Ahadi, A., Brennan, S., Kennedy, P.J., Hutvagner, G., Tran, N., Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes (2016) Sci Rep, 6, p. 24922
Aken, B.L., Achuthan, P., Akanni, W., Amode, M.R., Bernsdorff, F., Bhai, J., Billis, K., Clapham, P., Ensembl 2017 (2017) Nucleic Acids Res, 45, pp. D635-D642
Batagov, A.O., Kurochkin, I.V., Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3′-un-translated regions (2013) Biol Direct, 8, p. 12
Berrondo, C., Flax, J., Kucherov, V., Siebert, A., Osinski, T., Rosenberg, A., Fucile, C., Beckham, C.J., Expression of the long non-coding RNA HOTAIR correlates with disease progression in bladder cancer and is contained in bladder cancer patient urinary exosomes (2016) PLoS One, 11
Beuck, C., Williamson, J.R., Wüthrich, K., Serrano, P., The acidic domain is a unique structural feature of the splicing factor SYNCRIP (2016) Protein Sci, 25, pp. 1545-1550
Bolger, A.M., Lohse, M., Usadel, B., Trimmomatic: A flexible trimmer for Illumina sequence data (2014) Bioinformatics, 30, pp. 2114-2120
Cambier, L., De Couto, G., Ibrahim, A., Echavez, A.K., Valle, J., Liu, W., Kreke, M., Marbán, E., Y RNA fragment in extracellular vesicles confers cardioprotection via modulation of IL-10 expression and secretion (2017) EMBO Mol Med, 9, pp. 337-352
Chakrabortty, S.K., Prakash, A., Nechooshtan, G., Hearn, S., Gingeras, T.R., Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA (2015) RNA, 21, pp. 1966-1979
Challagundla, K.B., Wise, P.M., Neviani, P., Chava, H., Murtadha, M., Xu, T., Kennedy, R., Vannini, I., Exosome-mediated transfer of microRNAs within the tumor microenvironment and neuroblastoma resistance to chemotherapy (2015) J Natl Cancer Inst, 107, p. djv135
Chen, M., Xu, R., Ji, H., Greening, D.W., Rai, A., Izumikawa, K., Ishikawa, H., Simpson, R.J., Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line (2016) Sci Rep, 6, p. 38397
Choi, K.S., Mizutani, A., Lai, M.M.C., SYNCRIP, a member of the heterogeneous nuclear ribonucleoprotein family, is involved in mouse hepatitis virus RNA synthesis (2004) J Virol, 78, pp. 13153-13162
Crescitelli, R., Lässer, C., Szabó, T.G., Kittel, A., Eldh, M., Dianzani, I., Buzás, E.I., Lötvall, J., Distinct RNA profiles in subpopulations of extracellular vesicles: Apoptotic bodies, microvesicles and exosomes (2013) J Extracell Vesicles, 2, p. 20677
Duning, K., Buck, F., Barnekow, A., Kremerskothen, J., SYNCRIP, a component of dendritically localized mRNPs, binds to the translation regulator BC200 RNA (2008) J Neurochem, 105, pp. 351-359
Eliseeva, I.A., Kim, E.R., Guryanov, S.G., Ovchinnikov, L.P., Lyabin, D.N., Y-box-binding protein 1 (YB-1) and its functions (2011) Biochemistry, 76, pp. 1402-1433
Enderle, D., Spiel, A., Coticchia, C.M., Berghoff, E., Mueller, R., Schlumpberger, M., Sprenger-Haussels, M., Skog, J., Characterization of RNA from exosomes and other extracellular vesicles isolated by a novel spin column-based method (2015) PLoS One, 10
Farris, A.D., O’Brien, C.A., Harley, J.B., Y3 is the most conserved small RNA component of Ro ribonucleoprotein complexes in vertebrate species (1995) Gene, 154, pp. 193-198
Friand, V., David, G., Zimmermann, P., Syntenin and syndecan in the biogenesis of exosomes (2015) Biol Cell, 107, pp. 331-341
Fritz, J.V., Heintz-Buschart, A., Ghosal, A., Wampach, L., Etheridge, A., Galas, D., Wilmes, P., Sources and functions of extracellular small RNAs in human circulation (2016) Annu Rev Nutr, 36, pp. 301-336
