Novel genes and functional relationships in the adult mouse gastrointestinal tract identified by microarray analysis.
OBJECTIVE
A genome-level understanding of the molecular basis of segmental gene expression along the anterior-posterior (A-P) axis of the mammalian gastrointestinal (GI) tract is lacking. We hypothesized that functional patterning along the A-P axis of the GI tract could be defined at the molecular level by analyzing expression profiles of large numbers of genes.


METHODS
Incyte GEM1 microarrays containing 8638 complementary DNAs (cDNAs) were used to define expression profiles in adult mouse stomach, duodenum, jejunum, ileum, cecum, proximal colon, and distal colon. Highly expressed cDNAs were classified based on segmental expression patterns and protein function.


RESULTS
571 cDNAs were expressed 2-fold higher than reference in at least 1 GI tissue. Most of these genes displayed sharp segmental expression boundaries, the majority of which were at anatomically defined locations. Boundaries were particularly striking for genes encoding proteins that function in intermediary metabolism, transport, and cell-cell communication. Genes with distinctive expression profiles were compared with mouse and human genomic sequence for promoter analysis and gene discovery.


CONCLUSIONS
The anatomically defined organs of the GI tract (stomach, small intestine, colon) can be distinguished based on a genome-level analysis of gene expression profiles. However, distinctions between various regions of the small intestine and colon are much less striking. We have identified novel genes not previously known to be expressed in the adult GI tract. Identification of genes coordinately regulated along the A-P axis provides a basis for new insights and gene discovery relevant to GI development, differentiation, function, and disease.
Bates
Michael D
MD
Division of Gastroenterology, Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA. michael.bates@chmcc.org
Erwin
Christopher R
CR
Sanford
L Philip
LP
Wiginton
Dan
D
Bezerra
Jorge A
JA
Schatzman
Lynn C
LC
Jegga
Anil G
AG
Ley-Ebert
Cathy
C
Williams
Sarah S
SS
Steinbrecher
Kris A
KA
Warner
Brad W
BW
Cohen
Mitchell B
MB
Aronow
Bruce J
BJ
D000818:Animals; D004064:Digestive System / Q000378:metabolism*; D005786:Gene Expression Regulation; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis