(N)1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Oryctolagus Cuniculus (rabbit)
SUBMITTER: 
Sandip Kumar Patel
LAB HEAD: Anne E Willis
PROVIDER: PXD046445 | Pride | 2024-07-31
REPOSITORIES: pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| AspN_01.raw | Raw | |||
| AspN_02.raw | Raw | |||
| AspN_ProteinGroups.txt | Txt | |||
| AspN_Proteins.txt | Txt | |||
| Trypsin.raw | Raw |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:The WIN site of WDR5 is a druggable pocket that impairs WDR5 protein function and carries therapeutic potential for treating cancer. This study evaluates the protein interactions affected by small molecule blockade of this surface on WDR5. Inhibited and uninhibited WDR5-containing complexes from HEK293 cells were quantitatively compared by SILAC-based proteomics. Of the high confidence proteins affected by this inhibition, one protein, PDPK1, was investigated further by mass spectrometry for identification of post translational modifications that could influence binding to WDR5.
2021-01-25 | PXD019209 | Pride
Project description:Current human reproductive risk assessment methods rely on semen and serum hormone analyses, which are not easily comparable to the histopathological endpoints and mating studies used in animal testing. Because of these limitations, there is a need to develop universal evaluations that reliably reflect male reproductive function. We hypothesized that toxicant-induced testicular injury can be detected in sperm using mRNA transcripts as indicators of insult. To test this, we exposed adult male Fischer 344 rats to low doses of model testicular toxicants and classically characterized the testicular injury while simultaneously evaluating sperm mRNA transcripts from the same animals. Overall, this study aimed to: 1) identify sperm transcripts altered after exposure to the model testicular toxicant, 2,5-hexanedione (HD) using microarrays; 2) expand on the HD-induced transcript changes in a comprehensive time course experiment using qRT-PCR arrays; and 3) test these injury indicators after exposure to another model testicular toxicant, carbendazim (CBZ). Microarray analysis of HD-treated adult Fischer 344 rats identified 128 altered sperm mRNA transcripts when compared to control using linear models of microarray analysis (q < 0.05). All transcript alterations disappeared after 3 months of post-exposure recovery. In the time course experiment, time-dependent alterations were observed for 12 candidate transcripts selected from the microarray data based upon fold change and biological relevance, and 8 of these transcripts remained significantly altered after the 3-month recovery period (p < 0.05). In the last experiment, 8 candidate transcripts changed after exposure to CBZ (p < 0.05). The two testicular toxicants produced distinct molecular signatures with only 4 overlapping transcripts between them, each occurring in opposite directions. Overall, these results suggest that sperm mRNA transcripts are indicators of low dose toxicant-induced testicular injury in the rat. Rats were exposed to sub-chronic low doses of the Sertoli cell toxicant 2,5-hexanedione (HD) or water (control for HD) for 3 months. Some rats in each group underwent 3 months of post-exposure recovery.
2012-09-01 | E-GEOD-34641 | biostudies-arrayexpress
Project description:The piggyBac transposon system is widely used for biotechnology and genome engineering and is the founding member of a large superfamily of piggyBac-like elements. We investigated the role in transpositon of the nonconserved N-terminus in the piggyBac transposase, including the impact of predicted casein kinase phosphorylation sites within it.
2023-03-11 | PXD037132 | Pride
Project description:Our goal was to better understand the interaction between the Hsp70 Ssb1 and the atypical Hsp70 Ssz1, which we had uncovered by in vivo site-specific Bpa crosslinking. Ssz1 having Bpa incorporated was purified and incubated with purified Ssb1 and the J-domain protein Zuo1 during activation of photo cross-linking. After protein gel electrophoresis and protease digestion of excised bands, the resulting cross-linked peptides were analyzed by mass spectrometry and identified by StavroX.
