Binding Sites in Transcription Factors

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1

Hi @LindsayHayes , I was told to ask you about looking for binding sites between two genes, mine being Wnt6 and Elf5. I don’t remember how to do that so I was wondering if you could remind me how to. (Sorry if this is basic stuff, I just totally forgot about it…)

2

@Mark_Sandwich

  1. Go to the UCSC Genome Browser (Mouse mm10 chr12:56,694,976-56,714,605 UCSC Genome Browser v433)
  2. At the top click on the Genome Browser tab and select configure
  3. Scroll down to the Expression and Regulation panel
  4. Click on JASPAR Transcription Factors
  5. Select Display mode = full, checkbox JASPAR 2022 TFBS JASPAR CORE 2022, and click the configure link next to it
  6. In the select dropdown menu check Elf5 because its a transcription factor!
    Note: You can check on/off all if you need to unselect other transcription factors instead of clicking on everyone.
  7. Click the submit button at the top, then click the submit button again on the next page.
  8. Now you should see a track that labels all the Elf5 binding sites on the genome. Now you can go look up your other genes in your pathway or string network to see if you can find Elf5 sites nearby. You will need to be a bit of an explorer here to hunt them down.
    Can you find a Elf5 site near Wnt6 that is going in the same direction as Wnt6? Maybe that could be regulating Wnt6 gene expression? Can you think of an experiment to test that?
    Note: The direction of the arrows to know which direction that TF is regulating.

Happy Hunting!

3

Hi Lindsay, I followed your instructions and I got this result.

https://genome.ucsc.edu/trash/hgt/hgt_genome_22c4_550e0.png
https://genome.ucsc.edu/trash/hgt/hgt_genome_22c4_550e0.png1200×268 3.7 KB

We went over this in class and it looks like there are a lot more transcription factors than usual. Also, if zoomed in enough, you can see that the transcription (Elf5) regulates to the left while the gene itself (Wnt6) points to the right. (Every Elf5 points to the left this was just the biggest one)
image
image2843×640 85.7 KB

I’m not too sure what to make out of this though or if it’s anything interesting.

4

If you look one on the farthest left it is going the same direction as Wnt6. This one could potentially be regulating Wnt6. It is only maybe 1.5 kB away if you look at the scale bar at the top. In genomics work this is like your next door neighbor haha. Transcription factors that regulate a gene are often found outside of the gene structure. So being a little bit before the gene and in the right direction is a good sign.

Note: my screenshot won’t load :frowning:

Look about 1.5 kB before the start of Wnt6.

5

https://stemcellsjournals.onlinelibrary.wiley.com/doi/epdf/10.1002/stem.706
Check out Figure 6