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Effect of PTBP1 S-nitrosylation on SNO-proteome

ABSTRACT: After co-transfection with with NOS1 and either wild-type or C251S PTBP1, SNO-RAC was performed to capture S-nitrosylated (SNO-) proteins, and mass spectrometry was used to identify these SNO-proteins.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture, Early Embryonic Cell

DISEASE(S): Disease Free

SUBMITTER: Joseph Schindler

LAB HEAD: Jonathan Stamler

PROVIDER: PXD060478 | Pride | 2026-05-23

REPOSITORIES: Pride

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			Action	DRS
	251A.raw	Raw
	251B.raw	Raw
	251C.raw	Raw
	F006452.dat	Other
	F006452.mgf	Mgf

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Publications

Nitric oxide drives proteomic diversity through alternative splicing.

Schindler Joseph C JC Seth Puneet P Hausladen Alfred A Chan E Ricky ER Yang Jun J Qin Jun J Qian Zhaoxia Z Seth Divya D Lundberg Kathleen K Luna Joseph M JM Premont Richard T RT Stamler Jonathan S JS

Molecular cell 20260521 12

Redox signaling by nitric oxide (NO) is estimated to control a large part of the global proteome via S-nitrosylation (SNO-modification). Here, we report that RNA-binding proteins (RBPs) represent the most significantly enriched class of S-nitrosylation targets, with broad coverage of spliceosomal factors. We demonstrate that NO regulates alternative splicing (AS) and that S-nitrosylation of PTBP1, a central regulator of AS, can massively shift and contextually alter gene expression while further ...[more]

PMID: 42167237

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Effect of S-nitrosylation on PTBP1 interactome

Project description:Interacting proteins were co-immunoprecipitated with either wild-type or C251S PTBP1 after co-transfection with NOS1 for 48 hours. Mass spectrometry was used to identify interacting proteins.

2026-05-23 | PXD060476 | Pride

iiCLIP protocol benchmarking with PTBP1

Project description:We describe an improved individual nucleotide resolution CLIP protocol (iiCLIP), which can be completed within 4 days from UV crosslinking to libraries for sequencing. For benchmarking, we directly compared PTBP1 iiCLIP libraries with the iCLIP2 protocol produced under standardised conditions with 1 million HEK293 cells, and with public eCLIP and iCLIP PTBP1 data. There are 3 PTBP1 iiCLIP libraries, 1 input iiCLIP library and 1 PTBP1 iCLIP2 library produced in this study.

2022-08-01 | E-MTAB-10881 | biostudies-arrayexpress

Nitric oxide drives proteomic diversity through alternative splicing [HEK RNA-Seq]

Project description:Redox signaling by nitric oxide (NO) is estimated to control the large part of the global proteome via S-nitrosylation (SNO-modification). Here we report that RNA-binding proteins (RBPs) represent the most significantly enriched class of S-nitrosylation targets, with broad coverage of spliceosomal factors. We demonstrate that NO regulates alternative splicing (AS) and that S-nitrosylation of PTBP1, a central regulator of AS, can massively shift and contextually alter gene expression, while further enriching the transcriptome for SNO sites. PTBP1 S-nitrosylation changes RNA-binding domain conformation, RNA motif recognition, protein–RNA and protein–protein interactions, and intracellular trafficking to impact pathways for viral infection and neurodegeneration. Levels of SNO-PTBP1 are reduced in mouse and human Alzheimer’s brains and correlate with adverse clinical outcomes. Overall, SNO-RBPs are characterized by conservation across diverse lineages and SNO sites and provide a blueprint for redox regulation of both transcriptome and proteome in physiology and disease.

