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Quantitative Proteomics Identifies Profilin-1 as a Pseudouridine-Binding Protein

ABSTRACT: Quantitative Proteomics Identifies Profilin-1 as a Pseudouridine-Binding Protein

PROVIDER: PRJNA1062713 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27467451_1.fastq.gz	Fastqsanger.gz
	SRR27467451_2.fastq.gz	Fastqsanger.gz
	SRR27467452_1.fastq.gz	Fastqsanger.gz
	SRR27467452_2.fastq.gz	Fastqsanger.gz
	SRR27467453_1.fastq.gz	Fastqsanger.gz

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Quantitative Proteomics Identifies Profilin-1 as a Pseudouridine-Binding Protein

Project description:Pseudouridine (Ψ) is the most abundant RNA modification in nature; however, the exact biological functions of Ψ remain largely elusive. By employing an unbiased quantitative proteomics method, we identified multiple candidate reader proteins of Ψ in RNA, including a cytoskeleton protein profilin-1, whose mutations are linked with amyotrophic lateral sclerosis (ALS). We purified recombinant PFN1 and showed that it can bind directly and selectively to Ψ-containing RNA. We also found that PFN1 binds to thousands of transcripts in human cells, including a known Ψ site in the mRNA of TPI1. We showed that PFN1-Ψ interaction is crucial for regulating the stability and translation efficiency of TPI1 mRNA. Together, our data unveiled PFN1 as a reader protein of Ψ in RNA and illustrated the functions of PFN1-Ψ interaction in modulating the stability and translation efficiency of TPI1 mRNA, which provides new insights into the functions of Ψ in RNA biology and lays a strong foundation for the discovery of new mechanisms in disease pathogenesis

2025-01-22 | GSE252793 | GEO

Expression data from allergic patients to profilin

Project description:Prevalence and severity of allergic diseases have increased worldwide. To date, respiratory allergy phenotypes are not fully characterized and, along with inflammation progression, treatment is increasingly complex and expensive. Profilin sensitization constitutes a good model to study the progression of allergic inflammation. We have used microarrays to understand the underlying mechanisms of severe profilin-mediated reactions using a model that includes patients with different levels of sensitization to profilin (non-allergic, mild, moderate and severe)

2018-05-22 | GSE114707 | GEO

The effects of novel adjuvant complex and CpG ODN on host immune response to recombinant Eimeria profilin vaccine

Project description:This study investigated the ability of two novel adjuvant formulations, QCDC (Quil A/cholesterol/DDA/Carbopol) and QCDCR (QCDC/Bay R1005), in combination with a recombinant profilin vaccine, to modulate host protective immunity and to alter new gene expression during experimental avian coccidiosis. Four-condition experiment, Profilin only vs. Non-vaccination, Profilin only vs. Co-vaccination of QCDC plus profilin, Profilin only vs. Co-vaccination of QCDCR plus profilin, Biological replicates: 2 profilin only replicates, 2 Non-vaccination replicates, 2 QCDC plus profilin replicates, 2 QCDCR plus profilin replicates with dye-switching.

2010-10-28 | E-GEOD-24966 | biostudies-arrayexpress

BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution

Project description:Pseudouridine (Ψ) is an abundant RNA modification that is present in and impacts the functions of diverse non-coding RNA species, including rRNA, tRNA, snRNA, etc. Pseudouridine also exists in mammalian mRNA and likely exhibits functional roles; however, functional investigations of pseudouridine in mammalian mRNA have been hampered by the lack of a quantitative method that detects Ψ at base precision. We have recently developed Bisulfite-Induced Deletion sequencing (BID-seq), which provides the community with a quantitative method to map RNA Ψ distribution transcriptome-wide at single-base resolution. Here, we describe an optimized BID-seq protocol to generate highly reproducible results, displaying nearly zero background deletions at unmodified uridines after bisulfite treatment and uncovering 8,407 Ψ sites starting from as little as 10 ng mouse embryonic stem cell (mESC) polyA+ RNA, with the steps that are fast in both library preparation and data analysis. This optimized BID-seq workflow takes 5 days to complete and includes four main sections: RNA preparation, library construction, next-generation sequencing (NGS), and data analysis. The library construction can be completed by researchers who have basic knowledge and skills in molecular biology and genetics. In addition to the experimental protocol, we provide BID-pipe (https://github.com/y9c/pseudoU-BIDseq), a user-friendly data analysis pipeline for BID-seq, requiring only basic bioinformatic and computational skills to uncover Ψ signatures from NGS data.

