Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos

• Published in: iScience Vol. 7; pp. 16 - 29
• Main Authors: Biase, Fernando H, Wu, Qiuyang, Calandrelli, Riccardo, Rivas-Astroza, Marcelo, Zhou, Shuigeng, Chen, Zhen, Zhong, Sheng
• Format: Journal Article
• Language: English
• Published: United States Elsevier 28.09.2018
• Subjects: Single cell; Preimplantation; Cell fate; Lineage tracing; Transposon
• ISSN: 2589-0042; 2589-0042
• DOI: 10.1016/j.isci.2018.08.009

We developed the Rainbow-seq technology to trace cell division history and reveal single-cell transcriptomes. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA sequencing (RNA-seq) experiment to simultaneously decode the lineage marker genes and read single-cell transcriptomes. We triggered lineage tracking in each blastomere at the 2-cell stage, observed microscopically inequivalent contributions of the progeny to the two embryonic poles at the blastocyst stage, and analyzed every single cell at either 4- or 8-cell stage with deep paired-end sequencing of full-length transcripts. Although lineage difference was not marked unequivocally at a single-gene level, it became clear when the transcriptome was analyzed as a whole. Moreover, several groups of novel transcript isoforms with embedded repeat sequences exhibited lineage difference, suggesting a possible link between DNA demethylation and cell fate decision. Rainbow-seq bridged a critical gap between division history and single-cell RNA-seq assays.