Functional phenotyping of genomic variants using joint multiomic single-cell DNA–RNA sequencing
Genetic variants (both coding and noncoding) can impact gene function and expression, driving disease mechanisms such as cancer progression. The systematic study of endogenous genetic variants is hindered by inefficient precision editing tools, combined with technical limitations in confidently linking genotypes to gene expression at single-cell resolution. We developed single-cell DNA-RNA sequencing (SDR-seq) to simultaneously profile up to 480 genomic DNA loci and genes in thousands of single cells, enabling accurate determination of coding and noncoding variant zygosity alongside associated gene expression changes. Using SDR-seq, we associate coding and noncoding variants with distinct gene expression in human induced pluripotent stem cells. Furthermore, we demonstrate that in primary B cell lymphoma samples, cells with a higher mutational burden exhibit elevated B cell receptor signaling and tumorigenic gene expression. SDR-seq provides a powerful platform to dissect regulatory mechanisms encoded by genetic variants, advancing our understanding of gene expression regulation and its implications for disease.
Authors
- Lars Michael Steinmetz (ORCID: https://orcid.org/0000-0002-3962-2865)
- Donnacha Fitzgerald (ORCID: https://orcid.org/0000-0003-4927-7484)
- Anastasiia Korosteleva (ORCID: https://orcid.org/0000-0002-5326-9471)
- John A. Hawkins (ORCID: https://orcid.org/0000-0002-2943-9397)
- Moritz Kueblbeck (ORCID: https://orcid.org/0000-0001-6178-7140)
- Wolfgang K. Huber (ORCID: https://orcid.org/0000-0002-0474-2218)
- Judith B. Zaugg (ORCID: https://orcid.org/0000-0001-8324-4040)
- Mikael Marttinen (ORCID: https://orcid.org/0000-0001-5861-4601)
- Sascha Dietrich (ORCID: https://orcid.org/0000-0002-0648-1832)
- Dominik Lindenhofer (ORCID: https://orcid.org/0000-0001-8838-7163)
- Umut Yildiz
- Kyung‐Min Noh (ORCID: https://orcid.org/0000-0002-0708-787X)
- Julia Bauman (ORCID: https://orcid.org/0000-0001-9488-529X)
- Oliver Stegle (ORCID: https://orcid.org/0000-0002-8818-7193)
- Hyo Jin Jung
Institutions
- European Bioinformatics Institute (GB)
- Tampere University (FI)
- German Cancer Research Center (DE)
- University of Basel (CH)
- Aarhus University (DK)
- Heidelberg University (DE)
- University Hospital Heidelberg (DE)
- University Hospital of Basel (CH)
- Düsseldorf University Hospital (DE)
- German Centre for Cardiovascular Research (DE)
- Stanford Medicine (US)
- European Molecular Biology Laboratory (DE)
- European Molecular Biology Laboratory (DE)
- Heinrich Heine University Düsseldorf (DE)
- Stanford University (US)
Publication Details
- Journal
- Nature Methods
- Published
- 2025-09-01
- DOI
- https://doi.org/10.1038/s41592-025-02805-0
- Citations
- 10
- Primary Topic
- CRISPR and Genetic Engineering
- Type
- article
- Field-Weighted Citation Impact
- 8.06
Funders
- Human Frontier Science Program