title: Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans.
abstract: 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.
authors.affiliation: Center for Cancer Systems Biology, Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Denis
authors.initials: D
authors.lastname: Dupuy
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bertin
authors.forename: César A
authors.initials: CA
authors.lastname: Hidalgo
authors.forename: Kavitha
authors.initials: K
authors.lastname: Venkatesan
authors.forename: Domena
authors.initials: D
authors.lastname: Tu
authors.forename: David
authors.initials: D
authors.lastname: Lee
authors.forename: Jennifer
authors.initials: J
authors.lastname: Rosenberg
authors.forename: Nenad
authors.initials: N
authors.lastname: Svrzikapa
authors.forename: Aurélie
authors.initials: A
authors.lastname: Blanc
authors.forename: Alain
authors.initials: A
authors.lastname: Carnec
authors.forename: Anne-Ruxandra
authors.initials: AR
authors.lastname: Carvunis
authors.forename: Rock
authors.initials: R
authors.lastname: Pulak
authors.forename: Jane
authors.initials: J
authors.lastname: Shingles
authors.forename: John
authors.initials: J
authors.lastname: Reece-Hoyes
authors.forename: Rebecca
authors.initials: R
authors.lastname: Hunt-Newbury
authors.forename: Ryan
authors.initials: R
authors.lastname: Viveiros
authors.forename: William A
authors.initials: WA
authors.lastname: Mohler
authors.forename: Murat
authors.initials: M
authors.lastname: Tasan
authors.forename: Frederick P
authors.initials: FP
authors.lastname: Roth
authors.forename: Christian
authors.initials: C
authors.lastname: Le Peuch
authors.forename: Ian A
authors.initials: IA
authors.lastname: Hope
authors.forename: Robert
authors.initials: R
authors.lastname: Johnsen
authors.forename: Donald G
authors.initials: DG
authors.lastname: Moerman
authors.forename: Albert-László
authors.initials: AL
authors.lastname: Barabási
authors.forename: David
authors.initials: D
authors.lastname: Baillie
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
mesh_terms: 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
chemical_list: D029742:Caenorhabditis elegans Proteins; D020543:Proteome