Transcriptional and epigenetic regulations of cell fate decisions in early heart development revealed by single-cell analysis
Guangshuai Jia*, Jens Preussner*, Stefan Guether, Xuejun Yuan, Michail Yekelchyk, Ann Atzbergen, Yonggang Zhou and Thomas Braun
Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
The long-lasting challenges for understanding heart development are to characterize cell fate transition, specification and hierarchical lineage descendants of cardiac progenitor cells, and underlying gene regulatory networks that orchestrate such processes. However, the cell fate decisions of cardiac progenitor cells during cardiogenesis remain unclear due to limited cell numbers. Here, we comprehensively analyze ~1,700 of the first and second heart field cardiac progenitor cells across embryonic day E7.5 to E9.5 marked by Nkx2.5 and Isl1 respectively by single-cell RNA sequencing, representing an unprecedented transcriptome-wide in vivo interrogation of mouse early heart development. By identifying heterogeneous sub-populations and reconstructing developmental trajectories, we show Nkx2.5+ cardiac progenitor cells are unipotent towards a cardiomyocyte fate, whereas Isl1+ cardiac progenitor cells maintain a prolonged multipotent state, comprising a transitional cell population. Forced expression of Nkx2.5 in Isl1+ lineage eliminates the multipotency of Isl1+ cells. By harnessing ATAC-seq approach to measure chromatin accessibility, we show the lineage determinants, namely cardiac transcription factors progressively overcome epigenetic barriers to achieve open chromatin states associated with elevated expression. Moreover, using an Isl1 knockout mouse, we demonstrate the key role of Isl1 in subpopulation and lineage establishment in the second heart field through shaping the landscape of accessible chromatin. Our data not only provides a framework for studying early cardiogenesis at single-cell resolution which may facilitate congenital heart disease diagnosis and therapies, but also establishes a general model of transcriptional and epigenetic regulations in cardiac progenitor cell fate decisions.