%0 Journal Article %1 Johnson2007 %A Johnson, David S. %A Mortazavi, Ali %A Myers, Richard M. %A Wold, Barbara %D 2007 %J Science %K Algorithms Amino_Acid_Motifs Binding_Sites Chromatin_Immunoprecipitation DNA,_metabolism DNA-Binding_Proteins,_chemistry/metabolism Gene_Regulatory_Networks Genome,_Human Humans Insulin-Secreting_Cells,_cytology/physiology MicroRNAs,_genetics Neurons,_physiology Promoter_Regions_(Genetics) Protein_Binding Repressor_Proteins,_chemistry/genetics/metabolism Sensitivity_and_Specificity Sequence_Analysis,_DNA Synaptic_Transmission T-Lymphocytes,_metabolism Transcription,_Genetic Transcription_Factors,_chemistry/genetics/metabolism Zinc_Fingers %N 5830 %P 1497-1502 %R 10.1126/science.1141319 %T Genome-wide mapping of in vivo protein-DNA interactions. %U http://dx.doi.org/10.1126/science.1141319 %V 316 %X In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element-1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position +/-50 base pairs (bp), which facilitated our finding motifs and allowed us to identify noncanonical NRSF-binding motifs. These ChIPSeq data also have high sensitivity and specificity ROC (receiver operator characteristic) area >/= 0.96 and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development.

@article{Johnson2007, abstract = {In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element-1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [+/-50 base pairs (bp)], which facilitated our finding motifs and allowed us to identify noncanonical NRSF-binding motifs. These ChIPSeq data also have high sensitivity and specificity [ROC (receiver operator characteristic) area >/= 0.96] and statistical confidence (P <10(-4)), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development.}, added-at = {2010-01-26T20:35:53.000+0100}, author = {Johnson, David S. and Mortazavi, Ali and Myers, Richard M. and Wold, Barbara}, biburl = {https://www.bibsonomy.org/bibtex/2ceda8a146bb0dd48bc6e6f1f800a40a8/denilw}, doi = {10.1126/science.1141319}, institution = {Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305-5120, USA.}, interhash = {b00f1cb7dc87c620295403e9e47e9f21}, intrahash = {ceda8a146bb0dd48bc6e6f1f800a40a8}, journal = {Science}, keywords = {Algorithms Amino_Acid_Motifs Binding_Sites Chromatin_Immunoprecipitation DNA,_metabolism DNA-Binding_Proteins,_chemistry/metabolism Gene_Regulatory_Networks Genome,_Human Humans Insulin-Secreting_Cells,_cytology/physiology MicroRNAs,_genetics Neurons,_physiology Promoter_Regions_(Genetics) Protein_Binding Repressor_Proteins,_chemistry/genetics/metabolism Sensitivity_and_Specificity Sequence_Analysis,_DNA Synaptic_Transmission T-Lymphocytes,_metabolism Transcription,_Genetic Transcription_Factors,_chemistry/genetics/metabolism Zinc_Fingers}, month = Jun, number = 5830, owner = {denilw}, pages = {1497-1502}, pii = {1141319}, pmid = {17540862}, timestamp = {2010-01-26T20:35:59.000+0100}, title = {Genome-wide mapping of in vivo protein-DNA interactions.}, url = {http://dx.doi.org/10.1126/science.1141319}, volume = 316, year = 2007 }