Single cell RNA-seq and ATAC-seq indicate critical roles of Isl1 and Nkx2-5 for cardiac progenitor cell transition states and lineage settlement

Abstract

SUMMARYFormation and segregation of cell lineages building the vertebrate heart have been studied extensively by genetic cell tracing techniques and by analysis of single marker gene expression but the underlying gene regulatory networks driving cell fate transitions during early cardiogenesis are only partially understood. Here, we comprehensively characterized mouse cardiac progenitor cells (CPC) marked by Nkx2-5 and Isl1 expression from E7.5 to E9.5 using single-cell RNA sequencing. By leveraging on cell-to-cell heterogeneity, we identified different previously unknown cardiac sub-populations. Reconstruction of the developmental trajectory revealed that Isl1+ CPC represent a transitional cell population maintaining a prolonged multipotent state, whereas extended expression of Nkx2-5 commits CPC to a unidirectional cardiomyocyte fate. Furthermore, we show that CPC fate transitions are associated with distinct open chromatin states, which critically depend 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.

Single-cell transcriptome analysis during cardiogenesis reveals basis for organ level developmental anomalies

“…Human mutations in essential transcription factors and signaling proteins point to key nodes in regulating distinct heart regions but understanding how gene regulatory network disruption in individual cells contributes to CHD remains unknown. Early efforts to map cardiogenesis at the single-cell level by sequencing hundreds of cells were consistent with recognized heterogeneity of the major cell types [8][9][10] . However, to gain sufficient resolution to interrogate smaller pools of cellular subtypes required for cardiogenesis, and to investigate gene network disruption in those cell subsets, it may be necessary to study tens of thousands of cells, recognizing that only 1-2 % are specifically disrupted in disease.…”

Function of the Stem Cell Transcription Factor SALL4 in Hematopoiesis

“…SALL4 appears to be unique among the core ESC pluripotency regulators because it is also expressed in non-ESC stem cell fractions where Oct4 and/or Nanog are silenced. These include XEN cells, mesodermal progenitor cells [35], embryonic cardiac progenitor cells [36], fetal liver stem/progenitor cells [27], and adult stem cells such as bone marrow HSCs/HPCs [37]. In these cells, SALL4 regulates downstream networks in a cell type-specific manner.…”

A novel algorithm for the collective integration of single cell RNA-seq during embryogenesis

“…Single cell RNA-seq provides unprecedented opportunities to study the complex cellular dynamics during the entire embryonic developmental process by profiling the transcriptomes of single cells, from the zygote to the postnatal stage[1–9]. Due to the heterogeneity of underlying cell populations, separate studies usually focus on specific embryonic regions or subpopulations of cells that express specific gene markers, during a relatively narrow developmental window (e.g.…”