The Repeat Masker Tool Within the UCSC Genome Browser

This week I will continue to utilize the UCSC Genome Browser (http://genome.ucsc.edu/), this time using the Repeat Masker track to research the repeat elements of the PIR gene (Kent, Sugnet, Furey, et al., 2002). Repeat elements are sections of the genome that repeat themselves within the genome. The Screen Masker track is capable of displaying 10 separate classes of repeats: SINE, LINE, LTR, DNA, Simple, Low Complexity, Satellite, RNA, Others, and Unknown. Within each of these classes, areas of the PIR gene are shaded from a light grey to a very dark grey to indicate how many “Base mismatches, base deletions, and base insertions [are] associated with a repeat element,” with a higher number of these being indicated by light shading, while a lower number is indicated by darker shading. 





Utilizing this knowledge we can see that classes such as LINE and LTR have relatively high concentrations of repeats and classes such as LINE and DNA contain longer repeats. Understanding the presence of repeat elements such as SINEs (Short interspersed nuclear elements) and microsatellites in a gene is important as it allows us to understand what genetic material provides architectural and functional support and what material is strictly protein encoding. Furthermore, repeat elements can be used to determine the presence or absence of heritable traits by using them as markers within a chromosome (Holmes, 1994).


Throughout the entirety of my semester with the TRAIN program I have had the opportunity to research several experimental techniques that may be useful for my research in the future. Most recently this blog has discussed the use of microarrays to determine tissue specificity as well as utilizing Next Generation RNA-Seq technologies to map anything from individual codons to entire genomes. Furthermore, the very first week of this blog I briefly mentioned how I was interested in further researching the use of bacterial expression systems to aid in the research of protein expression. 




References

Holmes NG. Microsatellite markers and the analysis of genetic disease. Br Vet J. 1994
Sep-Oct;150(5):411-21. doi: 10.1016/S0007-1935(05)80190-3. PMID: 7953576.

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.

 

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