Molecular genetics of pattern formation (pintar + milliong)

Question 1

What causes most cases of Down Syndrome?

Answer 1

Usually a nondisjunction in meiosis I. This will make two diploid gametes rather than one so chances are higher.

Question 2

Other than 21, which other two chromosomal aneuploidies are not lethal

Answer 2

13: cleft lip, holoprosencephaly, micropthalmia (small eyes)
18: rocker bottom feet, clenches hands `

Question 3

What is thalidomide and when are risk of birth defects from teratogens highest?

Answer 3

Thalidomide is a sedative and insomnia treatment. Resulted in lack of long bone formation leading to short limbs.

Risk is highest during the embryonic period (3-8 weeks)

Question 4

Describe how TGF-beta starts the signal cascade.

Answer 4

TGF-beta proteins (nodal and BMP4) first dimerize and then bind to threonine, serine kinases.

From there receptor is phosphorylated.

Antagonists would bind the TGF-beta receptors and prevent the formation of TGF-beta dimers.

this will lead to phosphorylation of Smads which will unfold and they themselves, dimerize, enter the nucleus and activate gene expression

Question 5

How does BMP signaling and RA signaling differ from TGF-beta signaling?

Answer 5

BMP4 is also part of the TGF-beta family and antagonists (chordin and noggin) will bind to the monomers so they cannot produce a dimer to bind to the receptors.

RA (vitamin A) is hydrophobic and so does not need a receptor. It will enter the nucleus and activate genes.

Question 6

Describe FGF signaling

Answer 6

heparan sulfate presents FGF to tyrosine kinase receptors and help stablize an active dimeric receptor despite FGF being a monomer. The activity of a proteoglycan.

Question 7

Describe how the ICM is separated from the trophectoderm

Answer 7

At the 8 cell stage, two TFs are coexpressed. By the 16 cells stage, certain cells express one TF over the other. This allows for their segregation at the blastocyst stage into the ICM and the TE.

Question 8

What is the node and the nodal protein’s function

Answer 8

Nodal expression begins early in development, first initiating the formation of the AVe in the anterior visceral endoderm. AVE produces inhibitors that sequester nodal expression to only a region of the postrior.

The node is in the posterior region of the embryo. It is where gastrulation begins and the mesoderm will form. The node expresses nodal above a threshold level and a lack of nodal protein will result in no primitive streak and undeveloped mesoderm.

Question 9

Describe BMP4 and nodal’s relationship and the role of BMP4

Answer 9

BMP4 supresses mesoderm and CNS formation and promotes epidermis. It is antagonized by chordin and noggin which binds to its monomers.

BMP4 will first inhibit mesoderm and the node, especially dorsal mesoderm which gives rise to notochord and somites. once nodal expression is in the node, noggin and chordi n expression also begin. This allows for nodal expression and formation of dorsal mesoderm and neural induction

Question 10

What is goosecoid?

What is Brachyury?

Answer 10

Goosecoid-expressed in the node, allows anterior structures to be induced-
-too much goosecoild could lead to two heads.

Brachyury knockout leads to much reduced posterior mesoderm.

Question 11

What are 4 causes of reduced posterior mesoderm development?

Answer 11

1. Too litte Brachyury
2. Too little chordin, noggin to suppress BMP4
3. Too much retinoic acid
4. Too little FGF.

Question 12

What are the two functions of FGF

Answer 12

FGF is expressed in primitive cells.
1. It induces and maintains a second region of nodal expression which leads to left-right sidedness.

2. promotes chordin and noggin expression which continues to inhibit BMP4 and lead to dorsal mesoderm and neural tissue development

Question 13

Describe the role of RA.

Answer 13

RA negatively controls FGF.
RA is usually expressed in a gradient starting highest in the anterior and FGF is expressed highest in the posterior. Over time RA will expand further posteriorly and activate FGF from rostral to caudal.

If too much RA, FGF will be turned off prematurely leading to deficits in posteriro structures.

Too much RA means a lack of FGF (which promotes the formation of posterior structures)

RA is teratogic - it could activate receptors that shouldn’t be activated and lead to underdeveloped posterior.

Question 14

So too much RA shuts off FGF prematurely, why does this affect the posterior genes?

Answer 14

Well this is a result of homeobox genes, linearly organized with the 5’ end encoding for posterior organs and 3’ end encoding for the anterior. 5’ end genes require a more exposure to FGF to start their transcription. Premature removal of FGF leads to underdeveloped posterior .

Question 15

How are transgenics created?

Answer 15

They are insertion of DNA into the genome because the system hates free DNA ends and will fix it.

Transgenics are not deletions and are only addition of extra copies.

You take fertilized eggs from the fallopian tube and DNA is injected into the pronuclei, DNA will integrate randomnly into the genome and develop into an organism.

Question 16

Describe the fly and human homeobox. Include in your sexy discussion the promiscuous paralogs and obedient orthologs.

Answer 16

Homeobox is a gene 180 bp in legnth.

So the fly has one cluster of homeobox genes

Human and mice both have four clusters.

Homeobox genes encode for proteins with a homeodomain which binds to AT rich DNA regions. In vitro there is no specificity. So the remaining region of the protein impart specificity.

Orthologs: are homologous genes between species (fly red gene and mouse red gene)

Paralog (beside): are homologous genes in the same species - red genes on two of the four clusters

Question 17

What are spatial and temporal colinearities?

Answer 17

Spatial refers to how 3’ gene expression boundaries are more anterior.

Temporal refers to how 3’ gene expression is expressed earlier.

Question 18

Describe the hox code and three qualities of their deletion, amount of deletion, or insertion?

Answer 18

Certain cells will only express certain factors. As you go posterior, each body segment expresses the same factors as anteriorly along with additional factors.

Deletion of a homeobox genes: leads to more anterior morphology (because you will lack additional posterior factors but anterior TFs extend the length of the embryo)

Deletions show a semidominant pattern, the more deletions the more severe.

Gain of function mutations or transgenics tend to lead to more posterior transformations because posterior tend to express more or if expressed anteriorly would lead to posterior structure formation.

Question 19

How is head structure formed?

What if these factors were expressed in other tissues

Answer 19

None of the homeobox genes encode the head in both fly and human. This is the role of the Otd (fly) and Otx1 + Otx2 (human and mice). Otd and Otx have functional redundancy. Since they affect downstream genes. Replacing Otx with Otd will activate the same genes and rescue an Otx deletion.
Both Otd and Otx lead to develop of anterior brain regions.
Otx2 full deletion- lethal
Otx1 full deletion - smaller cortex
So Otx1 deletion is less severe.

Since these TFs sit quite upstream, expression in nonneuronal tissue induces neural structures. aka ectopic expression

Question 20

Which 5 factors can generate embryonic cells from differentiated cells?

Answer 20

OCT4, SOx2, NANOG, C-MYC, KLF4.

Question 21

Describe homeobox transcription factors.

Answer 21

The homeodomain is part of the TF DNA binding domain.

The homeodomain is comprised of three alpha helices.

Homeobox TFs will bind DNA in vitro.