{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/074/SRR21708474/SRR21708474_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/071/SRR21708471/SRR21708471.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/068/SRR21708468/SRR21708468.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/072/SRR21708472/SRR21708472_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/072/SRR21708472/SRR21708472_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/069/SRR21708469/SRR21708469.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/075/SRR21708475/SRR21708475_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/066/SRR21708466/SRR21708466.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/070/SRR21708470/SRR21708470.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/073/SRR21708473/SRR21708473_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/067/SRR21708467/SRR21708467.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/075/SRR21708475/SRR21708475_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/074/SRR21708474/SRR21708474_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/073/SRR21708473/SRR21708473_1.fastq.gz"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["Rama Natarajan, Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA884278"],"scientific_name":["Homo sapiens"],"long_description":["BACKGROUND: Obesity and diabetes are associated with elevated free fatty acids like palmitic acid (PA), which promote chronic inflammation and impaired inflammation resolution associated with cardiometabolic disorders. Long non-coding RNAs (lncRNAs) are implicated in inflammatory processes, however, their roles in PA-regulated inflammation and resolution are unclear. METHODS: We performed RNA-seq analysis to identify PA-regulated coding genes and novel lncRNAs in CD14+ monocytes from healthy volunteers. We investigated the regulation and function of an uncharacterized PA-induced lncRNA PARAIL (PA-regulated anti-inflammatory lncRNA). We examined its role in inflammation resolution employing knockdown and overexpression strategies in human and mouse macrophages. We also used RNA-pulldown coupled to mass spectrometry to identify PARAIL interacting nuclear proteins and their mechanistic involvement in PARAIL functions in human macrophages. RESULTS: Treatment of human CD14+ monocytes with PA induced several lncRNAs and genes associated with inflammatory phenotype. PA strongly induced lncRNA PARAIL expressed near RIPK2. PARAIL was also induced by cytokines and infectious agents in human monocytes/macrophages and was regulated by NF-kB. Time course studies showed PARAIL was induced during inflammation resolution phase in PA treated macrophages. Knockdown of PARAIL with antisense oligonucleotides upregulated key inflammatory genes and vice versa with PARAIL overexpression. We found that PARAIL interacts with Human Antigen R (HuR) protein via AU-rich elements (AREs). HuR knockdown inhibited the anti-inflammatory functions of PARAIL. Moreover, PARAIL knockdown increased cytosolic localization of HuR and increased the stability of ARE-containing inflammatory mRNAs. Mouse orthologous Parail was downregulated in macrophages from mice with diabetes and atherosclerosis. Parail overexpression attenuated pro-inflammatory genes in mouse macrophages. CONCLUSIONS: Upregulation of PARAIL under acute inflammatory conditions contributes to pro-resolution mechanisms via PARAIL-HuR interactions. Conversely, PARAIL downregulation in cardiometabolic diseases enhances HuR function and impairs inflammation resolution to further augment inflammation. Thus, inflammation-resolving lncRNAs like PARAIL represent novel tools to combat inflammatory cardiometabolic diseases. Overall design: We performed RNA-seq analysis to identify PA-regulated coding genes and novel lncRNAs in CD14+ monocytes from healthy volunteers. We investigated the regulation and function of an uncharacterized PA-induced lncRNA PARAIL (PA-regulated anti-inflammatory lncRNA). We examined its role in inflammation resolution employing knockdown and overexpression strategies in human and mouse macrophages. We also used RNA-pulldown coupled to mass spectrometry to identify PARAIL interacting nuclear proteins and their mechanistic involvement in PARAIL functions in human macrophages."],"tag":["xref:PubMed:40068774","xref:PubMed:37128912"],"repository":["ENA"],"description_synonyms":["Non-Translated RNA, Inflammatory Response, ds RNA-Binding, hur, Inflammations, Monocyte Derived Macrophages, Palmitic acid, LINC RNA, Sodium Palmitate, Double