Whole-organism clone tracing using single-cell sequencing

• Published in: Nature (London) 2018-04, Vol.556 (7699), p.108-112
• Main Authors: Alemany, Anna, Florescu, Maria, Baron, Chloé S., Peterson-Maduro, Josi, van Oudenaarden, Alexander
• Format: Article
• Language: English
• Subjects: 38/91; 45/23; 631/136; 631/1647/2017; Animal Fins - cytology; Animals; Biocompatibility; Biomedical materials; Blood cells; Brain; Brain - cytology; Cell Lineage - genetics; Cell Tracking - methods; Clone Cells - cytology; Clone Cells - metabolism; Cloning; CRISPR; CRISPR-Cas Systems - genetics; Danio rerio; DNA sequencing; Embryogenesis; Embryonic growth stage; Embryonic Stem Cells - cytology; Embryonic Stem Cells - metabolism; Eye - cytology; Female; Fluorescence; Gene expression; Genes, Reporter - genetics; Genetic code; Genomes; Glial stem cells; Hematopoietic Stem Cells - cytology; Hematopoietic Stem Cells - metabolism; Humanities and Social Sciences; Immune system; letter; Male; Mesenchyme; Methods; Microsatellites; multidisciplinary; Multipotent Stem Cells - cytology; Multipotent Stem Cells - metabolism; Nervous system; Organ Specificity; Organs; Osteoprogenitor cells; Physiological aspects; Proteins; Regeneration; Scars; Science; Sequence Analysis - methods; Single-Cell Analysis; Stem cells; Transcriptome; Whole Body Imaging; Zebrafish; Zebrafish - anatomy & histology; Zebrafish - embryology; Zebrafish - genetics
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature25969

A single-cell sequencing method is developed that uses transcriptomics and CRISPR–Cas9 technology to investigate clonal relationships in cells present in different zebrafish tissues. Tracing single cells from embryo to adult Determining the adult fate of progenitor cells present during embryonic development is a challenging task because it requires simultaneous knowledge about the lineage and identity of the cells at a single-cell level. Alexander van Oudenaarden and colleagues have developed a new method to tackle this challenge. ScarTrace relies on single-cell transcriptome sequencing and barcodes ('scars') introduced by CRISPR–Cas9 in individual progenitor cells. The authors use ScarTrace to investigate lineage relationships in cells present in different zebrafish tissues. In the future, such a method could make it possible to match all embryonic cell types to all adult cell types, and to reconstruct how the body emerges from a single cell. Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development 1 , 2 , monitoring the heritable expression of genetically encoded fluorescent proteins 3 and, more recently, using next-generation sequencing technologies that exploit somatic mutations 4 , microsatellite instability 5 , transposon tagging 6 , viral barcoding 7 , CRISPR–Cas9 genome editing 8 , 9 , 10 , 11 , 12 , 13 and Cre– loxP recombination 14 . Single-cell transcriptomics 15 provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors,