Fis Promoter Map

fispromoter.jpg DNA sequence from E.  coli in the
promoter region for the Fis gene.  Below the sequence are
sequence walkers for Fis sites in front of rectangles
(called petals) with various shades of pink to indicate
different information contents.  There are also a number of
sigma 70 promoters shown by walkers in front of blue boxes
(for the -35) and green boxes (for the -10).  It is clear
that Fis regulates itself from this genetic map. The image above will vary in width to fit the size of your browser window. The figure is also available as: Fis Promoter Map (PDF), Fis Promoter Map (jpg)

At the top, under the page number, you see the line that begins with 'piece 1 ...' which describes the graph. Below that is a bunch of numbers which are the positions of DNA bases on the chromosome of the Escherichia coli (E. coli) bacterial genome. So this is a place at 3.4 million bases from the (arbitrary!) start of the coordinate system, out of 4.6 million bases.

I picked this place because it is in front of the fis gene. The fis gene is turned on when a bacterial cell goes from being starved, when there are no Fis protein molecules, to having lots of nutrients, the number is then 50,000 Fis molecules in each cell!

The letters over pink and red rectangles are representing Fis sites. I call the letters 'sequence walkers' - we have a patent on the method. The colored rectangles, show how strong the site should be (using the mathematics of information theory). The cool thing about this new 'instrument' is that you can see which sites are strong and which are weak in a instant. Before now you had to read the labels, like 4.8 bits or 1.0 bits.

But I also like it because one can see so much in an instant.

See those purple and blue rectangles? They come in pairs, and there are dashed lines directly below the green bar of each that connect them. These represent the places RNA polymerase binds to the DNA to start making RNA. The RNA runs into the fis gene (and from that the Fis protein itself is made) and so this is the genetic control region for Fis.

The reason I love this region is that how it works is obvious. If the cell makes too much Fis protein (from the fis gene) then Fis protein will bind all over this region and turn off the promoters! So it is a nifty feed-back loop, and you can see that in an instant from this ... artwork :-)
Here's the same image with 'artmode' turned on and other parameters switched to remove the black lettering:
fispromoterArt.jpg DNA sequence from E. coli in the as artwork Art: Fis Promoter Map (PDF), Art: Fis Promoter Map (jpg)

2016 Oct 09: NEW: vertical bars connect the parts making it easy to see multi-part binding sites as a single object! The previous images without vertical bars: Fis Promoter Map (PDF), Fis Promoter Map (jpg). I also added a ribosome binding site model. The Shine/Dalgarno is in light green and the initiation codon; ATG in this case is in chartreuse. The resulting short reading frame is shown under the DNA sequence ending in a stop sign. The startpoint for Fis is about 1000 bp downstream from this region, past another gene, so it is not shown.

For the colored rectangles behind the walkers, called "petals", the HSB (hue saturation brightness) colors are set automatically by the script mkpetals. The brightness is set to 1 (full). For the hue (such as red, green and purple), the color spectrum is divided up evenly and assigned to the various sequence walker models. The saturation (white-pink-red) of each rectangle behind the walker is determined by the ratio between the walker total individual information and and the maximum information for the walker weight matrix (i.e., the information of the "consensus"). This turns out to work well visually. One can override the color choices but not the brightness and saturation.

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Schneider Lab

origin: 2004 Jul 27
updated: 2016 Oct 10
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