With the growing understanding of the importance of non-coding RNAs, one particular class, the piwi-interacting RNA, is garnering increased attention for its apparent role in regulating RNA silencing.
To support ongoing research into piRNAs, the National Institutes of Health last month awarded two grants that will fund projects examining the mechanisms behind their creation and their possible role in brain damage.
The first grant went to California Institute of Technology's Alexei Aravin for his work studying the molecular mechanisms of piRNA biogenesis.
Working with piwi proteins, piRNAs “recognize and silence endogenous genomic parasites called transposable elements,” Aravin wrote in his grant's abstract. “The silencing of transposons is critical in germline cells and the failure of piRNA-mediated repression leads to sterility in both Drosophila and mice.”
The ncRNAs are encoded in clusters and act as “memory banks to store inactive copies of past transposon invaders” and “produce long transcripts that are further processed to mature small RNA species,” he added. “Our goal is to dissect piRNA biogenesis from their transcription to processing into mature piRNAs, and to understand how these steps are regulated.”
Specifically, Aravin and his colleagues aim to understand how transcripts that are to be processed into piRNAs are selected and to identify the “enzymatic machinery responsible for processing” using Drosophila and other insect cell lines, according to the abstract.
The team will then investigate the genomic and chromatin structure of piRNA clusters and map their promoter regions in order to identify the regulatory elements needed for piRNA expression, and to pinpoint the role of chromatin in their transcription.
Aravin then proposes to identify the aspects of precursor transcripts that are required for piRNA biogenesis, and determine if processing of the ncRNAs depends on “distinct sequence elements” inside the transcripts or a specific protein complex.
“Finally, we will study the intracellular localization of piRNA precursor transcripts and the role of nuage granules in piRNA biogenesis,” he added. “Together, these experiments will comprehensively analyze all steps of piRNA biogenesis from transcription of precursor RNAs to processing into mature small RNAs.”
His grant began on June 6 and runs until the end of May 2015. It is worth $288,360 in its first year.
In the second grant, University of Wisconsin, Madison, researcher Raghu Vemuganti will focus on the possible role of piRNAs in ischemic brain damage.
Previous studies have shown that microRNA expression profiles change after a stroke and that modulating certain of these small RNAs can induce neuroprotection, he wrote in his grant's abstract.
“These studies indicate the role of ncRNAs in ischemic pathophysiology, but the significance of other ncRNAs like [piRNAs] to ischemic brain damage is not evaluated yet.”
In preliminary studies, Vemuganti and his lab found that more than 10 percent of the 40,000 piRNAs they evaluated are expressed in rat cerebral cortex.
“Furthermore, when rats were subjected to focal ischemia, 106 cortical piRNAs were either up- or down-regulated,” he wrote. “Bioinformatics showed that stroke-responsive piRNAs have several [retrotransposon] targets distributed throughout the genome, and the promoters of those piRNAs contain binding sites for multiple transcription factors.”
With the NIH funding, he plans to examine the temporal pattern of piRNA expression profiles following transient focal ischemia, and then to conduct bioinformatics analysis to find retrotransposons targeted by the ncRNAs altered after ischemia.
Afterward, a bioinformatics analysis will be performed to “identify transcription factor binding sites in the promoters of the stroke-responsive piRNAs,” according to the grant's abstract.
The researchers will then examine the effect of knocking down specific piRNAs on histological and behavioral outcomes after focal ischemia.
The grant began on June 1 and runs until May 31, 2013. It is worth $185,625 in the first year.