Gazestani Vahid H, Salavati Reza
Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Montreal, Quebec, Canada.
Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Montreal, Quebec, Canada; McGill Centre for Bioinformatics, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada; Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada.
PLoS One. 2015 Nov 3;10(11):e0142342. doi: 10.1371/journal.pone.0142342. eCollection 2015.
Trypanosoma brucei is a vector-borne parasite with intricate life cycle that can cause serious diseases in humans and animals. This pathogen relies on fine regulation of gene expression to respond and adapt to variable environments, with implications in transmission and infectivity. However, the involved regulatory elements and their mechanisms of actions are largely unknown. Here, benefiting from a new graph-based approach for finding functional regulatory elements in RNA (GRAFFER), we have predicted 88 new RNA regulatory elements that are potentially involved in the gene regulatory network of T. brucei. We show that many of these newly predicted elements are responsive to both transcriptomic and proteomic changes during the life cycle of the parasite. Moreover, we found that 11 of predicted elements strikingly resemble previously identified regulatory elements for the parasite. Additionally, comparison with previously predicted motifs on T. brucei suggested the superior performance of our approach based on the current limited knowledge of regulatory elements in T. brucei.
布氏锥虫是一种通过媒介传播的寄生虫，其生命周期复杂，可导致人类和动物患上严重疾病。这种病原体依靠基因表达的精细调控来应对和适应多变的环境，这对传播和感染性有影响。然而，所涉及的调控元件及其作用机制在很大程度上尚不清楚。在此，受益于一种新的基于图谱的方法来寻找RNA中的功能调控元件（GRAFFER），我们预测了88个新的RNA调控元件，它们可能参与布氏锥虫的基因调控网络。我们表明，这些新预测的元件中有许多在寄生虫的生命周期中对转录组和蛋白质组的变化都有反应。此外，我们发现预测的元件中有11个与该寄生虫先前鉴定的调控元件惊人地相似。此外，与先前对布氏锥虫预测的基序进行比较表明，基于目前对布氏锥虫调控元件的有限了解，我们的方法具有优越的性能。
