A 3D molecular atlas of the chick embryonic heart

Dev Biol. 2019 Dec 1;456(1):40-46. doi: 10.1016/j.ydbio.2019.07.003. Epub 2019 Jul 5.

Abstract

We present a detailed analysis of gene expression in the 2-day (HH12) embryonic chick heart. RNA-seq of 13 micro-dissected regions reveals regionalised expression of 15,570 genes. Of these, 132 were studied by in situ hybridisation and a subset (38 genes) was mapped by Optical Projection Tomography or serial sectioning to build a detailed 3-dimensional atlas of expression. We display this with a novel interactive 3-D viewer and as stacks of sections, revealing the boundaries of expression domains and regions of overlap. Analysis of the expression domains also defines some sub-regions distinct from those normally recognised by anatomical criteria at this stage of development, such as a previously undescribed subdivision of the atria into two orthogonal sets of domains (dorsoventral and left-right). We also include a detailed comparison of expression in the chick with the mouse and other species.

Keywords: Cardiac; Cardiovascular; Chick embryo; Molecular anatomy; RNAseq; Transcriptome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anatomy, Artistic / methods
  • Animals
  • Atlases as Topic
  • Chick Embryo
  • Chickens / genetics
  • Gene Expression / genetics
  • Gene Expression Regulation, Developmental / genetics
  • Heart / anatomy & histology*
  • Heart / embryology*
  • Imaging, Three-Dimensional / methods*
  • In Situ Hybridization / methods