More than 97% of the mammalian genome is non-protein coding, and repetitive elements account for more than 50% of noncoding space. However, the functional importance of many non-coding RNAs generated by these elements and their connection with pathologic processes remains elusive. We have previously shown that B2 RNAs, a class of non-coding RNAs that belong to the B2 family of SINE repeats, mediate the transcriptional activation of stress response genes (SRGs) upon application of a stimulus. Notably, B2 RNAs bind RNA Polymerase II (RNA Pol II) and suppress SRG transcription during pro-stimulation state. Upon application of a stimulus, B2 RNAs are processed into fragments and degraded, which in turn releases RNA Pol II from suppression and upregulates SRGs. Here, we demonstrate a novel role for B2 RNAs in transcriptome response to amyloid beta toxicity and pathology in mouse hippocampus. In healthy hippocampi, activation of SRGs is followed by a transient upregulation of pro-apoptotic factors, such as p53 and miRNA-34c, which target SRGs creating a negative feedback loop that facilitates return to the pro-stimulation state. Using an integrative RNA genomics approach, we show that in mouse hippocampi with amyloid pathology and in an in vitro cell culture model of amyloid beta toxicity, this regulatory loop is dysfunctional due to increased levels of B2 RNA processing, constitutively elevated SRG expression and high p53 levels. Evidence indicates that Hsf1, a master regulator of stress response, mediates B2 RNA processing in cells, and is upregulated during amyloid toxicity accelerating the processing of SINE RNAs and SRG hyper-activation. This data attributes a role to SINE RNA processing in a pathological process as well as a new function to Hsf1 that is independent of its transcription factor activity. Our study reveals that in mouse, SINE RNAs constitute a novel pathway deregulated in amyloid beta pathology, with potential implications for similar cases in the human brain, such as Alzheimer’s disease (AD).
Overall design: In this study, we employed a transgenic mouse model of amyloid pathology, APP NL−G−F (APP) (Saito et al., 2014) and the respective wild type control C57BL/6J (WT). We have tested three different mouse ages that correspond to different phases of amyloid beta pathology: i) pre-symptomatic stage with undetectable (very low) amyloid plaque load, (3 months - 3m/ APP: 3x mice, WT:2x mice), ii) stage of symptom manifestation (that coincides with the active neurodegeneration phase and appearance of amyloid plaques (6 months - 6m/ APP: 3x mice, WT:3x mice), and iii) terminal stage of the pathology (12 months - 3m/ APP: 3x mice, WT:3x mice). Whole hippocampi, (hippocampi separated from both the left (L) and right (R) hemishere of each mouse and pooled together), represented as hippocampus L+R, were isolated from the above mice, and the extracted RNA from each hippocampus was separated into two samples: one enriched in short-RNAs (sR) and one in long-RNAs (LR). Each sample was then subjected to next-generation sequencing (short-RNA-seq and long-RNA-seq, respectively). We also employed the hippocampal HT-22 cell line (Davis & Maher, 1994). We treated HT22 cells with either an LNA against Hsf1 (anti-Hsf1) or a scramble LNA (ctrl) followed by incubation with amyloid beta peptides (42/ 1-42 aa) or a control peptide with an inverted amino acid sequence (R/ reverse 42-1). Biological replicates were as follows: 42/Ctrl: x4, R/Ctrl: x4, 42/Anti-Hsf1:x3, R/Anti-Hsf1:x3 Subsequently RNA was extracted, separated into short-RNA and long-RNA samples as above, and subjected to next generation sequencing (short-RNA-seq and long-RNA-seq, respectively).
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