Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans

Denis Dupuy; Nicolas Bertin; César A. Hidalgo; Kavitha Venkatesan; Domena Tu; David Lee; Jennifer Rosenberg; Nenad Svrzikapa; Aurélie Blanc; Alain Carnec; Anne Ruxandra Carvunis; Rock Pulak; Jane Shingles; John Reece-Hoyes; Rebecca Hunt-Newbury; Ryan Viveiros; William A. Mohler; Murat Tasan; Frederick P. Roth; Christian Le Peuch; Ian A. Hope; Robert Johnsen; Donald G. Moerman; Albert László Barabási; David Baillie; Marc Vidal

doi:10.1038/nbt1305

Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans

Denis Dupuy, Nicolas Bertin, César A. Hidalgo, Kavitha Venkatesan, Domena Tu, David Lee, Jennifer Rosenberg, Nenad Svrzikapa, Aurélie Blanc, Alain Carnec, Anne Ruxandra Carvunis, Rock Pulak, Jane Shingles, John Reece-Hoyes, Rebecca Hunt-Newbury, Ryan Viveiros, William A. Mohler, Murat Tasan, Frederick P. Roth, Christian Le PeuchIan A. Hope, Robert Johnsen, Donald G. Moerman, Albert László Barabási^*, David Baillie, Marc Vidal

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract (may include machine translation)

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 ∼900 predicted C. elegans promoters (∼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.

Original language	English
Pages (from-to)	663-668
Number of pages	6
Journal	Nature Biotechnology
Volume	25
Issue number	6
DOIs	https://doi.org/10.1038/nbt1305
State	Published - Jun 2007
Externally published	Yes

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Dupuy, D., Bertin, N., Hidalgo, C. A., Venkatesan, K., Tu, D., Lee, D., Rosenberg, J., Svrzikapa, N., Blanc, A., Carnec, A., Carvunis, A. R., Pulak, R., Shingles, J., Reece-Hoyes, J., Hunt-Newbury, R., Viveiros, R., Mohler, W. A., Tasan, M., Roth, F. P., ... Vidal, M. (2007). Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nature Biotechnology, 25(6), 663-668. https://doi.org/10.1038/nbt1305

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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 ∼900 predicted C. elegans promoters (∼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.",

author = "Denis Dupuy and Nicolas Bertin and Hidalgo, {C{\'e}sar A.} and Kavitha Venkatesan and Domena Tu and David Lee and Jennifer Rosenberg and Nenad Svrzikapa and Aur{\'e}lie Blanc and Alain Carnec and Carvunis, {Anne Ruxandra} and Rock Pulak and Jane Shingles and John Reece-Hoyes and Rebecca Hunt-Newbury and Ryan Viveiros and Mohler, {William A.} and Murat Tasan and Roth, {Frederick P.} and {Le Peuch}, Christian and Hope, {Ian A.} and Robert Johnsen and Moerman, {Donald G.} and Barab{\'a}si, {Albert L{\'a}szl{\'o}} and David Baillie and Marc Vidal",

year = "2007",

month = jun,

doi = "10.1038/nbt1305",

language = "English",

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Dupuy, D, Bertin, N, Hidalgo, CA, Venkatesan, K, Tu, D, Lee, D, Rosenberg, J, Svrzikapa, N, Blanc, A, Carnec, A, Carvunis, AR, Pulak, R, Shingles, J, Reece-Hoyes, J, Hunt-Newbury, R, Viveiros, R, Mohler, WA, Tasan, M, Roth, FP, Le Peuch, C, Hope, IA, Johnsen, R, Moerman, DG, Barabási, AL, Baillie, D & Vidal, M 2007, 'Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans', Nature Biotechnology, vol. 25, no. 6, pp. 663-668. https://doi.org/10.1038/nbt1305

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T1 - Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans

AU - Dupuy, Denis

AU - Bertin, Nicolas

AU - Hidalgo, César A.

AU - Venkatesan, Kavitha

AU - Tu, Domena

AU - Lee, David

AU - Rosenberg, Jennifer

AU - Svrzikapa, Nenad

AU - Blanc, Aurélie

AU - Carnec, Alain

AU - Carvunis, Anne Ruxandra

AU - Pulak, Rock

AU - Shingles, Jane

AU - Reece-Hoyes, John

AU - Hunt-Newbury, Rebecca

AU - Viveiros, Ryan

AU - Mohler, William A.

AU - Tasan, Murat

AU - Roth, Frederick P.

AU - Le Peuch, Christian

AU - Hope, Ian A.

AU - Johnsen, Robert

AU - Moerman, Donald G.

AU - Barabási, Albert László

AU - Baillie, David

AU - Vidal, Marc

PY - 2007/6

Y1 - 2007/6

N2 - 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 ∼900 predicted C. elegans promoters (∼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.

AB - 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 ∼900 predicted C. elegans promoters (∼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.

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DO - 10.1038/nbt1305

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EP - 668

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 6

ER -

Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans

Abstract (may include machine translation)

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