Gao, Y., Wang, J., Zhao, F., CIRI: An efficient and unbiased algorithm for de novo circular RNA identification (2015) Genome Biol, 16, p. 4
Gezer, U., Özgür, E., Cetinkaya, M., Işin, M., Dalay, N., Long non-coding RNAs with low expression levels in cells are enriched in secreted exosomes (2014) Cell Biol Int, 38, pp. 1076-1079
Guo, T., Kong, J., Liu, Y., Li, Z., Xia, J., Zhang, Y., Zhao, S., Gu, C., Transcriptional activation of NANOG by YBX1 promotes lung cancer stem-like properties and metastasis (2017) Biochem Biophys Res Commun, 487, pp. 153-159
Hannafon, B.N., Ding, W.Q., Intercellular communication by exosome-derived microRNAs in cancer (2013) Int J Mol Sci, 14, pp. 14240-14269
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y.C., Laslo, P., Cheng, J.X., Glass, C.K., Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities (2010) Mol Cell, 38, pp. 576-589
Hewson, C., Capraro, D., Burdach, J., Whitaker, N., Morris, K.V., Extracellular vesicle associated long non-coding RNAs functionally enhance cell viability (2016) Non-Coding RNA Res, 1, pp. 3-11
Işin, M., Uysaler, E., Özgür, E., Köseoglu, H., Şanlı, Ö., Yücel, Ö.B., Gezer, U., Dalay, N., Exosomal lncRNA-p21 levels may help to distinguish prostate cancer from benign disease (2015) Front Genet, 6, p. 168
Jenjaroenpun, P., Kremenska, Y., Nair, V.M., Kremenskoy, M., Joseph, B., Kurochkin, I.V., Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing (2013) PeerJ, 1, p. e201
Ji, R., Zhang, B., Zhang, X., Xue, J., Yuan, X., Yan, Y., Wang, M., Xu, W., Exosomes derived from human mesenchymal stem cells confer drug resistance in gastric cancer (2015) Cell Cycle, 14, pp. 2473-2483
Joyce, D.P., Kerin, M.J., Dwyer, R.M., Exosome-encapsulated microRNAs as circulating biomarkers for breast cancer (2016) Int J Cancer, 139, pp. 1443-1448
Jung, K., Wu, F., Wang, P., Ye, X., Abdulkarim, B.S., Lai, R., YB-1 regulates Sox2 to coordinately sustain stemness and tumorigenic properties in a phenotypically distinct subset of breast cancer cells (2014) BMC Cancer, 14, p. 328
Kaudewitz, D., Skroblin, P., Bender, L.H., Barwari, T., Willeit, P., Pechlaner, R., Sunderland, N.P., Armstrong, P.C., Association of microRNAs and YRNAs with platelet function (2016) Circ Res, 118, pp. 420-432
Keerthikumar, S., Chisanga, D., Ariyaratne, D., Al Saffar, H., Anand, S., Zhao, K., Samuel, M., Chilamkurti, N., ExoCarta: A web-based compendium of exosomal cargo (2016) J Mol Biol, 428, pp. 688-692
Kosaka, N., Yoshioka, Y., Hagiwara, K., Tominaga, N., Ochiya, T., Functional analysis of exosomal microRNA in cell-cell communication research (2013) Methods Mol Biol, 1024, pp. 1-10
Kossinova, O.A., Gopanenko, A.V., Tamkovich, S.N., Krasheninina, O.A., Tupikin, A.E., Kiseleva, E., Yanshina, D.D., Kabilov, M.R., Cytosolic YB-1 and NSUN2 are the only proteins recognizing specific motifs present in mRNAs enriched in exosomes (2017) Biochim Biophys Acta, 1865, pp. 664-673
Kozomara, A., Griffiths-Jones, S., MiRBase: Annotating high confidence microRNAs using deep sequencing data (2014) Nucleic Acids Res, 42, pp. D68-D73
Lang, H.L., Hu, G.W., Chen, Y., Liu, Y., Tu, W., Lu, Y.M., Wu, L., Xu, G.H., Glioma cells promote angiogenesis through the release of exosomes containing long non-coding RNA POU3F3 (2017) Eur Rev Med Pharmacol Sci, 21, pp. 959-972
Langmead, B., Salzberg, S.L., Fast gapped-read alignment with Bowtie 2 (2012) Nat Methods, 9, pp. 357-359
