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Examining long non-coding RNA using Big Red II

The human body contains millions of microscopic units called ribonucleic acid (RNA) that work together to build muscle, create energy, and generally live in the world each day. While many of these molecules serve specific functions, some seem superfluous, like the “garbage” of the human biological makeup. It’s easy to skip past these seemingly insignificant specks, but one researcher’s trash is another’s molecular treasure.

While RNA performs many functions in the human body, most notably coding for amino acids that translate into proteins, one particular type of RNA remains a mystery. Long non-coding RNA (lncRNA) consists of a longer-than-200-nucleotide sequence that does not favor protein translation; due to its lack of apparent function, lncRNA is often dismissed as “junk” RNA. Felipe Porto, a Master’s student in Dr. Sarath Chandra Janga’s lab at IUPUI, seeks to annotate the function of lncRNA, which has previously been thought to have no function. His interest in the field of bioinformatics was piqued during an internship; during that time, Porto learned that the field is rife with potential for real discovery given its location at the intersection of several different disciplines.

Porto explains that his work looks at genomic sequences as a jumbled up sentence; he imagines the genes to be the words in the sentence, and the lncRNA as the punctuation marks. While many researchers would focus on the words, he focuses on the punctuation, looking for ways that their placement could change the overall meaning/function of the sentence/sequence. Porto examines lncRNA function within cancer cell lines, focusing on how mutations, such as the loss of a lncRNA, could affect alternative splicing of genes. When genes are alternatively spliced, like a change in punctuation or word placement, the differential gene expression can cause functional deviations. While many researchers focus on one specific lncRNA transcript or isoform, Porto focuses on many to observe the overall effect.

In order to look at the large sequences his work requires, Porto runs statistical models on Big Red II, IU’s main system for high performance parallel computing. These calculations could take months on a single PC, but Big Red II processes Porto’s work quickly and smoothly. Along with increased speed, Big Red II allows Porto and his colleagues access to other supercomputing resources such as Carbonate and Data Capacitor 2. As Porto notes, he and his colleagues are “avid users and big fans” of these resources, which make very difficult and time-consuming tasks possible, and offers his sincere thanks to the members of the Janga lab, the School of Informatics and Computing, and the UITS Research Technologies staff for helping him make the most of these HPC tools.