TFs and signaling Flashcards
What is a transcription factor?
A TF is a protein that specifically binds to DNA sequences, directly with a DNA binding domain or indirectly with adapter proteins. It can act as an activator or repressor for transcription.
How can be determined where TFs bind in the genome?
This can be done with ChIP-seq. In this technique the TFs are fixated to the DNA and the DNA is fragmented and purified for the target TF. This purified DNA is sequenced and mapped to the genome to show the binding locations of the TF.
How can you induce a pathway?
A pathway can be induced by providing extracellular factors that lead to an intracellular response, e.g. hormones, ions, light or heat.
Explain Notch signaling.
A notch ligand (Delta or Jagged) comes into contact with Notch receptor. This leads to cleavage of Notch and the Notch intracellular domain (NICD) translocates into the nucleus. It recruits additional proteins, and this complex regulates DNA transcription of different target genes.
How many molecules of TF are activated by Notch signaling?
One, because the Notch molecule is cleaved and the NICD acts as the TF.
What is the advantage of MAP kinase signaling?
The signal can get amplified because of the cascade of protein kinases.
How can the same signaling pathway give specific responses to different inputs?
Specificity in can be achieved to signal integration, where different inputs come together and converge. Also, spatial and temporal regulation of signaling events contributes to specificity.
Wnt signalling.
When Wnt ligands bind to the Frizzled (Fz) cell receptors, they induce a signal cascade which blocks the complex that degrades ß-catenin. This causes ß-catenin to accumulate and enter the nucleus where it activates the target genes (e.g. Lgr5).
How can there be different outputs considering there are so few signal transduction pathways which are utilized by all the cells?
The pathways combine in different ways (parallel, branch, converge, diverge). Also, the output is depending on the cell type and cellular environment. Signaling pathways also use feedback mechanisms and sensitivity adjustments after a stimulus, which increase complexity.
Explain 2 methods to visualize signaling activity.
FRET based biosensor: energy can be transferred when two fluorochromes are in proximity, because the emission spectrum of one overlaps with the excitation spectrum of the other. The change in fluorescence can be measured.
Translocation based biosensor: fusion of a fluorescent marker to a protein to measure the location in the cell.
What are tools that can be used to manipulate signaling in cells?
Tools to manipulate signaling:
- Add or remove natural signaling ligands like GFs, hormones, or cytokines
- Microfluidic systems to efficiently change media
- Chemical inhibitors: small, often unspecific molecules that can also be clinically used
- Inducible systems: systems that manipulate pathways which can be induced with chemicals or light (optogenetics)