Stranded RNA Binding Protein, Long Non-Translated, Long ncRNAs, Elra, Elav-like generic protein, elavl1, C16:0, Long Intergenic Non Protein Coding RNA, Protein Elavl1, 2410055N02Rik, melg, Noncoding RNA, Long Non Translated, Hexaectylic acid, Double Stranded RNA Binding Proteins, Long Non-Translated RNA, LincRNAs, MelG, ElrA, Long Non-Protein-Coding, Long Non-Coding, RNA Binding Proteins, lncRNA, ds RNA-Binding Protein, hexadecoic acid, n-hexadecoic acid, inflammatory response, abnormal vision, Hexadecylic acid, Non-Protein-Coding RNA, palmitic acid, Hexadecanoic, elav1, inflammation, Bone Marrow-Derived Macrophage, Palmitinic acid, INSDC_feature:ncRNA, ds RNA Binding Protein, Elavl1, Bone Marrow-Derived, Double-Stranded RNA-Binding Protein, Monocyte, Long Non-Protein-Coding RNA, Innate Inflammatory Response, ds RNA-Binding Proteins, 1-hexyldecanoic acid, Hexadecanoic Acid, RNA Binding Protein, ELAV1, Long Noncoding RNA, Long Untranslated, Long Untranslated RNA, RNA, Long Non-Coding RNA, 1-Pentadecanecarboxylic acid, ncRNA, ncRNAs, ds, C16 fatty acid, Monocyte Derived, Long ncRNA, Double-Stranded, isoform CRA_a, cetylic acid, Monocyte-Derived, Palmitate, C16, Non-Coding RNA, Pentadecanecarboxylic acid, Double-Stranded RNA-Binding Proteins, Protein, Hu-antigen R, Long Non Protein Coding RNA, Sodium, Drosophila)-like 1 (Hu antigen R) (Predicted), Hexadecanoate, CH3-[CH2]14-COOH, Long, ELAV (Embryonic lethal, Untranslated RNA, Double-Stranded RNA-Binding, RNA-Binding Protein, 16:00, Long Non Coding RNA, Monocyte-Derived Macrophages, Macrophage, Palmitic, Acid, Calcium, HuR, PALMITIC ACID, RNA-Binding Proteins, Macrophages, p36, Hua, Bone Marrow Derived Macrophages, FA 16:0, elrA, W91709, Calcium Palmitate, Monocyte-Derived Macrophage., HUR, Xel-1, Palmitinsaeure, Long Intergenic Non-Protein Coding RNA, Innate Inflammatory Responses, Bone Marrow-Derived Macrophages, n-hexadecanoic acid, LincRNA, hua, Innate"],"name_synonyms":["Non-Translated RNA, Inflammatory Response, ds RNA-Binding, hur, Inflammations, Monocyte Derived Macrophages, Palmitic acid, LINC RNA, Sodium Palmitate, Double Stranded RNA Binding Protein, Long Non-Translated, Long ncRNAs, Elra, Elav-like generic protein, elavl1, C16:0, Long Intergenic Non Protein Coding RNA, Protein Elavl1, 2410055N02Rik, melg, Noncoding RNA, Long Non Translated, Hexaectylic acid, Double Stranded RNA Binding Proteins, Long Non-Translated RNA, LincRNAs, MelG, ElrA, Long Non-Protein-Coding, Long Non-Coding, RNA Binding Proteins, lncRNA, ds RNA-Binding Protein, hexadecoic acid, n-hexadecoic acid, inflammatory response, abnormal vision, Hexadecylic acid, Non-Protein-Coding RNA, palmitic acid, Hexadecanoic, elav1, inflammation, Bone Marrow-Derived Macrophage, Palmitinic acid, INSDC_feature:ncRNA, ds RNA Binding Protein, Elavl1, Bone Marrow-Derived, Double-Stranded RNA-Binding Protein, Monocyte, Long Non-Protein-Coding RNA, Innate Inflammatory Response, ds RNA-Binding Proteins, 1-hexyldecanoic acid, Hexadecanoic Acid, RNA Binding Protein, ELAV1, Long Noncoding RNA, Long Untranslated, Long Untranslated RNA, RNA, Long Non-Coding RNA, 1-Pentadecanecarboxylic acid, ncRNA, ncRNAs, ds, C16 fatty acid, Monocyte Derived, Long ncRNA, Double-Stranded, isoform CRA_a, cetylic acid, Monocyte-Derived, Palmitate, C16, Non-Coding RNA, Pentadecanecarboxylic acid, Double-Stranded RNA-Binding Proteins, Protein, Hu-antigen R, Long Non Protein Coding RNA, Sodium, Drosophila)-like 1 (Hu antigen R) (Predicted), Hexadecanoate, CH3-[CH2]14-COOH, Long, ELAV (Embryonic lethal, Untranslated RNA, Double-Stranded RNA-Binding, RNA-Binding Protein, 16:00, Long Non Coding RNA, Monocyte-Derived Macrophages, Macrophage, Palmitic, Acid, Calcium, HuR, PALMITIC ACID, RNA-Binding Proteins, Macrophages, p36, Hua, Bone Marrow Derived Macrophages, FA 16:0, elrA, W91709, Calcium Palmitate, Monocyte-Derived Macrophage., HUR, Xel-1, Palmitinsaeure, Long Intergenic Non-Protein Coding RNA, Innate Inflammatory Responses, Bone Marrow-Derived Macrophages, n-hexadecanoic acid, LincRNA, hua, Innate"],"additional_accession":[]},"is_claimable":false,"name":"Palmitic acid induced lncRNA PARAIL regulates inflammation via interaction with RNA-binding protein HuR in monocytes and macrophages","description":"Palmitic acid induced lncRNA PARAIL regulates inflammation via interaction with RNA-binding protein HuR in monocytes and macrophages","dates":{"last_updated":"2025-09-24","first_public":"2024-09-26"},"accession":"PRJNA884278","cross_references":{"GEO":["GSE214160"],"taxon":["9606"],"PubMed":["40068774","37128912"]}}