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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Virus and Prion Research » Research » Publications at this Location » Publication #356745

Research Project: Intervention Strategies to Control Endemic and New and Emerging Viral Diseases of Swine

Location: Virus and Prion Research

Title: Pieces of a dream: A study in mapping transfer RNA fragments (tRFs) within the porcine genome

item FLEMING, DAMARIUS - Orise Fellow
item Miller, Laura

Submitted to: North American Porcine Reproductive and Respiratory Syndrome (NA-PRRS) Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 11/14/2018
Publication Date: 12/1/2018
Citation: Fleming, D.S., Miller, L.C. 2018. Pieces of a dream: A study in mapping transfer RNA fragments (tRFs) within the porcine genome [abstract]. North American Porcine Reproductive and Respiratory Syndrome (NA-PRRS) Symposium. Abstract No. PRRS 27.

Interpretive Summary:

Technical Abstract: Advancements in the study of porcine immunogenetic responses to highly pathogenic porcine reproductive and respiratory virus (HP-PRRSV) infections have served to uncover a litany of small non-coding RNAs involved in fostering tolerance or susceptibility to illness. Small non-coding RNAs (sncRNA) function as regulators of gene expression and epigenetic modifications. Some well-studied sncRNAs, such as miRNAs and tRNAs, have emerged as important modulators of the immune system and homeostatic regulation during HP-PRRSV infections. Unfortunately, there is little known about another class of sncRNA related to tRNAs referred to as tRNA fragments (tRFs) that can be similar in both size and function to miRNAs. It is possible that these tRFs, like miRNAs, also have modulating effects on the immune response in virally infected livestock. Regrettably, to date no list of expressed tRF molecules have been mapped for healthy or sick pigs; making it difficult to interrogate their expression during HP-PRRSV infections. Therefore, a study was undertaken to identify and quantify tRF expression in HP-PRRSV infected pigs. The study was conducted using porcine whole blood of 24 pigs split into two treatment groups (control/infected) and three time points (1, 3, and 8 dpi) to examine tRF differential expression. Discovery and mapping of possible porcine tRFs from the S. scrofa 10.2 reference genome were conducted using a comparative genomics approach. The results of the study showed that all five tRF classes (5', 3', 5'-halves, 3'-halves, i-tRFs) could be identified in both healthy and infected porcine blood and that expression levels differed between treatments. The results from this study highlights changes in tRF expression that has the potential to unlock new targets for understanding the effect HP-PRRSV has on the porcine immune response. Future studies will look to apply these methods to the updated porcine reference genome.