TF Regulatory Mechanisms Flashcards
Which two morphogens act on patterning the D-V axis by secreting morphogen from the dorsal side of the neural tube?
BMP and Wnt
Once morphogen gradients are established, describe how responding cells are “locked in” to a cellular program
Once a cell reacts to a morphogen and its cellular fate is determined, downstream target genes of the morphogen are activated and the cell can continue on this path independently of its exposure to a morphogen
Define a coherent feedforward loop
In a pathway x, y, z, the pathway from x > y > z is the same sign as the path from x directly to z
Define an incoherent feedforward loop
The sign of path X to Z is the opposite of the sign of the path from X to Z through transcription factor Y
What is the functional importance of incoherent feedforward loops? (3)
- can generate temporal pulses of Z response
- accelerate the response time of z
- act as a band-pass amplitude filter providing maximal Z activity for intermediate x activity
What types of variables affect feedforward loops? (3)
concentrations of x, y and z
time
post-transcriptional mechanisms
what is the advantage of a double-negative gate over direct activation from x > z?
More locations for regulation, and more control over the overall mechanism - can directly turn Z on and off instead of indirectly turning Z off
Describe the fruit fly antennapedia mutation
Legs develop where antennae should be
Define a homeotic selector gene
A gene which determines the positional identity of a segment
Who coined the term homeosis. Define homeosis
William Bateson in 1894 - definition: a being made like, resemblance
Describe the chromosomal organization of hox genes
They appear on the chromosome ordered as they would be expressed along the AP axis (anterior genes first for head, posterior genes last for feet)
In flies there are two major homeotic gene complexes, what are they called?
Antennapedia complex, bithorax complex
What are the 4 very general regions of the fly larval cuticle from most anterior to most posterior
Head (acron), thorax, abdomen, telson
The anterior hox genes in flies are located at the (5’, 3’) end of the chromosome
5’
Describe the common mechanism which prevents mutations such as the antennapedia mutation
Normally other genes repress hox genes dedicated to other body segments
Homeotic selector genes are sometimes also called…
Realisator genes
All homeodomain genes have… What is this motif called?
A 60 aa conserved region called the homeodomain
The homeodomain area of a gene codes for…
Transcription factor
Genes with homeodomains are called
Homeobox genes
Approximately how many homeobox genes are there in humans?
235
Describe the anatomy of the homeobox
3 alpha helix region where TFs bind
What is the core binding sequence on DNA to which homeobox proteins bind?
TAAT
Homeodomain sequence specificity is achieved at this location…
The 9th amino acid of helix 3
Flies have the Hom-C cluster of homeodomain genes. How many paralogous clusters exist in mammals? Why do mammals have more of these?
4 clusters
Have them from random gene duplication at some point in evolution
