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bioRxiv · 10.1101/829853

Diversification of Reprogramming Trajectories Revealed by Parallel Single-cell Transcriptome and Chromatin Accessibility Sequencing

Xing, Q.·Farran, C. E.·Gautam, P.·Chuah, Y. S.·Warrier, T.·Toh, C.-X. D.·Kang, N.-Y.·Sugii, S.·Chang, Y.-T.·Xu, J.·Collins, J.·Daley, G.·Li, H.·Zhang, L.-F.·Loh, Y.-H.
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Abstract

To unravel the mechanism of human cellular reprogramming process at single-cell resolution, we performed parallel scRNA-Seq and scATAC-Seq analysis. Our analysis reveals that the cells undergoing reprogramming proceed in an asynchronous trajectory and diversify into heterogeneous sub-populations. BDD2-C8 fluorescent probe staining and negative staining for CD13, CD44 and CD201 markers, could enrich for the GDF3+ early reprogrammed cells. Combinatory usage of the surface markers enables the fine segregation of the early-intermediate cells with diverse reprogramming propensities. scATAC-Seq analysis further uncovered the genomic partitions and transcription factors responsible for the regulatory phasing of reprogramming process. Binary choice between a FOSL1 or a TEAD4-centric regulatory network determines the outcome of a successful reprogramming. Altogether, our study illuminates the multitude of diverse routes transversed by individual reprogramming cells and presents an integrative roadmap for identifying the mechanistic part-list of the reprogramming machinery.

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Xing, Q., Farran, C. E., Gautam, P., Chuah, Y. S., Warrier, T., Toh, C.-X. D., Kang, N.-Y., Sugii, S., Chang, Y.-T., Xu, J., Collins, J., Daley, G., Li, H., Zhang, L.-F., Loh, Y.-H.. 2019-11-04. Diversification of Reprogramming Trajectories Revealed by Parallel Single-cell Transcriptome and Chromatin Accessibility Sequencing. https://doi.org/10.1101/829853

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