exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers.

Autor:	LaPlante EL; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Stürchler A; Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.; Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland., Fullem R; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA., Chen D; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Starner AC; Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 76706, USA., Esquivel E; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA., Alsop E; Neurogenomics Division, TGen, Phoenix, AZ 85004, USA., Jackson AR; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Ghiran I; Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA., Pereira G; Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA., Rozowsky J; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA., Chang J; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA., Gerstein MB; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA., Alexander RP; Extracellular RNA Communication Consortium, Phoenix, AZ 85254, USA., Roth ME; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA., Franklin JL; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA., Coffey RJ; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA., Raffai RL; Department of Veterans Affairs, Surgical Service (112G), San Francisco VA Medical Center, San Francisco, CA 94121, USA.; Division of Endovascular and Vascular Surgery, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA., Mansuy IM; Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland., Stavrakis S; Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland., deMello AJ; Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland., Laurent LC; Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA., Wang YT; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA., Tsai CF; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA., Liu T; Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA., Jones J; Laboratory of Pathology Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA., Van Keuren-Jensen K; Neurogenomics Division, TGen, Phoenix, AZ 85004, USA., Van Nostrand E; Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 76706, USA.; Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA., Mateescu B; Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland.; Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland., Milosavljevic A; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
Jazyk:	angličtina
Zdroj:	Cell genomics [Cell Genom] 2023 Apr 20; Vol. 3 (5), pp. 100303. Date of Electronic Publication: 2023 Apr 20 (Print Publication: 2023).
DOI:	10.1016/j.xgen.2023.100303
Abstrakt:	Although the role of RNA binding proteins (RBPs) in extracellular RNA (exRNA) biology is well established, their exRNA cargo and distribution across biofluids are largely unknown. To address this gap, we extend the exRNA Atlas resource by mapping exRNAs carried by extracellular RBPs (exRBPs). This map was developed through an integrative analysis of ENCODE enhanced crosslinking and immunoprecipitation (eCLIP) data (150 RBPs) and human exRNA profiles (6,930 samples). Computational analysis and experimental validation identified exRBPs in plasma, serum, saliva, urine, cerebrospinal fluid, and cell-culture-conditioned medium. exRBPs carry exRNA transcripts from small non-coding RNA biotypes, including microRNA (miRNA), piRNA, tRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), Y RNA, and lncRNA, as well as protein-coding mRNA fragments. Computational deconvolution of exRBP RNA cargo reveals associations of exRBPs with extracellular vesicles, lipoproteins, and ribonucleoproteins across human biofluids. Overall, we mapped the distribution of exRBPs across human biofluids, presenting a resource for the community. Competing Interests: E.V.N. is co-founder, member of the Board of Directors, on the SAB, equity holder, and paid consultant for Eclipse BioInnovations. E.V.N.’s interests have been reviewed and approved by the Baylor College of Medicine in accordance with its conflict of interest policies. (© 2023 The Authors.)
Databáze:	MEDLINE
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