Lázaro-Ibáñez, E., Lunavat, T.R., Jang, S.C., Escobedo-Lucea, C., La Cruz, O.-D.J., Siljander, P., Lötvall, J., Yliperttula, M., Distinct prostate cancer-related mRNA cargo in extracellular vesicle subsets from prostate cell lines (2017) BMC Cancer, 17, p. 92
Lerner, M.R., Boyle, J.A., Hardin, J.A., Steitz, J.A., Two novel classes of small ribonucleoproteins detected by antibodies associated with lupus erythematosus (1981) Science, 211, pp. 400-402
Lévesque, K., Halvorsen, M., Abrahamyan, L., Chatel-Chaix, L., Poupon, V., Gordon, H., DesGroseillers, L., Mouland, A.J., Trafficking of HIV-1 RNA is mediated by heterogeneous nuclear ribonucleoprotein A2 expression and impacts on viral assembly (2006) Traffic, 7, pp. 1177-1193
Li, L., Li, C., Wang, S., Wang, Z., Jiang, J., Wang, W., Li, X., Li, C., Exosomes derived from hypoxic oral squamous cell carcinoma cells deliver miR-21 to normoxic cells to elicit a prometa-static phenotype (2016) Cancer Res, 76, pp. 1770-1780
Li, Q., Shao, Y., Zhang, X., Zheng, T., Miao, M., Qin, L., Wang, B., Guo, J., Plasma long noncoding RNA protected by exosomes as a potential stable biomarker for gastric cancer (2015) Tumour Biol, 36, pp. 2007-2012
Lim, J.P., Shyamasundar, S., Gunaratne, J., Scully, O.J., Matsumoto, K., Bay, B.H., YBX1 gene silencing inhibits migratory and invasive potential via CORO1C in breast cancer in vitro (2017) BMC Cancer, 17, p. 201
Liu, H.M., Aizaki, H., Choi, K.S., Machida, K., Ou, J.J.H., Lai, M.M.C., SYNCRIP (synaptotagmin-binding, cytoplasmic RNA-interacting protein) is a host factor involved in hepatitis C virus RNA replication (2009) Virology, 386, pp. 249-256
Liu, T., Zhang, X., Gao, S., Jing, F., Yang, Y., Du, L., Zheng, G., Wang, C., Exosomal long noncoding RNA CRNDE-h as a novel serum-based biomarker for diagnosis and prognosis of colorectal cancer (2016) Oncotarget, 7, pp. 85551-85563
Lobb, R.J., Van Amerongen, R., Wiegmans, A., Ham, S., Larsen, J.E., Möller, A., Exosomes derived from mesenchymal non-small cell lung cancer cells promote chemoresistance (2017) Int J Cancer, 141, pp. 614-620
Lötvall, J., Hill, A.F., Hochberg, F., Buzás, E.I., Di Vizio, D., Gardiner, C., Gho, Y.S., Quesenberry, P., Minimal experimental requirements for definition of extracellular vesicles and their functions: A position statement from the International Society for Extracellular Vesicles (2014) J Extracell Vesicles, 3, p. 26913
Lv, J., Huang, Z., Liu, H., Liu, H., Cui, W., Li, B., He, H., Zhang, Y., Identification and characterization of long intergenic non-coding RNAs related to mouse liver development (2014) Mol Genet Genomics, 289, pp. 1225-1235
Lyabin, D.N., Eliseeva, I.A., Ovchinnikov, L.P., YB-1 protein: Functions and regulation (2014) Wiley Interdiscip Rev RNA, 5, pp. 95-110
Mateescu, B., Kowal, E.J.K., Van Balkom, B.W.M., Bartel, S., Bhattacharyya, S.N., Buzás, E.I., Buck, A.H., Das, S., Obstacles and opportunities in the functional analysis of extracellular vesicle RNA—an ISEV position paper (2017) J Extracell Vesicles, 6, p. 1286095
Mathivanan, S., Ji, H., Simpson, R.J., Exosomes: Extracellular organelles important in intercellular communication (2010) J Proteomics, 73, pp. 1907-1920
McCarthy, D.J., Chen, Y., Smyth, G.K., Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation (2012) Nucleic Acids Res, 40, pp. 4288-4297
Milane, L., Singh, A., Mattheolabakis, G., Suresh, M., Amiji, M.M., Exosome mediated communication within the tumor microenvironment (2015) J Control Release, 219, pp. 278-294
