Exploring Genetic Material Transfer, Chromosomal Conformation, And Genomes Sequencing

Horizontal Gene Transfer between Prokaryotes and Eukaryotes

Questions:

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in your textbook shows about 2,100 genomes and 94,000 genes (90,000 pan and about 4,000 core), so these numbers are out of date.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:40,000,000- 42,000,000 (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. 60,000,000- 62,000,000. 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      4. Angela   7. Karson   10. Shreya   13. Brianne
2. Maryam  5. Karina    8. Georgia  11. Hannah  14. Paulina
3. Conrad   6. Jared     9. Aashaka  12. Madison 15. Sam
 

1.Horizontal gene transfer, also known as lateral gene transfer, has been established to occur between prokaryotes and eukaryotes. This mode of genetic material transfer occurs between the symbiotic prokaryotes found within eukaryotic cells. The prokaryote’s genome gets inserted into the eukaryotic (host’s) genome and when successfully transcribed, it confers newer functions in the eukaryotes. The researcher’s used a common endosymbiont Wolbachia pipientis and computationally analyzed its host’s genomes for copies of the bacterial genes. Wolbachia pipientis’ genetic base sequences were identified and cross referenced with those of four insects and nematode species where entire Wolbachia genome and other short sequences of base pairs were identified as insertions in the test species being examined. Three other insect that are not common hosts for the bacteria had their genomes extracted and their sequences examined for the symbiont’s genome. This provided proof of lateral gene transfers in eukaryotic hosts that do not possess endosymbionts. The researchers also located specific regions of bacterial genome that had been transcribed in the eukaryotes and inferred the implication of translation of such genes (Julie et al, 1753-1756).

2.With newer sequences being added on a daily basis, successful complete Escherichia coli genomes sequenced add up to a total of 10120 genomes. Among th sequences identified, there are 94000 non-redundant genes established in Escherichia coli strains with 4000 core and 90000 pan genes.

3.Long Interspersed Nuclear Element (LINE) 1 (L1)

LINES are classified are class I transposable elements. The L1 is also referred to as clade LINE-1, and it is a non-Long terminal repeats (LTRs) retro transposon (Richard and Mark, 691-703). It is 6 kilobases (kb) long and contains a 5’ end untranslating region (UTR) that possess internal RNA polymerase II promoter activity. Its base sequence also contains two open Reading Frames (ORFs) each of which encodes a different functional unit (Babushok and Kazazian, 527-539): ORF1encodes a RNA-binding protein whereas ORF2 encodes a protein with endonuclease activity (Martin and Jose, 115).  L1 also has a 3’ end untranslating region that is made up of polyadenylation signals ending with an oligo dA-rich tail that varies in length for different sequences (Babushok and Kazazian, 527-539). This element causes genetic insertion mutation that result in most inherited diseases. LINE 1 insertion on the human factor VIII causes the production of un-functional clotting factor VIII that result in hemophilia. Also its insertion in the APC gene results in the development of colon cancer.

Alu element

This is another typical example of a non-LTRs retro transposon that contains a million copies in the human genome. They are mostly 300 base pairs in length with two sequences derived from 7SL RNA gene combining to form dimeric structures separated by A-rich linker regions (Kreigs et al, 158-61). They are similar in structure to the 3’ end of L1, however, their 5’ end has an internal RNA polymerase III promoter activity. It is also responsible for generating insertion mutations that alter gene expression of the affected gene. Insertion of Alu element on the human ALMS1 gene at exon 8, 10 and 16, results in Alström syndrome, a genetic disorder that is characterized by blindness and obesity. This is so as the gene encodes a protein responsible for insulin resistance, hypogonadism and heart disease (Songmi et al, 70-77). 

