Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA322081 | ENA |
REPOSITORIES: ENA
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Project description:NAD(P)H:quinone Oxidoreductase (NQO1) is essential for cell defense against reactive oxidative species, cancer, and metabolic stress. Recently, NQO1 was found in ribonucleoprotein (RNP) complexes, but NQO1-interacting mRNAs and the functional impact of such interactions are not known. Here, we used ribonucleoprotein immunoprecipitation (RIP) and microarray analysis to identify comprehensively the subset of NQO1 target mRNAs in human hepatoma HepG2 cells. One of its main targets, SERPINA1 mRNA, encodes the serine protease inhibitor α-1-antitrypsin, A1AT, which is associated with disorders including obesity-related metabolic inflammation, chronic obstructive pulmonary disease (COPD), liver cirrhosis and hepatocellular carcinoma. Biotin pulldown analysis indicated that NQO1 can bind the 3’ untranslated region (UTR) and the coding region (CR) of SERPINA1 mRNA. NQO1 did not affect SERPINA1 mRNA levels; instead, it enhanced the translation of SERPINA1 mRNA, as NQO1 silencing decreased the size of polysomes forming on SERPINA1 mRNA and lowered the abundance of A1AT. Luciferase reporter analysis further indicated that NQO1 regulates SERPINA1 mRNA translation through the SERPINA1 3’UTR. Accordingly, NQO1-KO mice had reduced hepatic and serum levels of A1AT and increased activity of neutrophil elastase, one of the main targets of A1AT. We propose that this novel mechanism of action of NQO1 as RNA-binding protein may help to explain its pleiotropic biological effects.
2017-05-22 | GSE81614 | GEO
Project description:The emergence and spread of Plasmodium falciparum human malaria parasites resistant to antimalarial drugs, including artemisinin, a first line antimalarial drug, is threatening malaria treatment and prompting fears of a resurgence of the disease. New drugs with novel mode of actions are thus urgently required. Several compounds with antimalarial activity are known to target protein translation, although few of these targets have been validated. Translation initiation in eukaryotes is known to require eukaryotic translation initiation factor 4F (eIF4F) complex, which binds to the 5′-cap structure on mature mRNA and recruits other proteins for translation of mRNA. The putative components of the eIF4F complex in P. falciparum have been identified in the genome including PfeIF4E, a 5′-cap-binding protein; PfeIF4A, a helicase protein for unwinding mRNA, and PfeIF4G, a PfeIF4E/PfeIF4A scaffold protein, which could constitute a novel antimalarial target. However, it is not known if these proteins constitute a P. falciparum eIF4F complex in vivo, nor what other proteins interact with the mRNA 5′-cap to control translation initiation in this species. Here, we investigated P. falciparum proteins that interact with the mRNA 5′-cap. Native protein extract from P. falciparum parasites was applied to m7GTP agarose beads and specific binding proteins eluted using m7GTP. LC-MS/MS based proteomic analysis of the m7GTP-eluted proteins demonstrated the presence of PfeIF4E, which was not found in control experiments with non-methylated GTP beads, verifying the native cap-binding function of PfeIF4E. PfeIF4A, PfeIF4G, and a putative polyadenylate-binding protein-interacting protein were present among m7GTP-eluted proteins but in low abundances. Interestingly, proteomics data clearly demonstrated P. falciparum enolase (Pfeno) in the m7GTP-eluted proteins.
2022-04-23 | PXD025583 | JPOST Repository
Project description:The emergence and spread of Plasmodium falciparum human malaria parasites resistant to antimalarial drugs, including artemisinin, a first line antimalarial drug, is threatening malaria treatment and prompting fears of a resurgence of the disease. New drugs with novel mode of actions are thus urgently required. Several compounds with antimalarial activity are known to target protein translation, although few of these targets have been validated. Translation initiation in eukaryotes is known to require eukaryotic translation initiation factor 4F (eIF4F) complex, which binds to the 5′-cap structure on mature mRNA and recruits other proteins for translation of mRNA. The putative components of the eIF4F complex in P. falciparum have been identified in the genome including PfeIF4E, a 5′-cap-binding protein; PfeIF4A, a helicase protein for unwinding mRNA, and PfeIF4G, a PfeIF4E/PfeIF4A scaffold protein, which could constitute a novel antimalarial target. However, it is not known if these proteins constitute a P. falciparum eIF4F complex in vivo, nor what other proteins interact with the mRNA 5′-cap to control translation initiation in this species. Here, we investigated P. falciparum proteins that interact with the mRNA 5′-cap. Native protein extract from P. falciparum parasites was applied to m7GTP agarose beads and specific binding proteins eluted using m7GTP. LC-MS/MS based proteomic analysis of the m7GTP-eluted proteins demonstrated the presence of PfeIF4E, which was not found in control experiments with non-methylated GTP beads, verifying the native cap-binding function of PfeIF4E. PfeIF4A, PfeIF4G, and a putative polyadenylate-binding protein-interacting protein were present among m7GTP-eluted proteins but in low abundances. Interestingly, proteomics data clearly demonstrated P. falciparum enolase (Pfeno) in the m7GTP-eluted proteins.