Miranda, K.C., Bond, D.T., Levin, J.Z., Adiconis, X., Sivachenko, A., Russ, C., Brown, D., Russo, L.M., Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA (2014) PLoS One, 9
Momen-Heravi, F., Saha, B., Kodys, K., Catalano, D., Satishchandran, A., Szabo, G., Increased number of circulating exosomes and their microRNA cargos are potential novel biomarkers in alcoholic hepatitis (2015) J Transl Med, 13, p. 261
Moser, J.J., Eystathioy, T., Chan, E.K.L., Fritzler, M.J., Markers of mRNA stabilization and degradation, and RNAi within astrocytoma GW bodies (2007) J Neurosci Res, 85, pp. 3619-3631
Munro, T.P., Magee, R.J., Kidd, G.J., Carson, J.H., Barbarese, E., Smith, L.M., Smith, R., Mutational analysis of a heterogeneous nuclear ribonucleoprotein A2 response element for RNA trafficking (1999) J Biol Chem, 274, pp. 34389-34395
Øverbye, A., Skotland, T., Koehler, C.J., Thiede, B., Seierstad, T., Berge, V., Sandvig, K., Llorente, A., Identification of prostate cancer biomarkers in urinary exosomes (2015) Oncotarget, 6, pp. 30357-30376
Pan, L., Liang, W., Fu, M., Huang, Z.H., Li, X., Zhang, W., Zhang, P., Xu, W.R., Exosomes-mediated transfer of long noncoding RNA ZFAS1 promotes gastric cancer progression (2017) J Cancer Res Clin Oncol, 143, pp. 991-1004
Peake, P.W., Pianta, T.J., Succar, L., Fernando, M., Pugh, D.J., McNamara, K., Endre, Z.H., A comparison of the ability of levels of urinary biomarker proteins and exosomal mRNA to predict outcomes after renal transplantation (2014) PLoS One, 9
Pignatelli, M., Vilella, A.J., Muffato, M., Gordon, L., White, S., Flicek, P., Herrero, J., NcRNA orthologies in the vertebrate lineage (2016) Database, 2016, p. bav127
Provencio, M., Rodríguez, M., Cantos, B., Sabín, P., Quero, C., García-Arroyo, F.R., Rueda, A., Sánchez, A., mRNA in exosomas as a liquid biopsy in non-Hodgkin lymphoma: A multicentric study by the Spanish Lymphoma Oncology Group (2017) Oncotarget, 8, pp. 50949-50957
Qu, L., Ding, J., Chen, C., Wu, Z.J., Liu, B., Gao, Y., Chen, W., Li, X.F., Exosome-transmitted lncARSR promotes suniti-nib resistance in renal cancer by acting as a competing endogenous RNA (2016) Cancer Cell, 29, pp. 653-668
Quek, C., Bellingham, S.A., Jung, C.H., Scicluna, B.J., Shambrook, M.C., Sharples, R.A., Cheng, L., Hill, A.F., Defining the purity of exosomes required for diagnostic profiling of small RNA suitable for biomarker discovery (2017) RNA Biol, 14, pp. 245-258
Repetto, E., Lichtenstein, L., Hizir, Z., Tekaya, N., Benahmed, M., Ruidavets, J.B., Zaragosi, L.E., Genoux, A., RNY-derived small RNAs as a signature of coronary artery disease (2015) BMC Med, 13, p. 259
Robinson, M.D., McCarthy, D.J., Smyth, G.K., EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data (2010) Bioinformatics, 26, pp. 139-140
Robinson, M.D., Oshlack, A., A scaling normalization method for differential expression analysis of RNA-seq data (2010) Genome Biol, 11, p. R25
Sánchez, C.A., Andahur, E.I., Valenzuela, R., Castellón, E.A., Fullá, J.A., Ramos, C.G., Triviño, J.C., Exosomes from bulk and stem cells from human prostate cancer have a differential microRNA content that contributes cooperatively over local and pre-metastatic niche (2016) Oncotarget, 7, pp. 3993-4008
Santangelo, L., Giurato, G., Cicchini, C., Montaldo, C., Mancone, C., Tarallo, R., Battistelli, C., Tripodi, M., The RNA-binding protein SYNCRIP is a component of the hepatocyte exosomal machinery controlling microRNA sorting (2016) Cell Rep, 17, pp. 799-808
