RNA structure profiling at single-cell resolution reveals new determinants of cell identity.
Jia Xu WangYu ZhangTong ZhangWen Ting TanFinnlay LambertJefferson DarmawanRoland G HuberYue WanPublished in: Nature methods (2024)
RNA structure is critical for multiple steps in gene regulation. However, how the structures of transcripts differ both within and between individual cells is unknown. Here we develop a SHAPE-inspired method called single-cell structure probing of RNA transcripts that enables simultaneous determination of transcript secondary structure and abundance at single-cell resolution. We apply single-cell structure probing of RNA transcripts to human embryonic stem cells and differentiating neurons. Remarkably, RNA structure is more homogeneous in human embryonic stem cells compared with neurons, with the greatest homogeneity found in coding regions. More extensive heterogeneity is found within 3' untranslated regions and is determined by specific RNA-binding proteins. Overall RNA structure profiles better discriminate cell type identity and differentiation stage than gene expression profiles alone. We further discover a cell-type variable region of 18S ribosomal RNA that is associated with cell cycle and translation control. Our method opens the door to the systematic characterization of RNA structure-function relationships at single-cell resolution.
Keyphrases
- single cell
- rna seq
- embryonic stem cells
- cell cycle
- high throughput
- nucleic acid
- simultaneous determination
- single molecule
- spinal cord
- stem cells
- mass spectrometry
- computed tomography
- magnetic resonance imaging
- spinal cord injury
- cell proliferation
- liquid chromatography tandem mass spectrometry
- dna methylation
- high resolution
- transcription factor
- mesenchymal stem cells
- copy number
- signaling pathway
- high performance liquid chromatography
- cell therapy
- resting state
- bone marrow