Part I – The study of limb phenotypes (10 min)

1.       What big processes of development are involved in the formation of a human limb?

The formation of three axes (AP, PD, and DV) is very important for limb development. The anterioposterior (AP) axis is formed first. These axes are caused by gradient differences in proteins like SHH and other molecules.

2.       Think about human limb development (wild-type or mutant) as a phenotype of interest. From a fundamental research perspective, why is it a useful phenotype to study? Why is it a good model system for the study of development? What are the advantages?

It is a good phenotype to study because it is very visual, caused by non-lethal mutations and changes in regulation, and it is a relatively complex model for even more complex systems. Limb malformation studies have been happening for a very long time even without genetic techniques.

3.       What is the difference between an isolated and a syndromic malformation, and what kinds of mutations are they postulated to be associated with?

isolated -> change in regulation of a gene in only one aspect of development. ie. SHH production is only effected in limb development but not everywhere else.

syndromic -> either a change in regulation in multiple areas or a mutation in the gene itself that causes phenotypic effects in many areas, leading to a group of symptoms that result in a syndrome

Part II – The study of cis-regulatory elements (20 min)

4.       Select one of the loci discussed in the review by Bhatia and Kleinjan. As a group, prepare a model of its regulation (can be in words, diagrams, a mixture thereof, etc). Then:

•   list the evidence that the authors use as a basis for each part of the model;

•   evaluate the evidence (decide if it is sufficient to support the various parts of the model);

•   if applicable, select a part of the model for which we do not (yet) have much supporting evidence. What additional piece(s) of evidence would help strengthen the model? What experiment(s) could you do to obtain them?

HoxD is surrounded by intergenic space and many regulatory islands that include enhancers. This includes the global control region (GCR) that has enhancing activity over many genes in a tissue specific manner; this is only one example of the many regulatory element groups surrounding HoxD. This information was found using histone markers that signify the presence of enhancers in the intergenic space surrounding HoxD. We think that finding histone makers that are often found near enhancers is a correlation rather than truly a signifier of enhancer sequences. Further investigation using enhancer traps and other techniques is necessary for verifying the presence of these regulatory islands.

5.       What is synteny? How does progress in our identification of cis-regulatory elements help explain some cases of synteny? (And thus making the connection between genome structure, function and evolution relevant?)

synteny -> physical co-localization of genes on the same chromosome

An understanding of the identity and location of cis-regulatory elements shows which aspects of regulation are essential for specific structure development. The conversation of these structures may lead to conservation of the regulation and groups of genes that are regulated by the same elements are more likely to remain together throughout speciation, resulting in syntenic regions.  

 Part III – Where do the cases are from, and who is the information for? (10 min)

6.       Think about all the research conducted on human limb malformation. How do you think the subjects for the study were recruited? How do you think the information gained from these studies was disseminated? Who had access to it? Who could it be useful or interesting for? How are the phenotypes under study depicted?

Subjects were likely recruited through doctors’ offices, medical histories, or speaking with people who have limb malformations. There may have also been some study of dead embryos (most likely in mice). The information gained from these studies was likely distributed through medical case studies, medical journals, and potentially in some scientific journals. Medical professionals, medical researchers and students, and other scientists would have had access to this information. This information would be interesting to medical students, science students, doctors, genetic counselors, researchers in the field, and people who are affected or know someone affected. The phenotypes are depicted in pictures, x-rays, and medical terms.