Escherichia Coli Genomes Sequencing

SVA elements

Also a non-LTRs retro transposon with up to 3000 copies in the human genome, SVA elements are often 2 kilobases long with various hexamer repeat region, Alu-like regions, a number of tandem repeats and HERV-K10-like region with the common 3’ polyadenylation signals that is typical of non-LTRs retro transposons (Wang et al, 994-1007). Also responsible for genetic insertion mutation, its nsertion into the α-spectin gene causes the inheritable familial elliptocytosis disorder (Eric et al, 1444-1445).

4.Hi-C is a typical example of the chromosomal conformation technologies (3C technologies) that are used in molecular biology to determine the spatial organization of chromatin within a cell. This technique uses high-throughput sequencing (Hakim, 1068) to simultaneously quantify the number of interactions of genomic loci between all possible pairs of fragments.  This thus provides a count of all the possible pairwise interactions between complete genomes. The method involves crosslinking of chromatin with formaldehyde followed by the digestion and re-ligation with biotin-labeled nucleotide at the junction between DNA fragments that are covalently bound to each other. The ligation products are sequences to produce heatmaps that identify Hi-C interactions as areas marked by dark red color (Belton et al, 268-276). The peaks of the red “triangles” indicate the first covalent interactions between sequences, that is, the initial point Hi-C interactions.

5.The segment outlines 24 comprehensive transcripts, hence 24 mRNAs. There are approximately 40 exons and 37 introns in the identified base sequence. The DNase 1 hypersensitivity for this segment is 0 meaning it cannot be spliced by DNase and hence, it is a stable region of the chromosome. The position of histone marks can be identified at point 1 and 4 within the DNA segment. The bound histone protein helps in protecting the DNA segment from attacks by endonucleases. This works to enhance the stability of the DNA segment. The DNA segment contains many tandem repeats of bases AAA and TTT with many highly conserved areas.   

Babushok D. V. and Kazazian H. H. Jr. Progress in Understanding the Biology of the Human Mutagen LINE-1. Hum Mutat. 2007; no 28: 527-539

Belton M., McCord P., Gibcus J. H., Naumova N., Zhan Y. and Dekker J. Hi-C: A Comprehensive Technique to Capture the Conformation of Genomes. Methods, 2012 Nov; Volume 58, no 3: 268-276

Eric M. Ostertag, John L. Goodier, Yue Zhang and Haig H. Kazazian Jr. SVA Elements are Nonautonomous Retro transposons that Cause Disease, Am J Hum Gen, Volume 73, no 6: 1444-14511

Julie C. Dunning Hotopp, Michael E. Clark, Deodoro C. S. G. Oliveira, Jeremy M. Foster, Peter Fischer and Monica C. Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes. Science 21 Sep 2007. Volume. 317, no. 5845, pp. 1753-1756

Hakim Ofir. “Snapshot: Chromosome Confirmation Capture. Cell, Volume 148, no 5: 1068.e1-2

Kreigs J.O., Churakov G., Jurka J., Brosius J. and Schmitz J. Review Evolutionary History of 7SL RNA-Derived SINES in Supraprimates. Trends Genet. 2007 Apr; Volume 23, no. 4: 158-61

Martin Munoz-Lopez and Jose L. Garcia-Perez. DNA Transposons: Nature and Applications in Genomics. Curr Genomics, 2010 Apr; Volume. 11, no. 2: 115-128

Songmi Kim, Chun-Sung Cho, Kyudong Han and Jungnam Lee. Structural Variations of Alu Element and Human Disease. Genomics Inform, 2016 Sep; Volume 14, no 3: 70-77

Richard Cordaux and Mark A. Batzer. The Impact of Retro transposons on Human Genome Evolution. Nat Rev Genet. Oct 2009. Volume. 10, no. 10: 691-703

Wang H., Xing J., Grover D., Hedges D. J., Han K., Walker J. A. and Betzer M. A. SVA Elements: A Hominid-Specific Retroposon Family. J Mol Biol. 2005 Dec 9; Volume 354, no 4: 9994-1007