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Updated: Aug 23, 2025
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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
Published on: April 30, 2011
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Spatial mapping of the total transcriptome by in situ polyadenylation
David W McKellar1, Madhav Mantri2, Meleana M Hinchman3
1Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
Nature Biotechnology
|November 4, 2022
Summary
This study introduces spatial total RNA-sequencing (STRS) to detect all RNA types, not just polyadenylated (A-tailed) RNA. STRS expands spatial transcriptomics to the whole transcriptome, offering deeper biological insights.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Spatial transcriptomics currently focuses on polyadenylated (A-tailed) RNA.
- This limitation restricts the analysis to a subset of the transcriptome.
- Understanding the full RNA landscape in spatial contexts is crucial for comprehensive biological insights.
Purpose of the Study:
- To develop a method for spatial transcriptomics that captures the entire RNA spectrum.
- To expand spatial transcriptomics beyond polyadenylated RNAs to the total transcriptome.
- To enable the study of noncoding and viral RNAs in their spatial context.
Main Methods:
- Enzymatic in situ polyadenylation of RNA was employed.
- This method was integrated into the Visium spatial total RNA-sequencing protocol.
- The developed spatial total RNA-sequencing (STRS) approach was applied to skeletal muscle regeneration and viral myocarditis models.
Main Results:
- STRS successfully detected coding RNAs, noncoding RNAs, and viral RNAs.
- The method achieved near-cellular resolution for noncoding RNA expression patterns.
- Spatially defined noncoding transcript expression was identified in skeletal muscle regeneration.
- Host transcriptional responses linked to local viral RNA abundance were highlighted.
Conclusions:
- STRS significantly expands the scope of spatial transcriptomics to the total transcriptome.
- The technique provides novel insights into spatial gene regulation, particularly for noncoding RNAs.
- STRS is easily adoptable, requiring minimal modification to existing protocols, thus facilitating broader research applications.
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