Increased processing of SINE B2 ncRNAs unveils a novel type of transcriptome deregulation in amyloid beta neuropathology

Abstract

The functional importance of many non-coding RNAs (ncRNAs) generated by repetitive elements and their connection with pathologic processes remains elusive. B2 RNAs, a class of ncRNAs of the B2 family of SINE repeats, mediate through their processing the transcriptional activation of various genes in response to stress. Here, we show that this response is dysfunctional during amyloid beta toxicity and pathology in the mouse hippocampus due to increased levels of B2 RNA processing, leading to constitutively elevated B2 RNA target gene expression and high Trp53 levels. Evidence indicates that Hsf1, a master regulator of stress response, mediates B2 RNA processing in hippocampal cells and is activated during amyloid toxicity, accelerating the processing of SINE RNAs and gene hyper-activation. 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).

Increased Alu RNA processing in Alzheimer brains is linked to gene expression changes

“…The identification, some years ago, of the critical ability of SINE B2 and SINE Alu RNAs to regulate transcription through suppression of RNA polymerase II, both in humans and in mouse, opened a totally new avenue of possibilities regarding their potential role in cellular function as well as their potential involvement in molecular pathologies (Espinoza et al, 2007;Mariner et al, 2008;Walters et al, 2009;Yakovchuk et al, 2009;Ponicsan et al, 2010Ponicsan et al, , 2015. Subsequently, our recent discovery of the SINE RNA ribozyme/riboswitch potential in response to cellular stress expanded further these possibilities (Zovoilis et al, 2016;Hernandez et al, 2020) and resulted in the identification of a connection between transcriptome deregulation observed in amyloid beta pathology in mouse brain and increased processing of SINE B2 RNAs accelerated by high Hsf1 levels (Cheng et al, 2020).…”

NERD-seq: A novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs

“…<200nt) ncRNAs with Illumina sequencing (short-RNA-seq) (45,48,52). This column-based approach enables for the significant enrichment of short transcripts (although it does not completely eliminate very long RNAs) (53).…”

“…Hippocampi exhibit high transcriptional activity and genomeenvironment interactions, while also being responsive to environmental and physiological changes (76)(77)(78)(79). Additionally, it is a tissue that has received considerable attention for its role in memory formation and learning, and its early dysfunction in disorders such as Alzheimer's and Parkinson's disease and during cancer treatment (45,52,(80)(81)(82)(83)(84)(85).…”

“…Mice were raised and had tissue extracted as described previously (45). Left and right mouse hippocampus tissue were homogenized separately in 1.0mL Trizol reagent: 15-minute incubation and subsequent grinding using a pestle until nothing but insoluble connective tissue remained.…”

“…In both the standard and the the NRED-seq protocol, ligations were performed for 15min instead of 10min, to increase yield. For NERD-seq, the standard protocol was further modified as follows: 1.5ug total RNA was separated into two fractions (short and long RNA) using the Invitrogen MirVana kit (AM1561) with a modified protocol as described before in our short RNA-seq approach for illumina (45)(46)(47)(48). 90uL of the short RNA elution fraction was polyadenylated using 12uL 10x polyA polymerase buffer (NEB, B0276), 12uL 10mM ATP (NEB, B0756A), 6uL polyA polymerase (NEB, M0276) and incubated at 37C for 30min.…”