This technology is an in vivo method for detecting non-coding RNA in primary cells using a knockout mouse model.
Unmet Need: Effective platform for measuring expression of a non-coding RNA transcriptome
Current methods for detecting non-coding RNA (ncRNA) in primary cells are ineffective due to the low amounts of basal ncRNA combined with their high rates of degradation. As a result, non-coding RNAs are not well understood; however, mounting evidence suggests that they are nevertheless important regulators of cell identity and disease transformation. The current methods for studying ncRNAs utilize transformed cell lines which have a different biological environment that could influence ncRNA concentrations and function. Thus, a system for in vivo analysis of ncRNAs in primary cells is needed.
The Technology: Mouse model for analyzing non-coding RNA in vivo
This technology offers a method for effectively measuring ncRNA transcriptomics in primary cells using a knockout mouse model. In this model, Dis3, a ncRNA-degrading exosome, is targeted for conditional knock-out, allowing accumulation of cellular ncRNA levels. Different primary cell types can then be harvested and isolated to perform transcriptomics on the accumulated ncRNA. The in vivo applicability of this method provides an accurate representation of the ncRNA landscape in a variety of primary cell types.
This technology has been validated in a generated mouse model.
Applications:
- In vivo ncRNA transcriptomics, genomics, and epigenomics
- Diagnostic assay for cancers and other ncRNA-related diseases
- Research tool for isolating ncRNA
- Research tool for measuring the effects of exosome-depletion at different developmental stages
- Research tool for the effect of pathogens and other diseases on ncRNA levels
- RNA neoantigen discovery
Advantages:
- In vivo application for accurate cellular environment
- Allows use of primary cells instead of cell lines
- Enables knockout of ncRNA degradation at any stage of development
- Effective measurement of ncRNA concentrations and transcriptomics
- Directly interferes with a primary ncRNA degradation mechanism
- Applicable to a range of cells including B cells, T cells, neurons, etc.
- Allows study of pathogen colonization effect on transcriptome
Lead Inventor:
Uttiya Basu, Ph.D.
Related Publications:
Nair L, Zhang W, Laffleur B, Jha MK, Lim J, Lee H, Wu L, Alvarez NS, Liu ZP, Munteanu EL, Swayne T, Hanna JH, Ding L, Rothschild G, Basu U. “Mechanism of noncoding RNA-associated N6-methyladenosine recognition by an RNA processing complex during IgH DNA recombination” Mol Cell. 2021 Oct 7; 81(19): 3949-3964.
Pefanis E, Wang J, Rothschild G, Lim J, Chao J, Rabadan R, Economides AN, Basu U. “Noncoding RNA transcription targets AID to divergently transcribed loci in B cells” Nature. 2014 Oct 16; 514(7522): 389-393.
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