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| Status |
Public on Aug 11, 2020 |
| Title |
Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction [Surface-FISHSeq] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Compared to proteins, glycans, and lipids, much less is known about RNAs on the cell surface. We developed a series of technologies to test for any nuclear-encoded RNAs that are stably attached to the cell surface and exposed to the extracellular space, hereafter called membrane-associated extracellular RNAs (maxRNAs). We visualized maxRNAs on the cell surface, sequenced selected maxRNAs, and validated two maxRNAs by RNA fluorescence in situ hybridization. To test for cell-type specificity of maxRNA, we used randomized antisense oligos to hybridize to single-stranded transcripts exposed on the surface of human peripheral blood mononuclear cells (PBMCs). Combining this strategy with imaging flow cytometry, single-cell RNA sequencing, and maxRNA sequencing, we identified monocyte as the major type of maxRNA+ PBMCs and prioritized 11 maxRNAs for functional tests. Extracellular hybridization of antisense oligos to the cell surface-exposed fragments of FNDC3B and CTSS transcripts inhibited monocyte adhesion to vascular endothelial cells. Collectively, these data highlight maxRNAs as a functional component of the cell surface, suggesting an expanded role for RNA in cell-cell interaction and communication.
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| Overall design |
Surface RNA sequencing using Surface-FISHSeq on human PBMCs.
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| Contributor(s) |
Huang N, Fan X, Rivera KZ, Nguyen TC, Zhou J, Luo Y, Fang RH, Chen ZB, Zhang L, Zhong S |
| Citation(s) |
32907628 |
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| Submission date |
May 11, 2020 |
| Last update date |
Jul 19, 2024 |
| Contact name |
Sheng Zhong |
| E-mail(s) |
szhong@ucsd.edu, szhong.ucsd@gmail.com
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| Phone |
2174190577
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| Organization name |
UCSD
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| Street address |
5556 Caminito Mundano
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| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92130 |
| Country |
USA |
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| Platforms (1) |
| GPL22790 |
Illumina MiniSeq (Homo sapiens) |
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| Samples (14)
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| This SubSeries is part of SuperSeries: |
| GSE150237 |
Natural display of nuclear-encoded RNA on the cell surface and its impact on cell interaction |
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| Relations |
| BioProject |
PRJNA631610 |
| SRA |
SRP261057 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE150234_RAW.tar |
69.3 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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