Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

Guangshuai Jia,Yonggang Zhou,Michail Yekelchyk,Thomas Braun,Jens Preussner,Xuejun Yuan,Carsten Kuenne,Sarah Teichmann,Stefan Guenther,Mario Looso,Xi Chen

doi:10.1038/s41467-018-07307-6

Abstract

Formation and segregation of cell lineages forming the heart have been studied extensively but the underlying gene regulatory networks and epigenetic changes driving cell fate transitions during early cardiogenesis are still only partially understood. Here, we comprehensively characterize mouse cardiac progenitor cells (CPCs) marked by Nkx2-5 and Isl1 expression from E7.5 to E9.5 using single-cell RNA sequencing and transposase-accessible chromatin profiling (ATAC-seq). By leveraging on cell-to-cell transcriptome and chromatin accessibility heterogeneity, we identify different previously unknown cardiac subpopulations. Reconstruction of developmental trajectories reveal that multipotent Isl1+ CPC pass through an attractor state before separating into different developmental branches, whereas extended expression of Nkx2-5 commits CPC to an unidirectional cardiomyocyte fate. Furthermore, we show that CPC fate transitions are associated with distinct open chromatin states critically depending on Isl1 and Nkx2-5. Our data provide a model of transcriptional and epigenetic regulations during cardiac progenitor cell fate decisions at single-cell resolution.

Highlights

Formation and segregation of cell lineages forming the heart have been studied extensively but the underlying gene regulatory networks and epigenetic changes driving cell fate transitions during early cardiogenesis are still only partially understood
Cell fate mapping experiments demonstrated that cardiac progenitor cells (CPCs) in the mouse form from Mesp1+ cells that leave the primitive streak during gastrulation at E6.5
We demonstrate by scRNA-seq and chromatin accessibility mapping that forced expression of Nkx[2,3,4,5] is associated with de novo chromatin opening and primes the cardiomyocyte fate

Summary

Introduction

Formation and segregation of cell lineages forming the heart have been studied extensively but the underlying gene regulatory networks and epigenetic changes driving cell fate transitions during early cardiogenesis are still only partially understood. We comprehensively characterize mouse cardiac progenitor cells (CPCs) marked by Nkx[2,3,4,5] and Isl[1] expression from E7.5 to E9.5 using single-cell RNA sequencing and transposase-accessible chromatin profiling (ATAC-seq). We show that CPC fate transitions are associated with distinct open chromatin states critically depending on Isl[1] and Nkx[2,3,4,5]. Single cell ATAC-seq (assay for transposase-accessible chromatin using sequencing) offers a similar power of resolution and generates additional information about gene regulatory processes[12,13]. We demonstrate by scRNA-seq and chromatin accessibility mapping that forced expression of Nkx[2,3,4,5] is associated with de novo chromatin opening and primes the cardiomyocyte fate

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Results

Conclusion