and transcriptional activity of homeodomain proteins?
A
- Other proteins interact with non-homeodomain regions of the homeodomain transcription factor to form protein complexes.
19
Q
What two classes of homeobox genes exist?
A
-
HOX genes
- clustered; mapped in same area of genome across species
-
Other genes with a homeodomain
- not clustered; mapped differently across species
20
Q
Function of HOX genes:
A
- patterning the body axes
- when mutated result in homeotic phenotypes
21
Q
HOX genes are clustered in one place in the genome.
How the genes are organized genomically within the cluster corresponds to:
A
- their expression pattern:
- 5’ end genes expressed in posterior domains of the adult.
- 3’ genes expressed in anterior domains of the adult.
22
Q
Within a HOX gene cluster, genes on the 5’ end are expressed where on the adult?
A
- posterior domains (tail)
23
Q
Within a HOX gene cluster, genes on the 3’ end are expressed where on the adult?
A
anterior domains (head)
24
Q
How many HOX gene clusters are in:
drosophilia?
mice?
humans?
A
- drosophilia = 1
- mice = 4
- humans = 4
25
The mouse and human Hox clusters are typically called:
* HOXa
* HOXb
* HOXc
* HOXd
26
Orthologs are:
* homologous genes between species.
27
Paralogs are:
* homologous genes within a species.
28
Posterior/anterior:
29
Mouse Hox genes are expressed where in the embryo?
* the developing neural tube
* the flanking somites
30
Spatial co-linearity:
* HOX genes further 3’ in the HOX gene cluster have more anterior expression boundaries
31
Temporal co-linearity:
* 3’ HOX genes in the HOX gene cluster are expressed earlier in development than 5’ HOX genes
32
The 5’- most HOX gene in the HOX cluster will be expressed when in development?
* at the latest developmental time point
* 3' end HOX gene are expressed first in development and more anteriorly
33
HOX Code:
* different groups of cells express distinct patterns of Hox genes (transcription factors) depending on their position along the anterior-posterior (A-P) axis.
* dictates the development of different structures along the A-P axis.
34
The HOX code is due to:
* spatial and temporal co-linearity
* cells that develop first will have a different set of HOX gene expression (HOX code) than those that develop later.
35
Loss of function HOX mutations (knock-outs) lead to:
* anterior transformations
* e.x. deletion of 5' HOX genes adjacent to a 3' HOX gene will lead to a duplication of the 3' HOX gene gene product (3' genes are expressed first and more anteriorly).
36
Gain of function HOX mutations lead to:
* posterior transformations
* e.x. 5' HOX genes are expressed too early, and more posterior structures are expressed too early
37
Single HOX mutants have less severe phenotypes than double or triple HOX mutations due to:
* redundancy
38
HOX genes encode for transcription factors that sit at the top of:
* a transcription cascade
* the HOX transcription factors will transcribe genes that are only supposed to be expressed in a particular cell type/structure.
* this is why DNA specificity is important
39
The generation of the head (Drosophila) and forebrain (mice) is the function of a different homeobox transcription factor (not part of the Hox cluster) called:
* Orthodenticle (Otd; drosophilia)
* Otx 1 and Otx2 (mice and humans)
40
What are the mice and human orthologs of the orthodenticle (Otd) homeobox transcription factor in drosophilia?
* Otx1 and Otx2
41
Drosophila null mutants for Otd result in:
* embryos without head and “brain” structures
* indicates this homeobox gene plays a fundamental role in generating these structures
42
Otx1-/- mouse mutants phenotype:
* survive embryogenesis
* different brain structures than normal
* cortex smaller
43
Otx2-/- mouse mutants phenotype:
* die early in embryogenesis
* The mutant deletes the portion of the developing CNS that will generate forebrain structures.
44
Otd and Otx transcription factors are essential for development of:
anterior brain structures
head/forebrain structures
45
Can any other genes in the genome substitute for the function of Otd and Otx1/2?
* No.
* indicates these homeobox transcription factors likely sit at the top of a transcriptional cascade that is important in generating these structures.
46
Does mis/overexpression of Otd or Otx1/2 lead to an enlarged brain?
* Yes.
* indicates that these homeobox transcription factors are **_both necessary and sufficient_** for generating these brain structures.
47
Three important facts about Otd and Otx1/2:
* all sit at the **top of a transcriptional cascade** responsible for development of the head/anterior brain.
* all are **necessary and sufficient** for development of the head/anterior brain.
* Otd and Otx1/2 are functionally and genetically redundant.
* conserved across drosophilia, mice, and humans
48
Cell type generation during development is determined in part by:
* a cascade of transcription factors
* Therefore, forced expression of a particular set of transcription factors in ES cells could result in the generation of different mature cell types.
49
Induced pluripotent (iPS) stem cells can be generated by:
* Introducing a specific set of transcription factors into mature cells:
* OCT4, SOX2, NANOG, C-MYC, KLF4
* These genes/transcription factors are sufficient to convert other cell types to ES cells.
50
What mutated HOX gene leads to synpolydactyly?
* *HOXd13*
* **important for patterning the vertebrate limbs
51
How was the HOXd13 gene identified as the cause of syndactyly?
1. Large syndactyly cohort.
2. Linkage analysis ran on affected versus healthy family members.
* causative gene found in HOXd gene cluster.
3. HOXd gene sequenced.
* three missense mutations found.
4. Experimental studies performed.
