exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers.
exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers.
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DOI：
10.1016/j.xgen.2023.100303
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发表时间：
2023-05-10
期刊：
影响因子：
--
通讯作者：
Milosavljevic, Aleksandar
中科院分区：
文献类型：
--
作者：
Laplante, Emily L.;Sturchler, Alessandra;Fullem, Robert;Chen, David;Starner, Anne C.;Esquivel, Emmanuel;Alsop, Eric;Jackson, Andrew R.;Ghiran, Ionita;Pereira, Getulio;Rozowsky, Joel;Chang, Justin;Gerstein, Mark B.;Alexander, Roger P.;Roth, Matthew E.;Franklin, Jeffrey L.;Coffey, Robert J.;Raffai, Robert L.;Mansuy, Isabelle M.;Stavrakis, Stavros;Demello, Andrew J.;Laurent, Louise C.;Wang, Yi-Ting;Tsai, Chia-Feng;Liu, Tao;Jones, Jennifer;Van Keuren-Jensen, Kendall;Van Nostrand, Eric;Mateescu, Bogdan;Milosavljevic, Aleksandar
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. Intersecting eCLIP and exRNA dataset predicts extracellular RBPs in human biofluids Deconvolution of RNA bound by RBPs associates RBPs with exRNA carrier classes Generated RNA-RBP coverage map of more than 6,900 biofluid samples across whole human genome Differential release of extracellular RBPs and their isoforms across different cell types By intersecting and deconvoluting extracellular RNAs (exRNAs) and eCLIP datasets, LaPlante and Stürchler et al. predict and validate novel extracellular RNA-binding proteins (exRBPs) associated with exRNA carriers in human biofluids and cell-conditioned medium. This work dramatically expands our current view on the role of exRBPs in cell-free RNA profiles.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
5.6
作者：
Nair-Menon, Joyce;Daulagala, Amanda C.;Kourtidis, Antonis
通讯作者：
Kourtidis, Antonis
缓冲密度梯度超速离心（C-DGUC）：一种用于隔离，表征和使用外泌体的精制和高性能方法。
DOI：
10.1007/978-1-4939-7652-2_7
发表时间：
2018
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Li K;Wong DK;Hong KY;Raffai RL
通讯作者：
Raffai RL
影响因子：
16
作者：
Subramanian SL;Kitchen RR;Alexander R;Carter BS;Cheung KH;Laurent LC;Pico A;Roberts LR;Roth ME;Rozowsky JS;Su AI;Gerstein MB;Milosavljevic A
通讯作者：
Milosavljevic A
影响因子：
10.5
作者：
Han, JJ;Lee, Y;Kim, VN
通讯作者：
Kim, VN