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Human Molecular Genetics Advance Access published online on February 9, 2005
Human Molecular Genetics, doi:10.1093/hmg/ddi083
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© The Author 2005. Published by Oxford University Press. All rights reserved

Article

Gene expression in pharyngeal arch 1 during human embryonic development

Juanliang Cai 1, David Ash 1, Lori E. Kotch 1, Ethylin Wang Jabs 2*, Tania Attie-Bitach 3, Joelle Auge 3, Geraldine Mattei 3, Heather Etchevers 3, Michel Vekemans 3, Yulia Korshunova 4, Rose Tidwell 4, David N. Messina 4, Julia B. Winston 4, and Michael Lovett 4

1 Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
2 McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University, 733 N Broadway, Room 419, Baltimore, MD 21205, USA
3 Department of Genetics and INSERM U-393, Hopital Necker Enfants Malades, 75743 Paris, France
4 Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA

* To whom correspondence should be addressed.
Ethylin Wang Jabs, E-mail: ejabs1{at}jhem.jhmi.edu


  Abstract

Craniofacial abnormalities are one of the most common birth defects in humans, but little is known about the human genes that control these important developmental processes. To identify relevant genes, we analyzed transcription profiles of human pharyngeal arch 1 (PA1), a conserved embryonic structure that develops into the palate and jaw. Using microdissected, normal human craniofacial structures, we constructed 12 SAGE (Serial Analysis of Gene Expression) libraries and sequenced 606,532 tags. We also performed Affymetrix microarray analysis on 25 craniofacial targets. Our data revealed not only genes "enriched" or differentially expressed in PA1 during 4th and 5th week of human development, but also 6,927 genes newly identified to be expressed in human PA1. Many of these genes are involved in biosynthetic processes and have binding function and catalytic activity. We compared expression profiles of human genes with those of mouse homologs to look for genes more specific to human craniofacial development and found 766 genes expressed in human, but not mouse PA1. We also identified 1,408 genes that were expressed in mouse as well as human PA1 and could be useful in creating mouse models for human conditions. We confirmed conservation of some human PA1 expression patterns in mouse embryonic samples with whole mount in situ hybridization and real-time RT-PCR. This comprehensive approach to expression profiling gives insights into the early development of the craniofacial region, and provides markers for developmental structures and candidate genes including SET and CCT3 for diseases such as orofacial clefting and micrognathia.


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