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Methods Mol Biol. 2008;441:163-73. doi: 10.1007/978-1-60327-047-2_11.

Immunoregulomics : a serum autoantibody-based platform for transcription factor profiling.

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Molecular Urology Laboratory, Division of Urology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.


Gene expression is regulated by a group of proteins known as transcription factors (TFs). By binding to specific DNA cis-elements, each TF contributes a different functional role in gene expression. Panomics has developed a TranSignal TF-TF Interaction Array, which enables the user to determine TF complexes of interest with multiple other TFs. The process works by immunoprecipitating cis-elements bound to native cell nuclear extract TFs using specific antibodies to the TFs, and hybridizing the corresponding cis-elements to a membrane array spotted with different consensus sequences. In this protocol, we adapt this technology to characterize and compare autoantibody reactivity to TFs between patients with and without disease. Using Panomics combination DNA/protein arrays with over 300 different cis-elements spotted on the membrane, we can monitor the differences in autoimmune-targeted regulatory TFs, a process we termed immunoregulomics. This method allows for a qualitative analysis of the interactions with some quantifiable data. The findings can then be verified with the use of gel-shift experiments. Autoantibodies; interactome microarrays; transcription factors.

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