8/19/14 - Gene Expression I Flashcards
What common structural motif is present in HLH transcription factors?
Leucine zipper
Do DNA elements behave differently depending on their orientation or distance from the coding region?
No, they are orientation and distance independent.
What is a bromodomain?
A region in a regulatory protein that recognizes acetylated lysines in histones.
What is a HAT?
Histone acetyl transferase, catalyzes the acetylation reaction.
What is a chromodomain?
A region in a regulatory protein that recognizes methylated lysines and arginines in histones.
What two amino acids are important for the function of Zn finger motifs?
Histidine, cysteine
What is a reporter gene?
A gene that is attached to the regulatory sequence of another gene. It allows us to measure the regulatory potential of an unknown DNA sequence.
Why do transcription factors generally bind to palindromic sequences?
Transcription factors are often active as dimers, and require symmetry in the DNA sequence so both subunits can bind.
What are CHIP assays used for?
Allows us to identify ALL the sites in a genome that a gene regulatory protein occupies in vivo.
Where does the RNA polymerase assemble on the gene?
Promoter region
Which gene region contains the TATA box?
Core promoter region
How does histone acetylation affect gene transcription?
Prior histone acetylation makes it easier for chaperone proteins to remove them from the nucleosome, increasing the accessibility of the DNA and therefore increasing transcription.
Which gene region contains the CCAAT box?
Proximal coding region
How does acetylation prevent the formation of heterochromatin?
Acetylation of lysines on the histones breaks the charge interactions between adjacent nucleosomes, allowing the chromatin structure to open.
What process allows us to identify regulatory regions in a gene, and what is the basic principle behind this process?
DNA footprinting. You add a protein of interest to a sample of DNA, then cleave the DNA with nuclease. If the protein binds to any region of that DNA, then it will be protected from cleavage. The protected region can be visualized following gel electrophoresis.
