Genome-wide identification of SCARECROW (SCR) direct targets using a custom Agilent promoter array

ABSTRACT: ChIP-chip analysis was used to identify direct targets of the transcription factor SCR SCARECROW (SCR) is a key regulatory of radial patterning and stem cell renewal in the primary root. We have shown in previous studies that SCR is a direct transcriptional regulator in Arabidopsis thaliana. With the aim of understanding the molecular pathway acting downstream of SCR in primary root development, we identified SCR direct targets at the genome-wide level in primary roots.To do this we designed a promoter microarray (chip) for Arabidopsis containing probes tiling the intergenic regions, first intron, and 3M-bM-^@M-^YUTR of all annotated genes. We performed Chromatin Immunoprecipitation (ChIP) using an antibody to Green Fluorescent Protein (GFP) on roots of transgenic plants expressing a functional fusion protein of SCR and GFP that is driven by the SCR promoter. Our control was performing ChIP in parallel using the same anti-GFP antibody on roots of Columbia-O wild-type plants. DNA recovered from the SCR and wild-type ChIP experiments with Cy5 and Cy3 dye, respectively, and then hybridized to the same microarray. The array was scanned using an Agilent scanner and the signal intensity for each channel was retrieved and normalized by Agilent feature extraction software. Two biological replicates of this ChIP-chip experiment were performed. Two biological replicates of the ChIP-chip experiment were performed using samples isolated from primary roots. Each Agilent array was hybridized with both SCR ChIP and wild-type control samples differentially labeled with Cy5 and Cy3 dye, respectively.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Anjali Iyer-Pascuzzi 

PROVIDER: E-GEOD-30104 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress