The protein-coding genes represent <2% of the eukaryotic genome as ~98% of the transcriptional output is non-coding (nc) RNAs. The ncRNAs are currently considered as the master controllers of the transcription and translation and hence any disruption in their function could lead to severe compromises in cellular homeostasis. Despite their abundance and paramount functional importance, very few studies to date evaluated the significance of ncRNAs in acute brain damage. We and others recently showed that miRNA expression profiles alter extensively following stroke;and modulating specific miRNAs induce neuroprotection. These studies indicate the role of ncRNAs in ischemic pathophysiology, but the significance of other ncRNAs like piwi-interacting RNA (piRNA) to ischemic brain damage is not evaluated yet. The piRNAs (26 to 31 nt long) are the most abundant of all ncRNAs with >40,000 piRNAs identified so far in eukaryotes. The major function attributed to them is to selectively target and silence the RNAs formed by the retrotransposons (RTs). As RTs are the predominant class of transposons (jumping genes) which mutate and disrupt the protein-coding genes, the piRNAs balance the fitness of the genome to maintain the cellular equilibrium. We hypothesize that """"""""Focal ischemia alters cerebral piRNAome with functional significance to ischemic brain damage"""""""". In preliminary studies, we observed that >10% of the 40,000 piRNAs evaluated are expressed in rat cerebral cortex. Furthermore, when rats were subjected to focal ischemia, 106 cortical piRNAs were either up- or down-regulated (>2.5 fold). Bioinformatics showed that stroke- responsive piRNAs have several RT targets distributed throughout the genome, and the promoters of those piRNAs contain binding sites for multiple transcription factors.
Aim 1 a is to study the temporal pattern of piRNA expression profiles following transient focal ischemia.
Aim 1 b is to conduct bioinformatics analysis to find RTs targeted by piRNAs altered after ischemia.
Aim 1 c is to conduct bioinformatics analysis to identify transcription factor binding sites in the promoters of the stroke-responsive piRNAs.
Aim 2 is to test the effect of knocking-down specific piRNAs on the histological and behavioral outcomes after focal ischemia.
Aim 1 results will generate a catalog of the piRNA profiles after experimental stroke, and will identify the putative down-stream targets and upstream controllers of stroke-responsive piRNAs.
Aim 2 results will show if piRNAs have a functional significance to stroke outcome.

Public Health Relevance

Stroke is a leading cause of death and disability in adult population. The mechanisms that lead to stroke-induced brain damage are not fully understood. This proposal wishes to evaluate if stroke-induced brain damage is mediated in part by a subtype of non- coding RNAs known as piRNAs.

National Institute of Health (NIH)
National Institute of Neurological Disorders and Stroke (NINDS)
Exploratory/Developmental Grants (R21)
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Molecular Neurogenetics Study Section (MNG)
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Jacobs, Tom P
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University of Wisconsin Madison
Schools of Medicine
United States
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Vemuganti, Raghu; Zhao, Heng (2015) Mechanisms and therapies for acute CNS insults. Metab Brain Dis 30:353
Vemuganti, Raghu; Silva, Vinícius R; Mehta, Suresh L et al. (2014) Acute liver failure-induced hepatic encephalopathy s associated with changes in microRNA expression rofiles in cerebral cortex of the mouse [corrected]. Metab Brain Dis 29:891-9
Mehta, Suresh L; Dharap, Ashutosh; Vemuganti, Raghu (2014) Expression of transcribed ultraconserved regions of genome in rat cerebral cortex. Neurochem Int 77:86-93
Vemuganti, Raghu (2014) Non-coding RNAs in CNS disorders--the long and short of it. Neurochem Int 77:1
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Dharap, Ashutosh; Pokrzywa, Courtney; Vemuganti, Raghu (2013) Increased binding of stroke-induced long non-coding RNAs to the transcriptional corepressors Sin3A and coREST. ASN Neuro 5:283-9
Vemuganti, Raghu (2013) All's well that transcribes well: non-coding RNAs and post-stroke brain damage. Neurochem Int 63:438-49
Alrfaei, Bahauddeen M; Vemuganti, Raghu; Kuo, John S (2013) microRNA-100 targets SMRT/NCOR2, reduces proliferation, and improves survival in glioblastoma animal models. PLoS One 8:e80865
Pandi, Gopal; Nakka, Venkata P; Dharap, Ashutosh et al. (2013) MicroRNA miR-29c down-regulation leading to de-repression of its target DNA methyltransferase 3a promotes ischemic brain damage. PLoS One 8:e58039
Dharap, Ashutosh; Nakka, Venkata Prasuja; Vemuganti, Raghu (2012) Effect of focal ischemia on long noncoding RNAs. Stroke 43:2800-2