Millonig - Molecular Gennetics of Pattern Formation 2

Question 1

orthologs vs. paralogs

Answer 1

o - homologous gene between species
p- homologous gene within species

For instance, orthologs would be if the same gene does the same thing in flies and mice. Paralogs would be if different genes within a mouse are responsible for developing the same part of the body.

Question 2

temporal co-linearity

spatial co-linearity

Answer 2

temporal - 3’ genes are expressed earlier than the 5’ genes
spatial - genes further 3’ have more anterior expression boundaries

It is important to note that not only one the one Hox gene that you would think is responsible for the development of a structure will be active. It is possible that 1) the paralog is also expressed and 2) the Hox gene that came before/after it is also expressed

Question 3

loss of function mutations vs gain of function mutation

Answer 3

loss - lead to anterior mutations because then the Hox gene that came before it will still be active so you will have duplication of that structure like in the C2/C3 example in the spine.
gain - lead to posterior mutations. Makes sense because if you have overexpression of a certain Hox gene then you will see it show up earlier than it should and in a greater ratio so it will take over something that was supposed to be developed first. Example is the C4.

Question 4

transcriptional mechanisms to explain Hox phenotypes

Answer 4

Basically as you get more posteriorly, more and more genes get turned on. However, the previous genes will need to stay on as well. For example, Hoxa2 and Hoxb2 are transcription factors resposible for turning on a set of genes in C2. Hoxa3, Hoxb3, and Hoxd3 are responsible for transcription factors that turn on genes in C3. However, Hoxa2 and Hoxa3 need to still be on in order for proper C3 formation. If there is a mutation in Hoxa3, Hoxb3, and Hoxd3 then we only Hoxa2 and Hoxb2 will be on so you will see “double C2.”

Question 5

Otd and Otx1/2

Answer 5

Otd is a homeobox gene responsible for brain development in flies. We have orthologs in humans called Otx1 and Otx2. A mutation in Otx1 will lead to smaller brain structures including the cortex. Mutation in Otx2 will lead to death. A mutation in Otd will lead to death. If you have a mutant Otx2 or Otd but express the protein at a non-neural location you will still see proper formtion of neural structures. If you have a mutant in Otx1, it can be rescued by using Otd.

Question 6

knockouts, knock-ins, transgenics

Answer 6

outs - delete a gene
in - replace one gene with a different one
transgenic - add extra copies of the gene

Question 7

Homeobox

Answer 7

180 bp domain that is responsible for encoding a protein that encodes a protein domain called homeodomain. Homeobox genes encode transcription factors that initiate a cascade of gene expression necessary for development of body structure. The homeodomain AA structure is responsible for binding and recognizing many AT rich areas found in promoters and enhancers. The 3’ end homeobox genes code for anterior structures (by the head), and 5’ end genes code for genes by the feet. 4 HOX clusters in humans and mice

Question 8

Why is it that in-vivo there is extreme specificity of the homeobox gene but in vitro there isn’t?

Answer 8

Because not the entire gene is responsible for creating the homeodomain. There are other proteins that bind to other parts of the DNA and alter the specificity.