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Landscape of mitochondrial RNA binding proteome [RNAseq_siDHX30_siTFam]

ABSTRACT: We combine RNA 5-ethynyluridine labelling, optimized mitochondria isolation, with click chemistry-based affinity purification to systematically capture the RBPs interacting with mitochondria-located RNAs. This methodology, termed mitochondrial RNA interactome using click chemistry (mitoRICK), unexpectedly revealed a rapid turnover of mitochondria-encoded RNAs compared to their nuclear-encoded counterparts. MitoRICK has identified 122 high-confidence and 25 lower-confidence mitochondrial RNA binding proteins, which expanded the repertoire of mitochondrial RNA binding proteome, and provided a new avenue for understanding mitochondrial RNA metabolism or inherited diseases. We found that MOV10, amongst many newly-identified RNA helicases, is a novel mitochondria-associated RBP. Functionally, MOV10 is important for MT-RNR1 expression or unwinding the mitochondrial double-strand RNAs. As a proof-of-concept, we applied mitoRICK to naïve-to-primed pluripotency transition for studying mitochondrial RBP dynamics, suggesting that intact mitochondrial RNA metabolism is essential for the cell fate transition. MitoRICK is broadly applicable to understand dynamics of mitochondrial RNA binding proteome in various cell contexts.

ORGANISM(S): Mus musculus

PROVIDER: GSE194140 | GEO | 2026/03/20

REPOSITORIES: GEO

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Landscape of mitochondrial RNA binding proteome [mitoRICK]

Project description:We combine RNA 5-ethynyluridine labelling, optimized mitochondria isolation, with click chemistry-based affinity purification to systematically capture the RBPs interacting with mitochondria-located RNAs. This methodology, termed mitochondrial RNA interactome using click chemistry (mitoRICK), unexpectedly revealed a rapid turnover of mitochondria-encoded RNAs compared to their nuclear-encoded counterparts. MitoRICK has identified 122 high-confidence and 25 lower-confidence mitochondrial RNA binding proteins, which expanded the repertoire of mitochondrial RNA binding proteome, and provided a new avenue for understanding mitochondrial RNA metabolism or inherited diseases. We found that MOV10, amongst many newly-identified RNA helicases, is a novel mitochondria-associated RBP. Functionally, MOV10 is important for MT-RNR1 expression or unwinding the mitochondrial double-strand RNAs. As a proof-of-concept, we applied mitoRICK to naïve-to-primed pluripotency transition for studying mitochondrial RBP dynamics, suggesting that intact mitochondrial RNA metabolism is essential for the cell fate transition. MitoRICK is broadly applicable to understand dynamics of mitochondrial RNA binding proteome in various cell contexts.

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Landscape of mitochondrial RNA binding proteome [Par_clip]

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NADcapPro Seq and CircNAD –Methods for Accurate Profiling of NAD and Non-Canonical RNA Caps in Eukaryotes

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Identification of the cellular RNAs bound by MOV10

Project description:Using the iCLIP protocol we have identified the cellular RNA entities that are bound by MOV10. We report the location and sequence of the MOV10 binding region on each RNA entity. To identify the RNAs that bound MOV10, we UV-cross-linked HEK293F cells and immunoprecipitated with an irrelevant antibody (ir or "control") followed by a MOV10-specific antibody (MOV10) to isolate associated RNAs after stringent washing.

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Mitochondrially-imported RNA in Drug Discovery

