{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR104/009/SRR1046759/SRR1046759.fastq.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics","Multiomics"],"center_name":["Uwe Ohler, BIMSM, MDC Berlin"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA231063"],"scientific_name":["Homo sapiens"],"long_description":["Tristetraprolin/ZFP36/TTP and ELAVL1/HuR are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embyonic kidney cells and examined combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1. Among the targets ZFP36 binds and negatively regulates the mRNA of genes encoding proteins necessary for immune function and cancer, and other RBPs. Using partial correlation analysis, we were able to quantify the association between ZFP36 binding sites and differential target RNA abundance from ZFP36 overexpression independent of effects from confounding features, such as 3’ UTR length. We identified thousands of overlapping ZFP36 and ELAVL1 binding sites, in 1,313 genes. ZFP36 preferentially interacts with and regulates AU-rich sequences while ELAVL1 prefers predominantly U- and CU-rich sequences. RNA target specificity identified by global in vivo ZFP36-mRNA interactions were quantitatively similar to previously reported in vitro binding affinities. ZFP36 and ELAVL1 both bind an overlapping spectrum of RNA sequences, yet with differential relative preferences that dictate combinatorial regulatory potential. Our findings and methodology delineate an approach to untangle the in vivo combinatorial regulation by RNA-binding proteins. Overall design: FLAG-HA ZFP36"],"tag":["xref:PubMed:24401661"],"repository":["ENA"],"description_synonyms":["Regulations, Ribonucleic, zfp-36, Microangiopathic hemolytic Anemia, Moschowitz disease, ZFP36, Gene, Zinc Finger Protein 36, protein, protein-containing complex, Social Controls, idiopathic thrombotic thrombocytopenic purpura., Protein TIS11A, Messenger, congenital, Gene Products, G0-G1 Switch Regulatory Protein 24, G0|G1 switch regulatory protein 24, protein aggregate, Non Polyadenylated, Formal Social Controls, RNA Gene Products, AU022812, Zfp-36, Polyadenylated Messenger, ligand, AA792898, messenger RNA, tectothalamic fibers, Social, Non-Polyadenylated RNA, template RNA, TIS11D, Schulman-Upshaw syndrome, tectothalamic pathway, sh3bp4, Upshaw Factor, RNF162A, USS, RNA, deficiency of, Polyadenylated, Formal Social Control, ribose nucleic acid, protein complex, Growth factor-inducible nuclear protein NUP475, Proteins, ribonucleic acids, familial, Messenger RNA, G0S24, RNS, Moschcowitz's syndrome, BOG25, Microangiopathic hemolytic Anaemia, thrombotic microangiopathy, Tristetraprolin Protein, native protein, Social Control, Poly(A)+ mRNA, yeast nucleic acid, Ribonukleinsaeure, Protein, INSDC_feature:mRNA, pentosenucleic acids, Ribonucleic acids, Polyadenylated RNA, Nup475, thiamine triphosphate ester, Polyadenylated Messenger RNA, ribonucleic acid, Acid, ZNF230, Poly(A)+ RNA, Non Polyadenylated mRNA, protein_coding_transcript, mRNA, Poly(A) Tail, Moschcowitz disease, Non Polyadenylated RNA, Tis11, Ttp, TTP, Non-Polyadenylated, Control, 2610110L04Rik, Ribonucleic Acid, Zinc finger protein 36 homolog, Controls, TISII, TIS11, Non-Polyadenylated mRNA, Moschowitz syndrome, Protein Gene Products, GOS24, Gene Proteins, Zinc finger protein 36, tectothalamic tract, NUP475, bog25, thrombotic thrombocytopenic purpura, TPA-induced sequence 11, Gos24, ttp, G0 G1 Switch Regulatory Protein 24, regulation, Polyadenylated mRNA, Regulation, Poly(A) RNA"],"name_synonyms":["Human, Modern., human being, Man (Taxonomy), Homo sapiens, man, Man, human, Modern Man"],"additional_accession":[]},"is_claimable":false,"name":"Homo sapiens","description":"Global Target mRNA Specification and Regulation by RNA-Binding Protein ZFP36/Tristetraprolin/TTP [PAR-CLIP]","dates":{"last_updated":"2025-09-24","first_public":"2013-12-26"},"accession":"PRJNA231063","cross_references":{"GEO":["GSE53184"],"taxon":["9606"],"PubMed":["24401661"]}}