Evolutionary emergence of the rac3b/ rfng/ sgca regulatory cluster refined mechanisms for hindbrain boundaries formation

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3731-E3740. doi: 10.1073/pnas.1719885115. Epub 2018 Apr 2.


Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cable assembly at hindbrain boundaries. We show that the novel rac3b/rfng/sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis-regulatory interactions. By combining 4C-seq, ATAC-seq, transgenesis, and CRISPR-induced deletions, we characterized this regulatory domain, identifying hindbrain boundary-specific cis-regulatory elements. Our results suggest that the capacity of boundaries to act as an elastic mesh for segregating rhombomeric cells evolved by cooption of critical genes to a novel regulatory block, refining the mechanisms for hindbrain segmentation.

Keywords: cis-regulatory elements; hindbrain boundaries; regulatory landscape; rhombomeres; segmentation.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • Actomyosin / physiology*
  • Animals
  • Body Patterning / genetics
  • CRISPR-Cas Systems
  • Cell Movement
  • Characidae / genetics
  • Characidae / physiology
  • Chromatin / genetics
  • Chromatin / ultrastructure
  • Evolution, Molecular
  • Fishes / classification
  • Fishes / genetics
  • Gene Expression Regulation, Developmental*
  • Morphogenesis
  • Mutagenesis, Site-Directed
  • Neurogenesis
  • Phylogeny
  • Rhombencephalon / embryology*
  • Sarcoglycans / genetics
  • Sarcoglycans / physiology*
  • Species Specificity
  • Zebrafish / embryology*
  • Zebrafish / genetics
  • Zebrafish Proteins / genetics
  • Zebrafish Proteins / physiology*
  • rac GTP-Binding Proteins / genetics
  • rac GTP-Binding Proteins / physiology*


  • Chromatin
  • Sarcoglycans
  • Zebrafish Proteins
  • rfng protein, zebrafish
  • sgca protein, zebrafish
  • Actomyosin
  • rac GTP-Binding Proteins
  • rac3b protein, zebrafish