Unknown,Transcriptomics,Genomics,Proteomics

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ChIP-Chip profiling of mouse MEF cell lines for genome-wide discovery of STAT3 functional binding sites


ABSTRACT: STAT3 is a transcription factor playing a crucial role in inflammation, immunity and oncogenesis, able to induce distinct subsets of target genes in different cell types or under different conditions. Identification of direct transcriptional targets however has only defined a relatively limited set of genes, not sufficient to explain its variegated functions. In order to improve our understanding of the STAT3 transcriptional network we decided to develop a computational approach for the discovery of STAT3 functional binding sites. Upon generating a Positional Weight Matrix to define STAT3 binding sites, we applied a loglikelihood ratio scoring function and were able to assign affinity scores with very high specificity (93.5%) as measured by EMSA. STAT3 binding sites scoring above a stringent threshold have been identified genome-wide in Homo sapiens and Mus musculus and selected for phylogenetic conservation by genomic sequence alignment using eight vertebrate species. Validation was carried out on a subset of predicted; sites within genes previously identified as STAT3-responsive by microarray analysis. The high percentage of sites able to bind STAT3 in vivo, as assessed by Chromatin Immunoprecipitation (ChIP) analysis, revealed the high predictive power of our method. Experiment Overall Design: Three prototypic situation were investigated using two replications for each experimental point: STAT3+/+ versus STAT3-/- MEFs , STAT3+/+ versus STAT3+/+ treated with OSM and STAT3-/- versus STAT3-/- treated with OSM.

ORGANISM(S): Mus musculus

SUBMITTER: Raffaele Calogero 

PROVIDER: E-GEOD-12262 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide discovery of functional transcription factor binding sites by comparative genomics: the case of Stat3.

Vallania Francesco F   Schiavone Davide D   Dewilde Sarah S   Pupo Emanuela E   Garbay Serge S   Calogero Raffaele R   Pontoglio Marco M   Provero Paolo P   Poli Valeria V  

Proceedings of the National Academy of Sciences of the United States of America 20090312 13


The identification of direct targets of transcription factors is a key problem in the study of gene regulatory networks. However, the use of high throughput experimental methods, such as ChIP-chip and ChIP-sequencing, is limited by their high cost and strong dependence on cellular type and context. We developed a computational method for the genome-wide identification of functional transcription factor binding sites based on positional weight matrices, comparative genomics, and gene expression p  ...[more]

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