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Genomics
BIOL 387/495
Spring 2018
Dr. Laten
Assignment 2
(Due Thursday, March 17 at 11:59 PM)
1. Use Google Scholar to find one recent (since 2014) journal report of primary research (not a review
article) detailing evidence for horizontal gene transfer(s) between eubacteria and archaea or between a
prokaryote and eukaryotes. Download the article to view it. If it is not open access, you may need to be
connected to the LUC library site to do this. If it is not available through the library, find another article
that you can download. Summarize the nature of the transfer and the kind of evidence/analysis the
researchers used to reach their conclusions. Provide the citation (author(s), article title, journal name,
volume, page numbers, year). [150-200 words].
2. Go to the NCBI web site and based on what we have covered about specific databases use the Resource
list, and/or the drop-down menu in the All Databases box, and the term Escherichia coli, find out exactly
how many total E. coli genomes have been sequenced as of this week and how many total non-redundant
genes (core plus pan) are in this species. You do not need to differentiate between core and pan. Note that
Figure 8.11 in your textbook shows about 2,100 genomes and 94,000 genes (90,000 pan and about 4,000
core), so these numbers are out of date.
3. Find five examples from the literature (Google Scholar is a good place to start) of independent examples
of transposable element insertions that cause a specific human disorder. Summarize the nature of the
transposable element, the location of the insertion, how gene function is altered, and the disease it causes.
[200-250 words]
4. The figure on the right represents a computer-generated heat
map of chromatin interactions within a 10 million base pair
region of human chromosome 18 detected by Hi-C. Numbers
at the corners represent the positions on the chromosome.
Explain how Hi-C works with respect to this figure. What do
the darkest red areas represent in general? Specifically, what
do the peaks of each of the five darker red “triangles” show?
Estimate the position numbers. [150-200 words]
5. Go to the UCSC genome browser (https://genome.ucsc.edu/cgi-bin/hgGateway) and go to the human
chromosome that corresponds to the number next to your name below. Type chrX:40,000,00042,000,000 (where X is your personal chromosome number - see list below) into the search box and hit
go. This will give you a 2 million base-pair window. If you get the message that one of these positions
can’t be found, just change the range to another two million base pair segment, e.g. 60,000,00062,000,000. Make sure you have annotated genes in the window. If not, choose another range. Zoom in
on a 200,000 bp-region containing one of the genes using the zoom and arrow boxes, and again zoom in
to cover the entire gene plus 10,000 bp on either side. Some annotations will be open by default in the
main window. Scroll down to see all the window options. Make sure the following windows are open:
NCBI Refseq on full; ENCODE regulation on show (click on ENCODE regulation and make sure the
following are designated: layered H3K4Me3 (full), layered H3K27Ac (full), and DNase clusters (dense));
OMIM alleles: hide; Common SNPs: hide; Human RNAs: full; Repeat Masker: dense; Conservation: full.
Once your window is organized, click on the name of the gene and sift through the links to determine as
best you can the function of the gene product. Are there different mRNAs? How many introns? Exons?
Possible alternative splicing? What are the positions and relevance of histone marks and DNase
sensitivity? Discuss sequence conservation and repetitive DNAs in the region – zoom in to see where
sequences are most conserved and repetitive DNAs are most dense. Include a screen shot of the upper part
of your zoomed window.
1. Vince
2. Maryam
3. Conrad
4. Angela
5. Karina
6. Jared
7. Karson
8. Georgia
9. Aashaka
10. Shreya
11. Hannah
12. Madison
13. Brianne
14. Paulina
15. Sam