San Diego State University Wk 2 Transcription Factor Binding Sites Lab Report

Week 2 Lab: Transcription Factor Binding Sites
Cells need to be able to modulate gene expression in response to the cell’s internal needs,
environmental conditions and signals from surrounding cells. In a multicellular organism,
differences in gene expression are critical for creating specialized cell types that can work
together.
Without differences in gene expression programs, specialized cell types such as olfactory
neurons would not function well. One of the most important gene expression tasks that needs
to happen in an olfactory neuron is the selection of a single receptor or receptor pair to express
while silencing other receptor genes. In carbon dioxide sensitive neurons on the fly antennae,
this means turning on Gr63a and Gr21a and shutting off other receptor genes. On the other
hand, a non-CO2 neuron would want to turn off expression of Gr21a and Gr63a.
Much of gene expression is regulated by DNA binding factors called transcription factors
(TFs). These types of TFs usually have at least two protein domains: a DNA binding domain
that is attracted to a particular sequence of DNA and an activator/repressor domain that
interacts with other proteins to control when and how strongly the gene is transcribed. Simply
speaking, expression of a particular gene can be controlled by A) the presence of a TF
binding site in its promoter and B) the presence or absence of the TF that binds that site.
Today we are going to take a closer look at Gr63a’s promoter region and the transcription
factors that could bind there.
1. Go to http://jaspar.genereg.net/genome-tracks/ and click on “Drosophila melanogaster:
dm6.”
2. This will take you to the UCSC genome browser and load the annotated fly genome with
a custom JASPAR track showing predicted TF binding sites. We are going to use it to
search for binding sites in Gr63a’s promoter region. Search for “Gr63a.”
3. This will take you to a screen asking which gene entry you mean. Click on the bottom
one:
4. This will take you to the gene span of Gr63a. Note that Gr63a is shown going from right
to left. This indicates that the CDS is on the minus (3’–>5’) strand in this standard
genome format. Scroll over to the right to see the promoter region directly upstream of
Gr63a’s TSS.

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