Integrating technologies for comparing 3D gene expression domains in the developing chick limb

Abstract

Chick embryos are good models for vertebrate development due to their accessibility and manipulability. Recent large increases in available genomic data from both whole genome sequencing and EST projects provide opportunities for identifying many new developmentally important chicken genes. Traditional methods of documenting when and where specific genes are expressed in embryos using wholemount and section in-situ hybridisation do not readily allow appreciation of 3-dimensional (3D) patterns of expression, but this can be accomplished by the recently developed microscopy technique, Optical Projection Tomography (OPT). Here we show that OPT data on the developing chick wing from different labs can be reliably integrated into a common database, that OPT is efficient in capturing 3D gene expression domains and that such domains can be meaningfully compared. Novel protocols are used to compare 3D expression domains of 7 genes known to be involved in chick wing development. This reveals previously unappreciated relationships and demonstrates the potential, using modern genomic resources, for building a large scale 3D atlas of gene expression. Such an atlas could be extended to include other types of data, such as fate maps, and the approach is also more generally applicable to embryos, organs and tissues.

Assembling models of embryo development: Image analysis and the construction of digital atlases

“…Quail (Ruffins et al, 2007) and chicken (Fisher et al, 2008;Fisher et al, 2011) are also used as vertebrate models and have interesting features for experimental embryology. The embryo can develop outside the egg, is quite well amenable to in vivo imaging ("Imaging modalities" section) and the construction of atlases with cellular resolution (see "Spatial scopes and resolutions" section).…”

“…Working at the mesoscopic scale of the multicellular structure is less demanding and has already provided useful information (Fisher et al, 2008;Frise et al, 2010).…”

“…Genomewide atlases (Fisher et al, 2008;Richardson et al, 2010) integrate gene expression patterns and multilevel information from various sources into anatomical atlases (Fig. 2D).…”

Live optical projection tomography

“…The range of species successfully imaged now includes human, 9 mouse, 10,11 chick, 12 reptile species, 13 zebrafish, 14 Drosophila 15 and Arabidopsis. 16 Mouse embryos are routinely imaged at E9.5 up to E12.5, 17 and, for older specimens, organs in isolation are scanned, for example, the developing limb 18 or brain 19 at E14.5.…”

Three-Dimensional (3D) Visualisation of the Cardiovascular System of Mouse Embryos and Fetus

“…OPT was introduced 2002 by James Sharp [68] (see also http://genex.hgu.mrc.ac.uk/OPT_Microscopy/optwebsite/fro ntpage/index.htm) and became an immediate success [69][70][71][72][73][74][75]. Within a few years it was commercialised and relatively easy to handle OPT scanners can be purchased from several companies.…”