Single-Cell Resolution of Temporal Gene Expression during Heart Development

Dev Cell. 2016 Nov 21;39(4):480-490. doi: 10.1016/j.devcel.2016.10.001. Epub 2016 Nov 10.


Activation of complex molecular programs in specific cell lineages governs mammalian heart development, from a primordial linear tube to a four-chamber organ. To characterize lineage-specific, spatiotemporal developmental programs, we performed single-cell RNA sequencing of >1,200 murine cells isolated at seven time points spanning embryonic day 9.5 (primordial heart tube) to postnatal day 21 (mature heart). Using unbiased transcriptional data, we classified cardiomyocytes, endothelial cells, and fibroblast-enriched cells, thus identifying markers for temporal and chamber-specific developmental programs. By harnessing these datasets, we defined developmental ages of human and mouse pluripotent stem-cell-derived cardiomyocytes and characterized lineage-specific maturation defects in hearts of mice with heterozygous mutations in Nkx2.5 that cause human heart malformations. This spatiotemporal transcriptome analysis of heart development reveals lineage-specific gene programs underlying normal cardiac development and congenital heart disease.

Keywords: ECM; Nkx2.5; RNA-seq; atria; cardiogenesis; cardiomyocyte maturation; heart; single cell; ventricle.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation / genetics
  • Cell Lineage / genetics
  • Endothelial Cells / cytology
  • Endothelial Cells / metabolism
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • Haploinsufficiency / genetics
  • Heart / embryology*
  • Heart Atria / cytology
  • Heart Ventricles / cytology
  • Homeobox Protein Nkx-2.5 / metabolism
  • Humans
  • Mice
  • Myocytes, Cardiac / cytology
  • Myocytes, Cardiac / metabolism
  • Sequence Analysis, RNA
  • Single-Cell Analysis / methods*
  • Time Factors
  • Transcriptome / genetics


  • Homeobox Protein Nkx-2.5
  • Nkx2-5 protein, mouse