We developed a two-pronged strategy to functionally probe the enormous repertoire of noncoding DNA within genomes. Our approach markedly improved signal-to-noise ratio and successfully intersected single-cell genomics with reporter assays. The result delivers a multiplex and highly quantitative readout of regulatory sequences’ activity in dynamic and multicellular systems.
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References
The ENCODE Project Consortium. et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583, 699–710 (2020). An overview article presenting the vast catalogue of regulatory elements in mammalian genomes.
Patwardhan, R. P. et al. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat. Biotechnol. 27, 1173–1175 (2009). This paper reports the massively parallel reporter assay strategy to profile the function of regulatory DNA at scale.
Litke, J. L. & Jaffrey, S. R. Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts. Nat. Biotechnol. 37, 667–675 (2019). This paper introduces the Tornado system to stabilize short polymerase III-driven RNAs.
Zhao, S. et al. A single-cell massively parallel reporter assay detects cell-type-specific gene regulation. Nat. Genet. 55, 346–354 (2023). This paper reports an assay that combines scRNA-seq with multiplex reporters.
Mangan, R. J. et al. Adaptive sequence divergence forged new neurodevelopmental enhancers in humans. Cell 185, 4587–4603.e23 (2022). This paper presents another example of an assay that combines scRNA-seq with STARR-seq.
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This is a summary of: Lalanne, J.-B. et al. Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters. Nat. Methods https://doi.org/10.1038/s41592-024-02260-3 (2024).
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Quantitative profiling of regulatory DNA activity at single-cell resolution. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02261-2
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DOI: https://doi.org/10.1038/s41592-024-02261-2
