Carver AP Biology 6: the exercise

Copy and paste this into a Word document and then procede.  Write if you have any problems!!

An Exercise in Comparitive Genomics

You will get DNA for an exon of an important gene and compare its sequence to those in species more and less closely-related to us.

1. Go to the UCSC Genome Browser (link on 2nd post on blog).  On the gateway page (Home, if you're already in the browser), press "Click here to reset" in order to clear what you have already done.  Now specify Human in the genome box, and in the gene box enter: RNA polymerase, and hit "Submit." 

2. In the UCSC Genes list at the top, find the last item: "DNA-directed RNA polymerase II A," and click it.

3. Find the RefSeq (reference sequence) track and click on its label on the left end.  From the beginning of the summary, what do you think the protein encoded by this gene does within a cell? _______________________________________________________________

4. Use the back-arrow to return to the browser window.  Find the RefSeq track again: it shows both ends of the gene, since you can see the untraslated part of the beginning and ending exons that are shown with a half-height bar.  How many exons does this gene contain?  _________   About what percentage of the whole gene would you say consists of exons, and actually encode a protein?  _________  Notice the "Mammal Cons" graph: it shows with a histogram how similar portions of this gene are to those in other mammals that have been sequenced.  Why do you suppose the exons show very strong similarity among species? ______________________________________________________________

Why do you suppose the introns (skinny line) are shown to vary much more (much less strongly-conserved) among species?

___________________________________________________________________________________

We will choose one exon that has been strongly conserved through time and see how similar it is in species closely-related to us, and some more distant.

5. At the top of the window, click on the scale at base position 7,405,000.  This will re-center the sequence at that position and zoom in 3X.  Re-center again at about 7,405,500.  You will see an exon at about 7,405,400 that has been almost entirely strongly conserved in mammals: the Mammal Cons histogram shows a nearly-continuous bar at that position. 

6. Now zoom-in using the 3X and 1.5X buttons and re-center, continuing until this exon almost fills the entire window.  You will notice that the POLR2A top track now shows the one-letter abbreviations for the amino acid sequence encoded by this exon.  Using the table on the 2nd entry of this blog, write out the first half-dozen amino acids, going in the direction of transcription shown by the track arrows.  ______________________________ 

7. We want the actual DNA sequence for this exon, and we will get it using position numbers.  Find the base positions of the ends of this exon.  One way to do this is to drag the track back and forth in the window and note the beginning and ending positions where each end of the exon hits the edge of the display window.  (You can write these numbers down, or simply write down one, Ctrl-c the position box, and correct the copy when you copy it.)  Write the position of this exon here: chr17:_________-__________. 

8. Click the DNA item in the blue menu bar at the top.  Enter the beginning and ending positions of the exon in the position box and click "Get DNA."  You will see the entire base sequence this exon.  (If you did this right, you will have four and a half lines of nucleotide bases--about 250 bases in all.)  Now Ctrl-c just these four and a half lines, hit the back-arrow, and open the BLAT software from the blue menu bar.  Paste the base sequence into the window.

Time to use BLAT to look for similar sequences in other species that are similar to the human exon we have been looking at. 

9. Change the genome in the window to "Chimp" and hit submit.  The chimpanzee is the animal long recognized as the living species most similar to us.  the "score" is the number of bases in the matching regions.  Look at the choice with the highest score.  How many bases in the human and chimp's exons match?  ________   See the matches by clicking "details" for that match region: the matches are shown in blue capitals.  The back-arrow will get you back to the previous screen.

10. Now hit the back arrow twice and change the genome to Mouse--still a mammal, but more distant in evolutionary relationship.  This may find more than one similar sequence; what is the highest score (base match) between humans and mice?  ______

11. Now try Chicken--separated from us by perhaps 300 million years, but still a tetrapod (descendant of the first land vertebrates).  Highest score: ______

12. A lancelet is a tiny marine creature so distantly related to us that it that all it barely has the rudiments of a backbone.  Score: ______

13. C. elegans (Caenorabdis elegans), a nematode worm, is from an entirely different phylum of the animal kingdom.  The score of this exon match is: ______

14. Finally, Saccharomyces cerviseae (S. cerviseae) is baker's yeast (which causes bread to rise by producing CO2 gas by cellular respiration).  This fungus, typically single-celled, is from a different kingdom, but is still a Eukaryote.  Its score for this exon is: ____ 

(Of course, a fungus like this yeast needs to transcribe its genes just as any other organism does, but it presumably does the job of this protein domain coded by exon with a quite different sequence.)

This use of the Genome Browser and BLAT search tool is a good segue into evolution!