2026-05-21 | GSE286544 | GEO

Nitric oxide drives proteomic diversity through alternative splicing [CLIP-Seq]

2026-05-21 | GSE286543 | GEO

Nitric oxide drives proteomic diversity through alternative splicing [Fibroblast RNA-Seq]

2026-05-21 | GSE286542 | GEO

Regulation of co-transcriptional splicing by RNA-binding protein PTBP1

Project description:We examined the role of PTBP1 in regulation of co-transcriptional splicing process by depleting this RNA-binding protein from embryonic stem cells using the auxin-inducible degron technology and analysing the total and chromatin-associated RNA fractions by RNA-seq. We also performed mNET-seq and ChIP-seq analyses using RNA polymerase II- and PTBP1-specific antibodies, respectively. Our data suggest that PTBP1 activates co-transcriptional splicing of hundreds of introns, a surprising effect given that PTBP1 is better known as a splicing repressor. Importantly, some co-transcriptionally activated introns fail to be spliced post-transcriptionally without PTBP1. In a striking example of this regulation, lasting retention of a PTBP1-dependent intron triggers nonsense-mediated decay of mRNAs encoding DNA methyltransferase DNMT3B, explaining their natural expression dynamics in development. Our further analyses suggest that this mechanism may protect differentiation-specific genes from aberrant methylation. We conclude that PTBP1-activated co-transcriptional splicing underlies biologically important decisions.

2023-01-08 | E-MTAB-11544 | biostudies-arrayexpress

S-nitrosylation of IRF7 induced by NOS1 expression in Melanoma suppresses anti-tumor immunity

Project description:Endogenous nitric oxide (NO) produced by nitric oxide synthases (NOSs) plays an important immunosuppressive role in the tumor microenvironment. In melanoma, NOS1 expression was increased with tumor progression and correlated with tumor immune escape through inhibition on type I interferon (IFN) signaling. However, the immune regulatory role and its related mechanism of NOS1 and its impacts on immune therapy such as immune checkpoint blockade (ICB) in melanoma is unclear. Here, we found that NOS1 expression induced IRF7 modification by s-nitrosylation at C435 site in mouse (C481 in human), which functionally promotes tumor growth in mouse models. Mechanically, IRF7-C435-SNO inhibited IFNβ transcription under PRR signal activation, leading to disorder in initiation of type I interferons response in melanoma cell. In melanoma mouse model, IRF7-C435-SNO decreased infiltration and activation of CD8 T cells in tumor microenvironment, by reducing antigen presentation processes in tumor cells and inhibits the maturation of DC1. Clinically, high expression of NOS1 correlated with poor survival prognosis and resistance with to ICB anti-tumor therapies in melanoma cases with less immune cell infiltration. Our study suggested that NOS1 expression in melanoma characterizes IFN-I signal disorders in response to innate immune stimulation by IRF7 s-nitrosylation. Targeting NOS1 signaling might benefit for overcome of immune therapeutically resistance particularly in immune cold melanoma phenotype.

2025-10-01 | GSE279140 | GEO

S-nitrosylation of IRF7 induced by NOS1 expression in Melanoma suppresses anti-tumor immunity [scRNA-seq]

2025-10-01 | GSE279235 | GEO

PTBP1 - Modified iCLIP

Project description:PTBP1 - Modified iCLIP

| PRJEB15236 | ENA

Proteome changes in PTBP1 deficient hematopoietic cells

Project description:Ribosomopathies constitute a range of disabling conditions associated with defective protein synthesis mainly affecting hematopoietic stem cells (HSCs) and erythroid development. Here we demonstrate that deletion of Polypyrimidine Tract Binding Protein 1 (PTBP1) in the hematopoietic compartment led to the development of a ribosomopathy-like condition. Specifically, loss of PTBP1 was associated with a decrease in HSC self-renewal, erythroid differentiation and protein synthesis. Consistent with its function as a splicing regulator, PTBP1 deficiency led to splicing defects in hundreds of genes and we demonstrate that the up-regulation of a specific isoform of CDC42 could partly mimic the protein synthesis defect associated with loss of PTBP1. Furthermore, PTBP1 deficiency was associated with a marked defect in ribosome biogenesis and a selective reduction in the translation of mRNAs encoding ribosomal proteins. Collectively, this work identifies PTBP1 as a key integrator of ribosomal functions and highlights the broad functional repertoire of RNA binding proteins.

2022-05-04 | PXD023879 | Pride

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