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

Fernando H Biase; Qiuyang Wu; Riccardo Calandrelli; Marcelo Rivas-Astroza; Shuigeng Zhou; Zhen Chen; Sheng Zhong

doi:10.1016/j.isci.2018.08.009

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

iScience. 2018 Sep 28:7:16-29. doi: 10.1016/j.isci.2018.08.009. Epub 2018 Aug 16.

Authors

Fernando H Biase¹, Qiuyang Wu², Riccardo Calandrelli¹, Marcelo Rivas-Astroza¹, Shuigeng Zhou³, Zhen Chen⁴, Sheng Zhong⁵

Affiliations

¹ Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA.
² Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA; Department of Computer Science and Technology, Tongji University, Shanghai 201804, China.
³ School of Computer Science, Fudan University, Shanghai 200433, China.
⁴ Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA 91010, USA.
⁵ Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA. Electronic address: szhong@ucsd.edu.

Abstract

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.

Keywords: Cell fate; Lineage tracing; Preimplantation; Single cell; Transposon.

Abstract

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