Research article

A systematic screen for genes expressed in definitive endoderm by Serial Analysis of Gene Expression (SAGE)

Juan Hou¹ , Anita M Charters² , Sam C Lee¹ , Yongjun Zhao² , Mona K Wu¹ , Steven JM Jones^2,3 , Marco A Marra^2,3 and Pamela A Hoodless^1,3,4

¹Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, Canada

²Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada

³Department of Medical Genetics, University of British Columbia, Vancouver, Canada

⁴Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10^th Avenue, Vancouver, BC, V5Z 1L3, Canada

author email corresponding author email

BMC Developmental Biology 2007, 7:92doi:10.1186/1471-213X-7-92

Published:	2 August 2007

Abstract

Background

The embryonic definitive endoderm (DE) gives rise to organs of the gastrointestinal and respiratory tract including the liver, pancreas and epithelia of the lung and colon. Understanding how DE progenitor cells generate these tissues is critical to understanding the cause of visceral organ disorders and cancers, and will ultimately lead to novel therapies including tissue and organ regeneration. However, investigation into the molecular mechanisms of DE differentiation has been hindered by the lack of early DE-specific markers.

Results

We describe the identification of novel as well as known genes that are expressed in DE using Serial Analysis of Gene Expression (SAGE). We generated and analyzed three longSAGE libraries from early DE of murine embryos: early whole definitive endoderm (0–6 somite stage), foregut (8–12 somite stage), and hindgut (8–12 somite stage). A list of candidate genes enriched for expression in endoderm was compiled through comparisons within these three endoderm libraries and against 133 mouse longSAGE libraries generated by the Mouse Atlas of Gene Expression Project encompassing multiple embryonic tissues and stages. Using whole mount in situ hybridization, we confirmed that 22/32 (69%) genes showed previously uncharacterized expression in the DE. Importantly, two genes identified, Pyy and 5730521E12Rik, showed exclusive DE expression at early stages of endoderm patterning.

Conclusion

The high efficiency of this endoderm screen indicates that our approach can be successfully used to analyze and validate the vast amount of data obtained by the Mouse Atlas of Gene Expression Project. Importantly, these novel early endoderm-expressing genes will be valuable for further investigation into the molecular mechanisms that regulate endoderm development.