Using the UCSC Genome Browser to Build a Further Understanding of the PIR Gene

  This week I will be using the UCSC Genome Browser (http://genome.ucsc.edu) to 

investigate the qualities and mechanisms of PIR, the gene that encodes the protein pirin. The

database was created by the Genome Bioinformatics Group for the purpose of compiling 

genomics information such as gene modifications, transcription factors, expression patterns,

and more. The strictly moderated database is capable of linking to genetic information 

available on other databases, but also directly cataloging scientist-submitted data (Kent, 

Sugnet, Furey, et al., 2002). 

The UCSC Genome Browser contains an absurd amount of data; it is truly a monumental feat of modern science. From the loci of every gene in a chromosome to the individual nucleotides in a specific modification of a specific gene, the UCSC Genome Browser is capable of generating imagery of it all. The database feels like the apotheosis of The Human Genome Project placed at the fingertips of anyone with an internet connection. Because of my lack of background in the language of biology, the database immediately comes across as overwhelming to me. The amalgam of technical vocabulary, user-settings, and search preferences crowding every square inch of the screen of the website’s homepage is nearly migraine inducing. I suppose this is the price of knowledge.

While the website and its functions are probably the most difficult to navigate out of the databases that I have encountered thus far, the Genome Browser does boast an impressive amount of customization and accessibility features. With a few mouse clicks one can resize the text or change the font of the entire website, save their current search session, resize the graphic-interface, or export the information gathered from their current session in a number of different file types utilizing any assortment of the export parameters offered by the website.

After getting my bearings I was able to navigate to the genetic assembly for the PIR gene. The assembly locates the gene in chromosome X at the coordinates “15,384,799-15,493,564.” The assembly presents a large range of information, from nucleotide/nitrogenous base sequences to information on allele variation. Scrolling down the page displays numerous display parameters to apply to the graphic. Changing the NCBI RefSeq track from a “dense display” to a “full display” expands the track to display the transcript variants of PIR catalogued by RefSeq. Clicking the heading of the new RefSeq track conveniently allows me to switch back to the “dense display," while clicking on the names or locations of the PIR variants navigates me to a summary page on said variant that includes numerous cross-links to other databases. These PIR variants include two mRNA variants (Locus NM_001018109.3 and Locus NM_003662.4) and, curiously, a non-coding variant (Locus NM_003662.4). Very little research has been conducted on the PIR ncRNA variant; the only article I was able to find even tangentially related to the topic was a study from the RIKEN Advanced Science Institute in Japan. The study was concerned with read-through transcription in general, and only uses the ncRNA PIR variant as one facet in a much broader investigation. The article concludes that the PIR variant rarely encodes a protein and is usually subject to decay (Prakash, Sharma, Adati, et al., 2002). Perhaps this could be a potential subject of further investigation?

Attached below is the genomic assembly for PIR that was provided to me by the UCSC Genome Browser. Unfortunately, due to Blogger's limitations I am not able to upload a higher quality version of the image. Instead I will paste a link to the Genome Browser beneath the image that displays the entire PIR assembly in higher quality.

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chrX%3A15384799%2D15493564&hgsid=1218417297_1j9sRI2MlRz25lykRxoZ7z6M14Hq

References

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D.  The
human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.
Prakash T, Sharma VK, Adati N, Ozawa R, Kumar N, Nishida Y, Fujikake T, Takeda T,
Taylor TD. Expression of conjoined genes: another mechanism for gene
regulation in eukaryotes. PLoS One. 2010 Oct 12;5(10):e13284. doi:
10.1371/journal.pone.0013284. PMID: 20967262; PMCID: PMC2953495.