PCBP-1 Regulates the Transcription and Alternative Splicing of Inflammation and Ubiquitination-Related Genes in PC12 Cell.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35795237", "kind": "science-record", "revision": 5, "content_hash": "sha256:d78e363d58e39c2a358d371deabe60a98287c356a49e7d7550b66ff051d3e2df", "created_at": "2026-11-01T18:14:50Z", "updated_at": "2026-11-01T22:49:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PCBP-1 Regulates the Transcription and Alternative Splicing of Inflammation and Ubiquitination-Related Genes in PC12 Cell.", "doi": "10.3389/fnagi.2022.884837", "pmid": "35795237", "authors": ["Aishanjiang Yusufujiang", "Shan Zeng", "Chen Yang", "Sha Jing", "Lijuan Yang", "Hongyan Li"], "journal": "Frontiers in aging neuroscience", "year": 2022, "abstract": "PCBP-1, a multifunctional RNA binding protein, is expressed in various human cell/tissue types and involved in post-transcriptional gene regulation. PCBP-1 has important roles in cellular Iron homeostasis, mitochondrial stability, and other cellular activities involved in the pathophysiological process of neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD). However, it remains enigmatic whether PCPB-1 is associated with the pathogenesis of PD. In this study, we cloned and constitutively overexpressed PCBP-1 in rat PC12 cells (PC12 cell is the common cell line studying neurodegenerative disease include PD). RNA-seq was performed to analyze PCBP-1-regulated differentially expressed genes (DEGs) and alternative splicing events (ASEs) between control and PCBP1-overexpressed cells. GO and KEGG pathway analyses were performed to identify functional DEGs and alternatively spliced genes. Consequently, we validated PCBP-1-regulated genes using RT-qPCR. Finally, we downloaded CLIP-seq data from GEO (GSE84700) to analyze the mechanisms of PCBP-1's regulation of gene expression and ASEs by revealing the binding profile of PCBP-1 on its target pre-mRNAs. Overexpression of PCBP-1 partially regulated the ASE and expression of genes enriched in neuroinflammation and protein ubiquitination, which were also associated with PD pathogenesis. Moreover, RT-qPCR assay verified the PCBP-1-modulated expression of neuroinflammatory genes, like LCN-2, and alternative splicing (AS) of ubiquitination-related gene WWP-2. Finally, CLIP-seq data analysis indicated that the first UC motif was the critical site for PCBP-1 binding to its targets. In this study, we provided evidence that PCBP-1 could regulate the expression of LCN-2 gene expression associated with neuroinflammation and AS of WWP-2 in relation to protein ubiquitination. These findings thus provided novel insights into the potential application of PCBP-1 as the disease pathophysiological or therapeutic target for neurodegenerative disease.", "claims": [{"id": "claim-method", "statement": "Differentially Expressed Genes (DEGs) were screened by R Bioconductor package edgeR (Robinson et al., 2010) by applying the false discovery rate (FDR) < 0.05, and fold change > 2 or <0.5 as the cut-off.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35795237", "locator": "sections[8] \"Analysis of Differentially Expressed Genes\" paragraph 2", "quote": "Differentially Expressed Genes (DEGs) were screened by R Bioconductor package edgeR (Robinson et al., 2010) by applying the false discovery rate (FDR) < 0.05, and fold change > 2 or <0.5 as the cut-off."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE196153.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35795237", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: https://www.ncbi.nlm.nih.gov/, GSE196153."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PCBP-1 overexpression altered the PC12-cell transcriptome, with 132 genes up-regulated and 58 genes down-regulated.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35795237", "locator": "sections[15] \"PCBP-1 Up-Regulates Genes Enriched in Inflammation Response in PC12 Cells\" paragraph 2", "quote": "Subsequently, we identified 132 up-regulated and 58 downregulated genes in PCBP1-OE cells by constructing the volcano plot (Figure 2A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PCBP-1 overexpression altered the PC12-cell transcriptome, with 132 genes up-regulated and 58 genes down-regulated.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35795237"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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Finally, we downloaded CLIP-seq data from G", "o associated with PD pathogenesis. Moreover, RT-qPCR assay verified the PCBP-1-modulated expressi", "we validated PCBP-1-regulated genes using RT-qPCR. Finally, we downloaded CLIP-seq data from G", "ssociated with PD pathogenesis. Moreover, RT-qPCR assay verified the PCBP-1-modulated expressi"], "order_basis": "paper_text_order:1077", "id": "assay:3"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ycin with 5% CO2 at 37°C. PCBP-1 plasmid was transfected in PC-12 cells by Lipofectamine-2000 reagent", "tocol, and cells were harvested at 48 h post-transfection for RT-qPCR analysis. 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