Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans.
Differential regulation of gene expression is essential for cell fate specification in metazoans. Characterizing the transcriptional activity of gene promoters, in time and in space, is therefore a critical step toward understanding complex biological systems. Here we present an in vivo spatiotemporal analysis for approximately 900 predicted C. elegans promoters (approximately 5% of the predicted protein-coding genes), each driving the expression of green fluorescent protein (GFP). Using a flow-cytometer adapted for nematode profiling, we generated 'chronograms', two-dimensional representations of fluorescence intensity along the body axis and throughout development from early larvae to adults. Automated comparison and clustering of the obtained in vivo expression patterns show that genes coexpressed in space and time tend to belong to common functional categories. Moreover, integration of this data set with C. elegans protein-protein interactome data sets enables prediction of anatomical and temporal interaction territories between protein partners.
Dupuy
Denis
D
Center for Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
Bertin
Nicolas
N
Hidalgo
César A
CA
Venkatesan
Kavitha
K
Tu
Domena
D
Lee
David
D
Rosenberg
Jennifer
J
Svrzikapa
Nenad
N
Blanc
Aurélie
A
Carnec
Alain
A
Carvunis
Anne-Ruxandra
AR
Pulak
Rock
R
Shingles
Jane
J
Reece-Hoyes
John
J
Hunt-Newbury
Rebecca
R
Viveiros
Ryan
R
Mohler
William A
WA
Tasan
Murat
M
Roth
Frederick P
FP
Le Peuch
Christian
C
Hope
Ian A
IA
Johnsen
Robert
R
Moerman
Donald G
DG
Barabási
Albert-László
AL
Baillie
David
D
Vidal
Marc
M
D000375:Aging / Q000378:metabolism*; D000818:Animals; D017173:Caenorhabditis elegans / Q000254:growth & development / Q000378:metabolism*; D029742:Caenorhabditis elegans Proteins / Q000502:physiology*; D002874:Chromosome Mapping / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental / Q000502:physiology; D008856:Microscopy, Fluorescence; D011401:Promoter Regions, Genetic / Q000235:genetics*; D020543:Proteome / Q000235:genetics / Q000378:metabolism*; D014018:Tissue Distribution
D029742:Caenorhabditis elegans Proteins; D020543:Proteome