2023-08-07 | GSE238245 | GEO

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Illumina)

Project description:Pseudouridine (Ψ) is an abundant mRNA modification in the mammalian transcriptome, but its function has remained elusive due to the difficulty of transcriptome-wide mapping. We develop nanopore native RNA sequencing for quantitative Ψ analysis that utilizes native content training, machine learning model prediction, and single read coordination. We find interferon inducible Ψ modifications in the interferon stimulated gene transcripts, consistent with a role of Ψ in the efficacy of mRNA vaccines.

2021-11-18 | GSE180655 | GEO

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling (Nanopore)

2021-11-18 | GSE180654 | GEO

Cancer-associated exportin-6 upregulation inhibits the transcriptional repressive and anticancer effects of nuclear profilin-1

Project description:Aberrant expression of nuclear transporters and altered subcellular localization of their cargo proteins are increasingly recognized as drivers and therapeutic targets of cancer. Here, we report that exportin-6, a nuclear exporter specific for actin/profilin-1, is upregulated in a broad range of cancers and associated with poor prognosis. Exportin-6 loss triggers antitumor effects in breast cancer cells in a profilin-1-dependent fashion. Nuclear profilin-1 interacts with the Super Elongation Complex (SEC), a positive transcriptional regulator of pro-cancer genes including MYC. Exportin-6 loss, by increasing nuclear profilin-1, inhibits SEC-dependent transcription and sensitizes breast cancer cells to inhibition of BET domain proteins. Thus, exportin-6 upregulation is a previously unrecognized cancer addiction that reduces the transcriptional inhibitory and anticancer activities of nuclear profilin-1.

2021-04-07 | GSE144372 | GEO

Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

Project description:Interferon inducible pseudouridine modification in human mRNA by quantitative nanopore profiling

| PRJNA749031 | ENA

Potential binding partners of profilin protein from Leishmania donovani

Project description:For identifying potential ligands of Leishmania profilin (LdPfn) protein, full length profilin was cloned and expressed with GST tag. Only GST tag protein was used as a negative control. Employing pull down assay and with the help of LC-MS, the potential binding partners of profilin protein in Leishmania promastigotes were detected.

2022-03-10 | PXD026036 | Pride

Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome

Project description:Pseudouridine (Ψ) is one of the most abundant modifications in cellular RNA. However, its function remains elusive, mainly due to the lack of highly sensitive and accurate detection methods. To address this challenge, we introduced 2-bromoacrylamide-assisted cyclization sequencing (BACS) for quantitative profiling of Ψ at single-base resolution. Based on novel bromoacrylamide cyclization chemistry, BACS enables a Ψ-to-C transition. Compared to previous methods, BACS allowed the precise identification of Ψ positions, especially in densely modified Ψ regions and consecutive uridine sequences. BACS successfully detected all known Ψ sites in human rRNA and spliceosomal snRNAs and generated the first quantitative Ψ map of human snoRNA and tRNA. Furthermore, BACS simultaneously detected adenosine-to-inosine (A-to-I) editing sites and N1-methyladenosine (m1A). Depletion of three key pseudouridine synthases (PUS) enabled us to elucidate the targets and sequence motifs of TRUB1, PUS7, and PUS1 in HeLa cells. We further applied BACS to Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) and identified a highly abundant Ψ114 site in EBER2. Surprisingly, applying BACS to a panel of RNA viruses demonstrated the absence of Ψ in their viral transcripts or genomes, shedding light on differences in pseudouridylation between virus families. We anticipate BACS to serve as a powerful tool to uncover the biological importance of Ψ in future studies.

2024-07-31 | GSE241849 | GEO

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