RNA-RNA interaction analysis of functional SINE repeat elements-derived transcripts
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE224533 | GEO | 2023/02/06
REPOSITORIES: GEO
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Project description:SINEUPs are long non-coding RNAs which contain a functionally crucial SINE repeat element and positively regulate target mRNA translation at post-transcription level. To study secondary (2D) structure of these functional SINE-derived RNAs, various SINEUP-GFP plasmids containing different mouse SINEB2 repeat elements or human SINE FRAM repeat were transfected along with sense EGFP plasmid in HEK293T/17 cells. Total RNA in transfected cells were probed at flexible regions with NAI-N3 reagent and icSHAPE (in-vivo click selective hydroxyl acylation and profiling experiment) libraries were prepared. To further understand the structure dynamics of SINE transcripts in subcellular locations, cells were fractionated in nuclear and cytoplasmic fractions after 24 h of transfection and fraction-specific icSHAPE libraries were constructed.
2023-02-06 | GSE224534 | GEO
Project description:Short interspersed element (SINE) RNAs are upregulated by cellular stresses1 (heat shock, DNA damage and viral infection) and accumulate in human diseases (macular degeneration2, lupus3, and Alzheimer’s disease4). These transcripts activate inflammasomes5, a family of cytoplasmic multiprotein complexes that sense danger molecules and initiate innate immune responses by activating caspase-1-dependent cytokine production and inflammatory death6, but the molecular sensor of SINE RNAs is unknown. Here, we identify DDX17, a member of the DEAD box family of RNA helicases7, as a sensor of SINE RNAs requisite for inflammasome activation. Induction of caspase-1 cleavage and release of IL-1 and IL-18 by SINE RNAs requires dual recruitment of NLRP3 and NLRC4 but proceeds independent of NAIPs, immune sensors required for canonical NLRC4 activation by bacterial proteins8,9. Instead, SINE RNAs trigger DDX17–NLRC4 interaction, which licenses inflammasome activation. We also report increased levels of DDX17 protein and association of DDX17 and NLRC4 in the retinal pigmented epithelium (RPE) of human eyes with an advanced, untreatable form of age-related macular degeneration (AMD). Disrupting DDX17–NLRC4 signalling blocks SINE RNA-induced inflammasome activation in human RPE cells and RPE degeneration in an animal model of AMD. Our findings uncover a non-canonical mode of inflammasome activation by endogenous retrotransposon transcripts, and provide new potential targets for macular degeneration and potentially other diseases.
2022-06-09 | PXD016019 | Pride
Project description:SINEUPs are SINE repeat element containig long non-coding RNAs (lncRNAs)which positively regulate target mRNA translation at post-transcription level. SINE RNA region is crucial for SINEUP function. To analyze the effect of sequence deletion on RNA secondary structure of SINEB2 RNA derived from mouse natural antisense lncRNA to Gadd45α gene, RNA structure of four deletion mutants were chemically probed inside cells. For this, different structure mutants and target EGFP mRNA plasmids were co-transfected in HEK293 cells and icSHAPE libraries were prepared.
2023-09-19 | GSE243220 | GEO
Project description:We found novel functional long non-coding RNAs (lncRNAs) that contain a SINE element, and which up-regulate the translation of target mRNA, named SINEUPs. To investigate the network of translational regulation, we focused on the sub-cellular distribution of target mRNAs and SINEUP RNAs and SINEUP RNA binding proteins (RBPs). We identified PTBP1 and HNRNPK as essential RBPs. These proteins contributed to SINEUP RNA sub-cellular distribution and to assembly of translational initiation complexes, leading to enhancement of the target mRNA translation. To prove the SINEUP RBPs binding regions on SINEUP-GFP transcripts, we performed seCLIP; single-end enhanced crosslinking and immunoprecipitation assay to determine the specific binding sites of PTBP1 and HNRNPK on SINEUP-GFP RNA. These findings will promote a better understanding of the mechanisms on the fate of regulatory RNAs implicated in efficient protein translation.
2020-02-09 | GSE144345 | GEO
Project description:Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28,270 SINE loci, with ~50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA-RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation.
2016-10-31 | GSE85518 | GEO
Project description:We identified a novel long non-coding RNA Lx8-SINE B2, that is a marker of pluripotency. Depletion of Lx8-SINE B2 impacts embryonic stem cell self-renewal. RNA-seq analysis of Lx8-SINE B2 depletion revealed that a number of glycolytic genes with decreased expression. Mechanistically, we found that the Lx8-SINE B2 activates the glycolysis pathway by binding to Eno1. Collectively, our data suggest that Lx8-SINE B2 maintains the self-renewal of mESCs through glycolysis.
2022-09-19 | GSE182247 | GEO
Project description: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).
2020-11-19 | GSE149243 | GEO
Project description:RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Direct determination of RNA structures and interactions in living cells remain a major challenge in biology. Crosslinking and proximity-ligation-based approaches, such as PARIS (Psoralen Analysis of RNA Interactions and Structures), offer many advantages, such as the ability to directly capture complex RNA duplexes in cells with single molecule accuracy, near base pair resolution in high throughput and without size limit. Based on a systematic optimization of the photochemistry and enzymology, here we present PARIS2, a re-invented method for capturing RNA duplexes with >3000-fold improved efficiency. PARIS2 captures ribosome small subunit binding sites on mRNAs, thus reporting translation process. PARIS2 also captures the snRNP binding sites on various types of RNA targets. We applied PARIS2 to enterovirus D-68, a re-emerging viral pathogen associated with severe neurological symptoms and discovered dynamic/alternative conformations in the 5’UTR. The new photochemical and enzymological improvements and the PARIS2 method should be widely applicable to basic RNA research and RNA-related diseases.
2021-03-04 | GSE149493 | GEO
Project description:SINE transposons in multiple lepidopteran insects Raw sequence reads
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Project description:Developing a psoralen probe (PP)-based method for RNA tagging and RNA-protein complex (RP-complex) enrichment, isolating of both coding and noncoding RNAs from HeLa cells was achieved by PP enrichment. Exploring the type and relative distribution of the PP isolated RNAs by RNA-sequencing analysis.
2021-06-30 | GSE163230 | GEO