Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA

Chakrabortty, Sudipto K.; Prakash, Ashwin; Nechooshtan, Gal; Hearn, Stephen; Gingeras, T

doi:10.1261/rna.053629.115

Cited by 68 publications

(71 citation statements)

References 55 publications

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“…As mentioned before, in the plasma samples ~63% of the reads assigned to the human genome align to YRNAs in our samples. The presence of YRNA fragments has been reported previously16171819. Figure 2B (lower panel) illustrates the proportion of reads aligning to YRFs in plasma exceeds those found in saliva and urine (Wilcoxin p-value < 1.3E-16).…”

Section: Resultssupporting

confidence: 75%

Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects

Yeri

Courtright

Reiman

et al. 2017

Sci Rep

143

151

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Interest in circulating RNAs for monitoring and diagnosing human health has grown significantly. There are few datasets describing baseline expression levels for total cell-free circulating RNA from healthy control subjects. In this study, total extracellular RNA (exRNA) was isolated and sequenced from 183 plasma samples, 204 urine samples and 46 saliva samples from 55 male college athletes ages 18–25 years. Many participants provided more than one sample, allowing us to investigate variability in an individual’s exRNA expression levels over time. Here we provide a systematic analysis of small exRNAs present in each biofluid, as well as an analysis of exogenous RNAs. The small RNA profile of each biofluid is distinct. We find that a large number of RNA fragments in plasma (63%) and urine (54%) have sequences that are assigned to YRNA and tRNA fragments respectively. Surprisingly, while many miRNAs can be detected, there are few miRNAs that are consistently detected in all samples from a single biofluid, and profiles of miRNA are different for each biofluid. Not unexpectedly, saliva samples have high levels of exogenous sequence that can be traced to bacteria. These data significantly contribute to the current number of sequenced exRNA samples from normal healthy individuals.

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Section: Resultssupporting

confidence: 75%

Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects

Yeri

Courtright

Reiman

et al. 2017

Sci Rep

143

151

View full text Add to dashboard Cite

show abstract

“…See also Figures S4-S7, Table S1, and STAR Methods. higher abundance of Y RNAs than other cargo types, consistent with previously observed abundance of Y RNAs in whole biofluids (Chakrabortty et al, 2015;Dhahbi et al, 2013;Yeri et al, 2017). These results should be considered in the context of large sample-to-sample variability in biotype proportions observed across Atlas studies ( Figure S7B) and in the context of differences in library preparation protocols ( Figure S5D).…”

Section: Cargo Types Show Distinct Rna Biotype Compositionsupporting

confidence: 88%

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

Murillo

Thistlethwaite

Rozowsky

et al. 2019

Cell

246

261

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Graphical Abstract Highlights d The exRNA Atlas provides access to human exRNA profiles and web-accessible tools d Atlas analysis reveals six exRNA cargo types present across five human biofluids d Five of the cargo types associate with specific vesicular and non-vesicular carriers d These findings and resources empower studies of extracellular RNA communication An extracellular RNA atlas from five human biofluids (serum, plasma, cerebrospinal fluid, saliva, and urine) reveals six extracellular RNA cargo types, including both vesicular and nonvesicular carriers. SUMMARY To develop a map of cell-cell communication mediated by extracellular RNA (exRNA), the NIH Extracellular RNA Communication Consortium created the exRNA Atlas resource (https://exrna-atlas.org). The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools. To analyze variation between profiles, we apply computational deconvolution. The analysis leads to a model with six exRNA cargo types (CT1, CT2, CT3A, CT3B, CT3C, CT4), each detectable in multiple biofluids (serum, plasma, CSF, saliva, urine). Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers. To validate utility of this model, we re-analyze an exercise response study by deconvolution to identify physiologically relevant response pathways that were not detected previously.To enable wide application of this model, as part of the exRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.

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“…They have been found as biomarkers of coronary artery disease (Repetto et al 2015) and they are involved in cardioprotection via IL-10 expression regulation (Cambier et al 2017). Besides this, in the past couple of years, a few studies have detected circulating levels of these yRNA in serum and plasma (Fritz et al 2016;Kaudewitz et al 2016), and later on in extracellular vesicles such as exosomes (Chakrabortty et al 2015;van Balkom et al 2015;Cambier et al 2017). In our samples, we were able to identify these RNAs in the small RNA libraries among the fragments ranging in sizes from 30 to 34 nt.…”

Section: Discussionmentioning

confidence: 99%

Exploring the RNA landscape of endothelial exosomes

Pérez-Boza

Lion

Struman

2017

RNA

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Exosomes are small extracellular vesicles of around 100 nm of diameter produced by most cell types. These vesicles carry nucleic acids, proteins, lipids, and other biomolecules and function as carriers of biological information in processes of extracellular communication. The content of exosomes is regulated by the external and internal microenvironment of the parent cell, but the intrinsic mechanisms of loading of molecules into exosomes are still not completely elucidated. In this study, by the use of next-generation sequencing we have characterized in depth the RNA composition of healthy endothelial cells and exosomes and provided an accurate profile of the different coding and noncoding RNA species found per compartment. We have also discovered a set of unique genes preferentially included (or excluded) into vesicles. Moreover, after studying the enrichment of RNA motifs in the genes unequally distributed between cells and exosomes, we have detected a set of enriched sequences for several classes of RNA. In conclusion, our results provide the basis for studying the involvement of RNA-binding proteins capable of recognizing RNA sequences and their role in the export of RNAs into exosomes.

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Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA

Cited by 68 publications

References 55 publications

Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects

Total Extracellular Small RNA Profiles from Plasma, Saliva, and Urine of Healthy Subjects

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids

Exploring the RNA landscape of endothelial exosomes

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