Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1282644 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole proteome and ribosome-nascent-chain complex (RNC) changes of A549 cisplatin-resistant cells after treated with aurintricarboxylic acid
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Project description:The cancer cells selectively promote translation of specific oncogenic transcripts to facilitate cancer survival and progression, while the underlying mechanisms are poorly understood. N7-methylguanosine (m7G) tRNA modification and its methyltransferase complex METTL1/WDR4 are significantly up-regulated in intrahepatic cholangiocarcinoma (ICC) and associated with poor prognosis. We developed tRNA reduction and cleavage sequencing (TRAC-Seq) to reveal the m7G tRNA methylome inICC cell line and ribosome nascent-chain complex-bound mRNAs sequencing(RNC-seq) and ribosome profiling(Ribo-seq) to study the differential translated genes and reveal the ribosome pausing. A subset of 22 tRNAs is modified at a ‘RAGGU’ motif within the variable loop. We observe increased ribosome occupancy at the corresponding codons in the Mettl1 knockdown ICC cell line implying widespread effects on tRNA function, ribosome pausing, and mRNA translation. Translation of cell cycle genes and EGFR signaling pathway genes is particularly affected. Our study uncovers the important physiological function and mechanism of METTL1-mediated m7G tRNA modification in the regulation of cancer progression.
2021-08-07 | GSE161319 | GEO
Project description:In order to explore the effect of betaine on NAFLD and its mechanism, we divided mice into high-fat diet (HF) and high-fat diet with betaine (HB) groups, and used N6-methyladenosine sequence (m6A-seq), RNA-seq and mRNAs bound to ribosome-nascent chain complex sequencing (RNC-seq) to evaluate the gene expression levels in the liver of each group.
2021-05-20 | GSE174550 | GEO
Project description:To investigate the role of METTL3-mediated m6A modification and mRNA translation, we performed m6A-sequencing and Ribosome-nascent chain (RNC)-RNA sequencing in high glucose treated control or METTL3 knockdown HTR8/SVneo cells.
2020-12-01 | GSE148962 | GEO
Project description:Various proteins in the cell begin to fold during synthesis at the ribosome, many with the assistance of molecular chaperones. While the cotranslational activity of ribosome-associated chaperones and Hsp70 is frequently studied, the role of Hsp60 chaperonins during protein synthesis remains poorly understood. Here, we studied the binding of E. coli chaperonin GroEL to ribosome-nascent chain complexes (RNCs), to understand GroEL activity during nascent chain (NC) synthesis and folding. Using biochemical reconstitution, structural proteomics and electron microscopy we describe the physical architecture of GroEL:RNC and ATP/BeFx-GroEL/ES:RNC complexes. We show that GroEL engages destabilised nascent chains on the inside of its cavity via the apical domains and disordered C-terminal tails. This GroEL:RNC complex can be capped by GroES on the NC-bound ring, with GroEL but not GroEL/ES binding promoting nascent chain destabilisation. Lastly, we observe that GroEL directly competes with Hsp70 for nascent chain binding. Our findings thus show that GroEL is a versatile chaperone which in addition to its well characterised post-translational activity can affect folding of nascent chains undergoing synthesis.
2025-10-14 | PXD054379 | Pride
Project description:Various proteins in the cell begin to fold during synthesis at the ribosome, many with the assistance of molecular chaperones. While the cotranslational activity of ribosome-associated chaperones and Hsp70 is frequently studied, the role of Hsp60 chaperonins during protein synthesis remains poorly understood. Here, we studied the binding of E. coli chaperonin GroEL to ribosome-nascent chain complexes (RNCs), to understand GroEL activity during nascent chain (NC) synthesis and folding. Using biochemical reconstitution, structural proteomics and electron microscopy we describe the physical architecture of GroEL:RNC and ATP/BeFx-GroEL/ES:RNC complexes. We show that GroEL engages destabilised nascent chains on the inside of its cavity via the apical domains and disordered C-terminal tails. This GroEL:RNC complex can be capped by GroES on the NC-bound ring, with GroEL but not GroEL/ES binding promoting nascent chain destabilisation. Lastly, we observe that GroEL directly competes with Hsp70 for nascent chain binding. Our findings thus show that GroEL is a versatile chaperone which in addition to its well characterised post-translational activity can affect folding of nascent chains undergoing synthesis.
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Project description:Various proteins in the cell begin to fold during synthesis at the ribosome, many with the assistance of molecular chaperones. While the cotranslational activity of ribosome-associated chaperones and Hsp70 is frequently studied, the role of Hsp60 chaperonins during protein synthesis remains poorly understood. Here, we studied the binding of E. coli chaperonin GroEL to ribosome-nascent chain complexes (RNCs), to understand GroEL activity during nascent chain (NC) synthesis and folding. Using biochemical reconstitution, structural proteomics and electron microscopy we describe the physical architecture of GroEL:RNC and ATP/BeFx-GroEL/ES:RNC complexes. We show that GroEL engages destabilised nascent chains on the inside of its cavity via the apical domains and disordered C-terminal tails. This GroEL:RNC complex can be capped by GroES on the NC-bound ring, with GroEL but not GroEL/ES binding promoting nascent chain destabilisation. Lastly, we observe that GroEL directly competes with Hsp70 for nascent chain binding. Our findings thus show that GroEL is a versatile chaperone which in addition to its well characterised post-translational activity can affect folding of nascent chains undergoing synthesis.
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Project description:Folding newly synthesized proteins relies on the ribosome intricately coordinating mRNA translation with a network of ribosome-associated machinery. The principles that drive the coordination of this diverse machinery remain poorly understood. Here, we use selective ribosome profiling to determine how the essential chaperonin TRiC/CCT and the Hsp70 Ssb are recruited to ribosome-nascent chain complexes to mediate cotranslational protein folding. Whereas substrate localization and nascent chain sequence are the major determinants of cotranslational recruitment of Ssb, we found that temporal and structural elements drive TRiC engagement. For both chaperones, however, local slowdowns in translation enhance chaperone enrichment. This work helps define the principles that dictate the coordinated activity of ribosome-associated factors to perform their critical role in maintaining a properly folded nascent proteome.
2019-08-22 | GSE114882 | GEO
Project description:Mass Spectrometry of NOT gene-related purifications, including NOT5 Tap Tag in WT and not4 deletion, the Ribosome Nascent Chain Complex, and aggregates in NOT5 Delta,
2022-07-26 | PXD021580 | Pride