2021-08-26 | PXD024065 | Pride
Project description:The use of multiple proteases has been shown to increase protein sequence coverage in proteomics experiments, but due to the additional sample preparation and analysis time required, it has not been widely adapted in routine proteomic workflows. While data-independent acquisition (DIA) has been primarily optimized for fragmenting tryptic peptides with beam type (bt)-CID, it has the potential to analyze multiplexed samples from different protease digests. Here we evaluate a DIA multiplexing method that combines three proteolytic digests (Trypsin, AspN, and GluC) into a single sample. We first optimize DIA conditions for both resonance excitation (re-CID) and bt-CID to determine the optimal consensus fragmentation conditions for tryptic and non-tryptic peptides, and apply these methods to a human cell line. We demonstrate that using this multiplexed approach results in similar protein identifications and quantitative performance as compared to trypsin alone, but enables up to a 63% increase in peptide detections, resulting in up to a 8% increase in average sequence coverage. Importantly, this resulted in 100% sequence coverage for numerous proteins, suggesting the utility of this approach in applications where sequence coverage is critical, such as proteoform analysis.
2022-03-18 | PXD027242 | Pride
Project description:Anoplocephala perfoliata is a neglected gastro-intestinal tapeworm, commonly infecting horses worldwide. Molecular investigation of A. perfoliata is hampered by a lack of tools to better un-derstand the host-parasite interface. This interface is likely influenced by parasite derived immune modulators released in the secretome as free proteins or components of extracellular vesicles (EVs). Therefore, adult RNA was sequenced and de novo assembled to generate the first A. perfoliata transcriptome. In addition, excretory secretory products (ESP) from adult A. perfoliata were col-lected and EVs isolated using size exclusion chromatography, prior to proteomic analysis of the EVs, the EV surface and EV depleted ESP. Transcriptome analysis revealed 454 sequences ho-mologous to known helminth immune modulators including 2 novel Sigma class GSTs, 5 α-HSP90s and 3 α-enolases with isoforms of all three observed within the proteomic analysis of the secretome. Furthermore, secretome proteomics identified common helminth proteins across each sample with known EV markers, such as annexins and tetraspanins, observed in EV fractions. Importantly, 49 of the 454 putative immune modulators were identified across the secretome proteomics contained within and on the surface of EVs in addition to those identified in free ESP. This work provides the molecular tools for A. perfoliata to reveal key players in the host-parasite interaction within the horse host.
2021-07-26 | PXD027105 | Pride
Project description:Chromatin modifications instruct genome function through spatiotemporal recruitment of regulatory factors to the genome. However, how these modifications define the proteome composition at distinct chromatin states remains to be fully characterized. Here, we made use of natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for histone and DNA modifications. By stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localisation, genomic distribution and histone-PTM-binding preference, we first demonstrate their applicability as selective chromatin binders in living cells. Finally, we exploit the binding specificity of eCRs to establish ChromID, a new method for chromatin-dependent proteome identification based on proximity biotinylation. We use ChromID to reveal the proteome at distinct chromatin states in mouse stem cells, and by using a synthetic dual-modification reader, we furthermore uncover the protein composition at bivalent promoters marked by H3K4me3 and H3K27me3. These results highlight the applicability of ChromID as novel method to obtain a detailed view of the protein interaction network determined by the chemical language on chromatin.
2020-04-30 | PXD017235 | Pride
Project description:In this study, pull down assays combined with mass spectrometry analysis were performed in HL-1 cardiomyocytes transfected with control plasmid (OE-Vector) or LOC107984012-overexpression plasmid to identify the repertoire of LOC107984012 interacting proteins.
2024-01-26 | PXD036966 | Pride
Project description:Axonemal dynein motors drive ciliary motility and can consist of up to twenty distinct components with a combined mass of ~2 MDa. In mammals, failure of dyneins to assemble within the axonemal superstructure leads to primary ciliary dyskinesia. Syndromic phenotypes include infertility, rhinitis, severe bronchial conditions, and situs inversus. Nineteen specific cytosolic factors (DNAAFs) are necessary for axonemal dynein assembly although the detailed mechanisms involved remain very unclear. Here we identify the assembly factor DNAAF3 as a structural ortholog of S-adenosyl methionine-dependent methyltransferases. We further demonstrate that dynein heavy chains, especially those forming the ciliary outer arms, are methylated on key residues within various nucleotide-binding sites and on microtubule-binding domain helices directly involved in the transition to low binding affinity. These variable modifications, which are generally missing in a Chlamydomonas null mutant for the DNAAF3 ortholog PF22 (DAB1), likely impact on motor mechanochemistry fine-tuning the activities of individual dynein complexes.
2024-02-12 | PXD045935 | Pride
Project description:Allergenicity Assessment and Allergen Profile Analysis of Different Chinese Wheat Cultivars
2021-03-02 | PXD023612 | Pride