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{
  "pmid": "38724692",
  "doi": "10.1038/s41592-024-02260-3",
  "abstract": "The inability to scalably and precisely measure the activity of developmental cis-regulatory elements (CREs) in multicellular systems is a bottleneck in genomics. Here we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays. The resulting measurement of reporter expression is accurate over multiple orders of magnitude, with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode stabilization via circularization, these scalable single-cell quantitative expression reporters provide high-contrast readouts, analogous to classic in situ assays but entirely from sequencing. Screening >200 regions of accessible chromatin in a multicellular in vitro model of early mammalian development, we identify 13 (8 previously uncharacterized) autonomous and cell-type-specific developmental CREs. We further demonstrate that chimeric CRE pairs generate cognate two-cell-type activity profiles and assess gain- and loss-of-function multicellular expression phenotypes from CRE variants with perturbed transcription factor binding sites. Single-cell quantitative expression reporters can be applied in developmental and multicellular systems to quantitatively characterize native, perturbed and synthetic CREs at scale, with high sensitivity and at single-cell resolution.",
  "journal": "Nature Methods",
  "year": 2024,
  "authors": "Jean‐Benoît Lalanne, Samuel G. Regalado, Silvia Domcke, Diego Calderon, Beth Martin et al.",
  "external_ids": {
    "doi": "10.1038/s41592-024-02260-3",
    "pmid": "38724692"
  },
  "citation_count": 45
}