Project description:The import of nuclear transcribed RNAs into mitochondria is an emerging area that presents tremendous opportunity to develop human metabolic therapeutics. However, our knowledge base is quite limited. Much remains to be discovered regarding specific RNA localization and mechanisms of import. In order to identify novel RNAs imported into mitochondria, all RNAs within the mitochondria were characterized using next generation sequencing technology. Several nuclear transcribed RNAs were found within mitochondrial RNA samples, including nuclear ribosomal RNAs, gamma satellite RNA and VL30 retroelement RNA. The presence of these RNAs within mitochondria coupled with RNA sequencing data (RNAseq) from other laboratories investigating mitochondrial RNA processing, lead us to hypothesize that nuclease treatment of mitoplasts is insufficient for removing contaminating cytoplasmic RNAs. In contrast to traditional methodology, mitochondrial import was evaluated by qRT-PCR after stepwise removal of the outer mitochondrial membrane and subsequent lysis of mitochondria. This allowed identification of RNAs lost from the mitochondria with the same kinetics as mtDNA-transcribed RNAs. This approach provided an improved evaluation of nuclear RNA enrichment within mitochondrial membranes in order to characterize nuclease protection and mitochondrial import and identify false-positive detection errors. qRT-PCR results confirmed the presence of VL30 retroelement RNA within mitochondria and question the hypothesis that the RNA component of RNase P is imported. These results illustrate a reliable approach for evaluating the presence of RNAs within mitochondria and open new avenues of investigation relating to mitochondrial RNA biology and in targeting mitochondrial based therapeutics.

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Mov10 in developing brain suppresses retroelements and regulates neuronal development and function

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FMRP-associated MOV10 facilitates and antagonizes miRNA-mediated regulation

Project description:The fragile X mental retardation protein FMRP is an RNA binding protein that regulates translation of its bound mRNAs through incompletely defined mechanisms. FMRP has been linked to the microRNA pathway and we show here that it is associated with MOV10, a putative helicase that is also associated with the microRNA pathway. We show that FMRP associates with MOV10 in an RNA-dependent manner and facilitates MOV10-association with RNAs in brain. We identified the RNA sequences recognized by MOV10 using iCLIP and found an increased number of G-quadruplexes in the CLIP sites. We provide evidence that MOV10 facilitates microRNA-mediated translation regulation and also has the novel role of increasing the expression of a subset of RNAs by sterically hindering Argonaute2 association. In summary, we have identified a new mechanism for FMRP-mediated translational regulation through its association with MOV10. Comparison of MOV10 siRNA knockdown, irrelevant siRNA control and MOV10 overexpression on total RNA levels

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Poly (A) Click-seq for U937 control and PMA-treated (6h and 24h) cells

Project description:Poly(A)-ClickSeq: click-chemistry for next-generation 3'-end sequencing without RNA enrichment or fragmentation enabling simultaneous genomewide poly(A)-site identification and differential expression analysis

2023-01-12 | GSE169140 | GEO

FMRP-associated MOV10 facilitates and antagonizes miRNA-mediated regulation

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Biological and RNA Regulatory Function of MOV10 in Mammalian Germ Cells

Project description:Background: RNA regulation by RNA-binding proteins (RBPs) involve extremely complicated mechanisms. MOV10 and MOV10L1 are two homologous RNA helicases implicated in distinct intracellular pathways. MOV10L1 participates specifically in Piwi-interacting RNA (piRNA) biogenesis and protects mouse male fertility. In contrast, the functional complexity of MOV10 remains incompletely understood, and its role in the mammalian germline is unknown. Here we report a study of the biological and molecular functions of the RNA helicase MOV10 in mammalian male germ cells. Results: MOV10 is a nucleocytoplasmic protein mainly expressed in spermatogonia. Knockdown and transplantation experiments show that MOV10 deficiency has a negative effect on spermatogonial progenitor cells (SPCs), limiting proliferation and in vivo repopulation capacity. This effect is concurrent with a global disturbance of RNA homeostasis and downregulation of factors critical for SPC proliferation and/or self-renewal. Unexpectedly, microRNA (miRNA) biogenesis is impaired due partially to decrease of miRNA primary transcript levels and/or retention of miRNA via splicing control. Genome-wide analysis of RNA targetome reveals that MOV10 binds preferentially to mRNAs with long 3'-UTR, and also interacts with various non-coding RNA species including those in the nucleus. Intriguingly, nuclear MOV10 associates with an array of splicing factors, particularly with SRSF1, and its intronic binding sites tend to reside in proximity to splice sites. Conclusions: These data expand the landscape of MOV10 function and highlight a previously unidentified role initiated from the nucleus, suggesting that MOV10 is a versatile RBP involved in a broader RNA regulatory network.

2017-08-08 | GSE102303 | GEO

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