2022-04-22 | PXD025553 | JPOST Repository
Project description:Quinone oxidoreductase I (NQO1), an important antioxidant enzyme which plays an important role in monitoring cellular redox state, was altered in the brain tissues of Alzheimer’s disease (AD) patients. In addition to its traditional antioxidant effect, NQO1 is also a multifunctional RNA-binding protein (RBP) in post-transcriptional regulation. However, NQO1 in AD pathology by acting as an RBP is not studied. In the present study, the RBP functions of NQO1 in rat PC12 cells, a cell line widely used in neurological disease studies, were investigated using siRNA knock-down (KD) and following whole transcriptome (RNA-seq) analysis. Reduced levels of NQO1 led to a significant increase in cellular apoptosis, compared with control cells. Notably, RNA-seq analysis of the transcriptome of PC12 cells by NQO1-KD revealed that genes in certain apoptosis pathways, were under global transcriptional and alternative splicing regulation. Quantitative RT-PCR confirmed the NQO1-regulated transcription of apoptotic genes Cryab, Lgmn , Ngf, Apoe, Brd7, Stat3, and alternative splicing of Bin1, Picalm, Fyn. These NQO1-regulated genes have been found to be closely related to AD pathogenesis. Our findings suggest that NQO1 acts as an RBP and participates in the pathology of AD by regulating expression and alternative splicing of genes involved in apoptosis. The results of present study extend our understanding of the cellular and molecular mechanisms in AD pathogenesis, which might contribute to the development of novel therapeutic targets.
2023-10-20 | GSE185633 | GEO
Project description:mRNA cap addition occurs early during RNA pol II transcription, facilitating pre-mRNA processing and translation. We report that the mammalian mRNA cap methyltransferase, RNMT-RAM, promotes RNA pol II transcription, independently of mRNA capping and translation. In cells, sub-lethal suppression of RNMT-RAM reduces RNA pol II occupancy, net mRNA synthesis and pre-mRNA levels. Conversely, expression of RNMT-RAM increases transcription independently of cap methyltransferase activity. In isolated nuclei, recombinant RNMT-RAM stimulates transcriptional output; this requires the RAM RNA-binding domain. RNMT-RAM interacts with nascent transcripts along their entire length and with transcription associated factors including RNA pol II subunits, SPT4, SPT6 and PAFc. Suppression of RNMT-RAM inhibits transcriptional markers including histone H2B K120 ubiquitination, H3 K4 and K36 methylation, RNA pol II S5 and S2 phosphorylation and PAFc recruitment. These findings suggest that multiple interactions between RNMT-RAM, RNA pol II factors and RNA along the transcription unit stimulate transcription.
2018-05-01 | GSE87767 | GEO
Project description:N6-methyladenosine (m6A) is the most abundant internal messenger (mRNA) modification in mammalian mRNA. This modification is reversible and non-stoichiometric, which potentially adds an additional layer of variety and dynamic control of mRNA metabolism. The m6A-modified mRNA can be selectively recognized by the YTH family “reader” proteins. The preferential binding of m6A-containing mRNA by YTHDF2 is known to reduce the stability of the target transcripts; however, the exact effects of m6A on translation has yet to be elucidated. Here we show that another m6A reader protein, YTHDF1, promotes ribosome loading of its target transcripts. YTHDF1 forms a complex with translation initiation factors to elevate the translation efficiency of its bound mRNA. In a unified mechanism of translation control through m6A, the YTHDF2-mediated decay controls the lifetime of target transcripts; whereas, the YTHDF1-based translation promotion increases the translation efficiency to ensure effective protein production from relatively short-lived transcripts that are marked by m6A. PAR-CLIP and RIP was used to identify YTHDF1 binding sites followed by ribosome profling and RNA seq to assess the consequences of YTHDF1 siRNA knock-down
2015-06-09 | E-GEOD-63591 | biostudies-arrayexpress
Project description:N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis [RNA-Seq]
| PRJNA376775 | ENA
Project description:Many of the regulatory features governing erythrocyte specification, maturation, and associated disorders remain enigmatic. To identify new regulators of erythropoiesis, we performed a functional genomic screen for genes affecting expression of the erythroid marker CD235a/GYPA. Among validating hits were genes coding for the N6-methyladenosine (m6A) mRNA methyltransferase (MTase) complex, including, METTL14, METTL3, and WTAP. We found that m6A MTase activity promotes erythroid gene expression programs through selective translation of ~300 m6A marked mRNAs, including those coding for SETD histone methyltransferases, ribosomal components, and polyA RNA binding proteins, and novel genes. Remarkably, loss of m6A marks resulted in dramatic loss of H3K4me3 marks across key erythroid-specific KLF1 transcriptional targets (e.g., Heme biosynthesis genes). Further, each m6A MTase subunit and a subset of their mRNAs targets are required for human erythroid specification in primary bone-marrow derived progenitors. Thus, m6A mRNA marks promote the translation of a network of genes required for human erythropoiesis.
2019-08-12 | GSE105779 | GEO