Schwarzenbach, H., The clinical relevance of circulating, exosomal miRNAs as biomarkers for cancer (2015) Expert Rev Mol Diagn, 15, pp. 1159-1169
Shurtleff, M.J., Temoche-Diaz, M.M., Karfilis, K.V., Ri, S., Schekman, R., Y-box protein 1 is required to sort microRNAs into exosomes in cells and in a cell-free reaction (2016) eLife, 5, p. e19276
Simons, M., Raposo, G., Exosomes—vesicular carriers for intercellular communication (2009) Curr Opin Cell Biol, 21, pp. 575-581
Skogberg, G., Gudmundsdottir, J., Van Der Post, S., Sandström, K., Bruhn, S., Benson, M., Mincheva-Nilsson, L., Ekwall, O., Characterization of human thymic exosomes (2013) PLoS ONE, 8, p. e67554
Solé, C., Cortés-Hernández, J., Felip, M.L., Vidal, M., Ordi-Ros, J., MiR-29c in urinary exosomes as predictor of early renal fibrosis in lupus nephritis (2015) Nephrol Dial Transplant, 30, pp. 1488-1496
Suzuki, H., Matsuoka, M., HnRNPA1 autoregulates its own mRNA expression to remain non-cytotoxic (2017) Mol Cell Biochem, 427, pp. 123-131
Tsochandaridis, M., Nasca, L., Toga, C., Levy-Mozziconacci, A., Circulating microRNAs as clinical biomarkers in the predictions of pregnancy complications (2015) BioMed Res Int, 2015, p. 294954
Umezu, T., Tadokoro, H., Azuma, K., Yoshizawa, S., Ohyashiki, K., Ohyashiki, J.H., Exosomal miR-135b shed from hypoxic multiple myeloma cells enhances angiogenesis by targeting factor-inhibiting HIF-1 (2014) Blood, 124, pp. 3748-3757
Van Balkom, B.W.M., Eisele, A.S., Pegtel, D.M., Bervoets, S., Verhaar, M.C., Quantitative and qualitative analysis of small RNAs in human endothelial cells and exosomes provides insights into localized RNA processing, degradation and sorting (2015) J Extracell Vesicles, 4, p. 26760
Villarroya-Beltri, C., Gutiérrez-Vázquez, C., Sánchez-Cabo, F., Pérez-Hernández, D., Vázquez, J., Martin-Cofreces, N., Martinez-Herrera, D.J., Sánchez-Madrid, F., Sumoylated hnRNPA2B1 controls the sorting of miRNAs into exosomes through binding to specific motifs (2013) Nat Commun, 4, p. 2980
Wang, J., Zhou, Y., Lu, J., Sun, Y., Xiao, H., Liu, M., Tian, L., Combined detection of serum exosomal miR-21 and HOTAIR as diagnostic and prognostic biomarkers for laryngeal squamous cell carcinoma (2014) Med Oncol, 31, p. 148
Wu, S.L., Fu, X., Huang, J., Jia, T.T., Zong, F.Y., Mu, S.R., Zhu, H., Wu, Q., Genome-wide analysis of YB-1-RNA interactions reveals a novel role of YB-1 in miRNA processing in glioblastoma multiforme (2015) Nucleic Acids Res, 43, pp. 8516-8528
Xu, J.F., Wang, Y., Zhang, S.J., Chen, Y., Gu, H.F., Dou, X.F., Xia, B., Fan, S.W., Exosomes containing differential expression of microRNA and mRNA in osteosarcoma that can predict response to chemotherapy (2017) Oncotarget, 5, pp. 75968-75978
Yoon, C., Kim, J., Park, G., Kim, S., Kim, D., Hur, D.Y., Kim, B., Kim, Y.S., Delivery of miR-155 to retinal pigment epithelial cells mediated by Burkitt’s lymphoma exosomes (2016) Tumour Biol, 37, pp. 313-321
Zhang, J., Kong, L., Guo, S., Bu, M., Guo, Q., Xiong, Y., Zhu, N., Chen, Q., HnRNPs and ELAVL1 cooperate with uORFs to inhibit protein translation (2017) Nucleic Acids Res, 45, pp. 2849-2864
Zhao, X., Liu, Y., Yu, S., Long noncoding RNA AWPPH promotes hepatocellular carcinoma progression through YBX1 and serves as a prognostic biomarker (2017) Biochim Biophys Acta, 1863, pp. 1805-1816
Zhou, J., Gong, G., Tan, H., Dai, F., Zhu, X., Chen, Y., Wang, J., Wu, X., Urinary microRNA-30a-5p is a potential biomarker for ovarian serous adenocarcinoma (2015) Oncol Rep, 33, pp. 2915-2923
