Transcriptional Regulatory Networks in Saccharomyces cerevisiae

We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, thi...

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Published in	Science (American Association for the Advancement of Science) Vol. 298; no. 5594; pp. 799 - 804
Main Authors	Lee, Tong Ihn, Rinaldi, Nicola J., Robert, François, Odom, Duncan T., Bar-Joseph, Ziv, Gerber, Georg K., Hannett, Nancy M., Harbison, Christopher T., Thompson, Craig M., Simon, Itamar, Zeitlinger, Julia, Jennings, Ezra G., Murray, Heather L., Gordon, D. Benjamin, Ren, Bing, Wyrick, John J., Tagne, Jean-Bosco, Volkert, Thomas L., Fraenkel, Ernest, Gifford, David K., Young, Richard A.
Format	Journal Article
Language	English
Published	Washington, DC American Association for the Advancement of Science 25.10.2002 The American Association for the Advancement of Science
Subjects	Algorithms Biological and medical sciences Brewer's yeast Cell Cycle Cell cycle proteins Cellular biology Coding Computational Biology Control loops cytology DNA, Fungal DNA, Fungal - genetics DNA, Fungal - metabolism Feedback, Physiological Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Profiling Gene expression regulation Gene Expression Regulation, Fungal Genes Genes, Fungal Genetic regulation genetics genome Genome, Fungal Genomes Genomics growth & development metabolism Models, Genetic Molecular and cellular biology Molecular genetics Networks P values Promoter regions Promoter Regions, Genetic Protein Binding Quality Control Regulator genes Research Design Saccharomyces cerevisiae Saccharomyces cerevisiae - cytology Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - growth & development Saccharomyces cerevisiae - metabolism Saccharomyces cerevisiae Proteins Saccharomyces cerevisiae Proteins - genetics Saccharomyces cerevisiae Proteins - metabolism transcription (genetics) transcription factors Transcription Factors - genetics Transcription Factors - metabolism Transcription, Genetic Transcription. Transcription factor. Splicing. Rna processing Transcriptional regulatory elements Yeast Yeasts Fungi Regulation(control) Yeast Transcription Ascomycetes Saccharomyces cerevisiae Thallophyta
Online Access	Get full text
ISSN	0036-8075 1095-9203 1095-9203
DOI	10.1126/science.1075090

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Abstract	We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We use this information to identify network motifs, the simplest units of network architecture, and demonstrate that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators.
AbstractList	We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We use this information to identify network motifs, the simplest units of network architecture, and demonstrate that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators. We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We use this information to identify network motifs, the simplest units of network architecture, and demonstrate that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators. We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in tiring cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We use this information to identify network motifs, the simplest units of network architecture, and demonstrate that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators. We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We use this information to identify network motifs, the simplest units of network architecture, and demonstrate that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators.We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We use this information to identify network motifs, the simplest units of network architecture, and demonstrate that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators.
Audience	Academic
Author	Thompson, Craig M. Young, Richard A. Gifford, David K. Odom, Duncan T. Hannett, Nancy M. Simon, Itamar Fraenkel, Ernest Ren, Bing Lee, Tong Ihn Bar-Joseph, Ziv Jennings, Ezra G. Wyrick, John J. Harbison, Christopher T. Volkert, Thomas L. Tagne, Jean-Bosco Robert, François Zeitlinger, Julia Gerber, Georg K. Murray, Heather L. Rinaldi, Nicola J. Gordon, D. Benjamin
Author_xml	– sequence: 1 givenname: Tong Ihn surname: Lee fullname: Lee, Tong Ihn – sequence: 2 givenname: Nicola J. surname: Rinaldi fullname: Rinaldi, Nicola J. – sequence: 3 givenname: François surname: Robert fullname: Robert, François – sequence: 4 givenname: Duncan T. surname: Odom fullname: Odom, Duncan T. – sequence: 5 givenname: Ziv surname: Bar-Joseph fullname: Bar-Joseph, Ziv – sequence: 6 givenname: Georg K. surname: Gerber fullname: Gerber, Georg K. – sequence: 7 givenname: Nancy M. surname: Hannett fullname: Hannett, Nancy M. – sequence: 8 givenname: Christopher T. surname: Harbison fullname: Harbison, Christopher T. – sequence: 9 givenname: Craig M. surname: Thompson fullname: Thompson, Craig M. – sequence: 10 givenname: Itamar surname: Simon fullname: Simon, Itamar – sequence: 11 givenname: Julia surname: Zeitlinger fullname: Zeitlinger, Julia – sequence: 12 givenname: Ezra G. surname: Jennings fullname: Jennings, Ezra G. – sequence: 13 givenname: Heather L. surname: Murray fullname: Murray, Heather L. – sequence: 14 givenname: D. Benjamin surname: Gordon fullname: Gordon, D. Benjamin – sequence: 15 givenname: Bing surname: Ren fullname: Ren, Bing – sequence: 16 givenname: John J. surname: Wyrick fullname: Wyrick, John J. – sequence: 17 givenname: Jean-Bosco surname: Tagne fullname: Tagne, Jean-Bosco – sequence: 18 givenname: Thomas L. surname: Volkert fullname: Volkert, Thomas L. – sequence: 19 givenname: Ernest surname: Fraenkel fullname: Fraenkel, Ernest – sequence: 20 givenname: David K. surname: Gifford fullname: Gifford, David K. – sequence: 21 givenname: Richard A. surname: Young fullname: Young, Richard A.
BackLink	http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=13991991$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/12399584$$D View this record in MEDLINE/PubMed
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ClassificationCodes	2099 2099425
ContentType	Journal Article
Copyright	Copyright 2002 American Association for the Advancement of Science 2002 INIST-CNRS COPYRIGHT 2002 American Association for the Advancement of Science COPYRIGHT 2002 American Association for the Advancement of Science Copyright American Association for the Advancement of Science Oct 25, 2002
Copyright_xml	– notice: Copyright 2002 American Association for the Advancement of Science – notice: 2002 INIST-CNRS – notice: COPYRIGHT 2002 American Association for the Advancement of Science – notice: COPYRIGHT 2002 American Association for the Advancement of Science – notice: Copyright American Association for the Advancement of Science Oct 25, 2002
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DOI	10.1126/science.1075090
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Snippet	We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in... We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in...
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SubjectTerms	Algorithms Biological and medical sciences Brewer's yeast Cell Cycle Cell cycle proteins Cellular biology Coding Computational Biology Control loops cytology DNA, Fungal DNA, Fungal - genetics DNA, Fungal - metabolism Feedback, Physiological Fundamental and applied biological sciences. Psychology Gene expression Gene Expression Profiling Gene expression regulation Gene Expression Regulation, Fungal Genes Genes, Fungal Genetic regulation genetics genome Genome, Fungal Genomes Genomics growth & development metabolism Models, Genetic Molecular and cellular biology Molecular genetics Networks P values Promoter regions Promoter Regions, Genetic Protein Binding Quality Control Regulator genes Research Design Saccharomyces cerevisiae Saccharomyces cerevisiae - cytology Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - growth & development Saccharomyces cerevisiae - metabolism Saccharomyces cerevisiae Proteins Saccharomyces cerevisiae Proteins - genetics Saccharomyces cerevisiae Proteins - metabolism transcription (genetics) transcription factors Transcription Factors - genetics Transcription Factors - metabolism Transcription, Genetic Transcription. Transcription factor. Splicing. Rna processing Transcriptional regulatory elements Yeast Yeasts
Title	Transcriptional Regulatory Networks in Saccharomyces cerevisiae
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