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Targeting GI-SINE (Growth inducing B2-SINE) RNA in DRG neurons by Antisense Oligonucleotides (ASO)

ABSTRACT: Targeting GI-SINE (Growth inducing B2-SINE) RNA in DRG neurons by Antisense Oligonucleotides (ASO)

PROVIDER: PRJNA1090485 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28411573_1.fastq.gz	Fastqsanger.gz
	SRR28411573_2.fastq.gz	Fastqsanger.gz
	SRR28411574_1.fastq.gz	Fastqsanger.gz
	SRR28411574_2.fastq.gz	Fastqsanger.gz
	SRR28411575_1.fastq.gz	Fastqsanger.gz

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Targeting GI-SINE (Growth inducing B2-SINE) RNA in DRG neurons by Antisense Oligonucleotides (ASO)

Project description:We identified 2 specific motifs that are enriched in GI-SINE RNA expressed in sciatic-nerve injured DRG neurons compared to non-regulated B2-SINE RNAs. We designed a mix of 5 ASOs (21nt phosphorothioate DNA with LNA-flanks) that target these motifs and transfected those into cultured dorsal root ganglia (DRG) neurons. Control ASO was based on a 21nt non-targetting sequence from shControl backbone (addgene plasmid #85741). Primary DRG neurons were transfected using Dharmafect-4 with ASO at 50nM final concentration 1 hour after plating. Cultures were processed for RNA extraction 48h after transfection for RNA sequencing to identify changes in B2-SINE expression.

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GI-SINE Analyses

Project description:GI-SINE Analyses

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Role of ATF3 in the transcription of GI-SINEs (growth inducing B2-SINEs) in DRG neurons in response to sciatic nerve crush

Project description:Injury of the sciatic nerve upregulates a specific subset of B2-SINE RNAs in Dorsal Root Ganglia (DRG) neurons that enhances axon regeneration, which we termed GI-SINEs (growth inducing SINEs). Based on ATAC-seq and transcription factor binding site analysis and in-culture perturbation of AP-1 TFs, we hypotheiszed that GI-SINEs specifically regulated by injury activated AP-1 TFs. Here we experimentally tested the role of ATF3, a CREB TF that belongs to the AP-1 TF superfamily, in the transcriptional upregulation of GI-SINEs. ATF3 was previously identified and characterized as a key activator of nerve-injury induced regeneration associated genes (RAGs) mRNA. Cre recombinase expressed under the Advillin promoter was used for ATF3-exon3 excision in a broad and specific manner in the DRG. Sciatic nerve injury was carried on on mice with a conditional knockout of ATF3 in sensory neurons and ATF3-wt mice and total RNAseq was carried on RNA extracred from on sciatic innervating DRGs (L4-L6) from the injured side ("Inj") and non-injured side (naive / "Na").

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Analysis of the interactome of B2-SINE RNA transcripts

Project description:B2-SINEs are noncoding RNAs which are transcribed by RNA polymerase III (Pol III) from short interspersed nuclear elements (SINEs), which are high copy number transposable elements in the mouse genome. Unexpectedly have observed significant induction of non-coding RNAs from the B2-SINE subclass of repeat element RNAs in DRG neurons following sciatic nerve injury. We next sought to identify intracellular targets of GI-SINEs, by protein pull-down from sciatic nerve axoplasm using biotinylated B2-SINE RNA as bait. We generated two constructs from the B2 consensus sequence, comprising 5’ (1-75nt) and 3’ (75-166nt) sequences, both predicted to retain their respective structures, and used the constructs to pull down axoplasm proteins for mass spectrometry analysis. Further confirmatory experiments were performed using the mentioned -175nt sequence vs a control U1 SL3+4 RNA

2025-05-05 | PXD060976 | Pride

HF liver: Control vs. Plin2-ASO treated

Project description:Transcriptional profiling of mouse liver comparing control, scrambled-oligonucleotides (Cont)-treated mice with Perilipin 2-antisense oligonucleotides (Plin2-ASO)-treated mice. C57BL/6 mice on a high-fat diet were treated with oligonucleotides in vivo. The goal was to determine the effects of Plin2 down-regulation in the liver on global gene expression. Two-condition experiment, control oligonucleotides vs. Plin2-antisense oligonucleotides. Biological replicates: 4 control replicates, 4 Plin2-ASO replicates.

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HF liver: Control vs. Plin2-ASO treated

2012-12-05 | GSE37011 | GEO

Gene expression profile of modified gapmer antisense oligonucleotides treated mouse liver

Project description:To investigate gene expression change induced by modified gapmer antisense oligonucleotides, we performed transcriptome analysis of Scarb1 ASO or PBS treated mouse livers.

2025-03-28 | GSE289964 | GEO

Sciatic nerve crush upregulation of B2-SINE expression at specific genomic loci

Project description:To map the loci of B2-SINE expressed in DRG which are regulated by sciatic nerve injury, paired-end RNAseq was carried on DRG neurons following sciatic nerve injury at 24h and 72h (3d) after injury. Mice were subjected to crush of the sciatic nerve in one side, while the other nerve was spared and used as naive control condition.

2025-05-16 | GSE230720 | GEO

Lipid nanoparticle delivery promotes cell-type-specific distribution of antisense oligonucleotides in the brain

Project description:Antisense oligonucleotides (ASOs) are being actively investigated as potential therapeutics for a broad range of neurodegenerative diseases. While these small oligonucleotides have been effective in the clinic, many basic questions regarding ASO internalization, trafficking, and modes of enhancing delivery remain. To address these questions, we investigated how lipid nanoparticle (LNP) delivery affects ASO uptake and distribution in the brain. We show that ASOs are internalized and active in central nervous system (CNS) cell types both in vivo and in vitro. While differential cellular activity and polarization states do not affect ASO potency, encapsulating ASOs in LNPs increases ASO activity up to 100-fold in cultured CNS cells. This dramatic increase in efficacy is facilitated by the intracellular trafficking of ASOs away from lysosomes or enhanced ASO uptake, which is cell-type-specific. We assessed the translatability of these results by screening ASO-LNPs in vitro and intracerebroventricularly injecting top performing formulations in mice. ASO-LNP delivery induced a strong ASO-dependent microgliosis response in the brain revealing that LNP encapsulation cannot mask ASO-mediated toxicity. However, LNP-delivered ASOs did not downregulate mRNA levels in bulk tissue due to changes in ASO distribution. While ASOs distribute widely across the brain after bulk injection, ASO-LNPs are preferentially internalized by cells lining the blood vessels and ventricles. Consistent with our findings in cells, ASOs localize to the endolysosomal system following both ASO and ASO-LNP delivery in the brain as determined using immunoelectron microscopy. These data provide valuable insights into how LNPs regulate ASO uptake and distribution in the brain, and support further development of ASO-LNPs for treating CNS disorders.

2023-05-15 | GSE220777 | GEO

AP-1 inhibition in DRG neurons by A-Fos dominant negative construct

Project description:Prior analysis suggsted that that AP-1 TFs play a role in expression of specific B2-SINE following in-vivo nerve injury. We thus sought to experimnetally test the role of AP-1 transcription factors in upregulation of B2-SINE RNA expression in DRG neurons. Neurons were transduced with PHP.S-AAV vectors expressing either A-Fos (dominant negative construct that targets Fos-interacting transcription factors), GFP control or were left untransduced. RNA was extracted 7 days later and analyzed to identify effects on B2-SINE expression and known AP-1 targetted mRNAs.

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