ChIP-RAPD as a possible new methodology to identify genes regulated by chromatin related proteins

PASCUAL M AND BERNABEU R

Huerta Grande, Cordoba

Congreso; IIRCN; 2010

Sociedad Argentina de Neurociencias

Cells respond to their environment by sensing signals and translating them into changes in gene expression. In particular, the central nervous system is good stru8cture to apply techniques for gene expression paradigms. In recent years, there has been an extensive search for gene regulatory mechanisms using different techniques. Technical and experimental advances in RNA amplification, quantitative real-time polymerase chain reaction (qPCR), cDNA microarray, and chromatin immunoprecipitation (ChIP) analysis have led to an increase in the number of studies of gene expression. The most used are qPCR, and chromatin immunoprecipitation (ChIP). Our question was related to identify activated genes in response to a specific stimulus, and where chromatin remodeling is implicated. To reduce the large number of gene expression that is obtained by microarrays or ChIP-seq, we decided to combine to techniques that had never been used together, ChIP and random amplified polymorphic DNA (RAPD). To approach this strategy, we chose a simple cellular model as PC12 cells, which allow us to use in a near future with nicotine, our interest drug. To obtain a clear and strong stimulus we used NGF to test different ChIP grade antibodies against histone modifications. For RAPD, around 10 randomized primers we used to find different unknown amplicons, to sequence them later.