Heart morphogenesis gene regulatory networks revealed by temporal expression analysis

Development. 2017 Oct 1;144(19):3487-3498. doi: 10.1242/dev.154146. Epub 2017 Aug 14.


During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks (GRNs) driving this phase of heart development, during which many congenital heart disease malformations likely arise, we conducted an RNA-seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern, identified transcription factor binding motifs enriched in each cluster, and generated a model GRN for the major gene batteries in heart morphogenesis. This approach predicted hundreds of regulatory interactions and found batteries enriched in specific cell and tissue types, indicating that the approach can be used to narrow the search for novel genetic markers and regulatory interactions. Subsequent analyses confirmed the GRN using two mutants, Tbx5 and nkx2-5, and identified sets of duplicated zebrafish genes that do not show temporal subfunctionalization. This dataset provides an essential resource for future studies on the genetic/epigenetic pathways implicated in congenital heart defects and the mechanisms of cardiac transcriptional regulation.

Keywords: Gene regulatory network; Heart development; RNA-seq; Timecourse; Zebrafish.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Cluster Analysis
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • Gene Regulatory Networks*
  • Genes, Duplicate
  • Heart / embryology*
  • Mice
  • Morphogenesis / genetics*
  • Mutation / genetics
  • Nucleotide Motifs / genetics
  • Organ Specificity / genetics
  • Protein Binding
  • Sequence Analysis, RNA
  • Time Factors
  • Transcription Factors / metabolism
  • Zebrafish / embryology
  • Zebrafish / genetics


  • Transcription Factors