Comparison of gene expression in wild-type and rpl-1 Arabidopsis inflorescence apices

The Arabidopsis thaliana REPLUMLESS gene (RPL), also known as PENNYWISE (PNY) and BELLRINGER (BLR) encodes a BEL1-like TALE homeodomain (BLH) transcription factor that controls multiple aspects of meristem and floral development, including meristem maintenance, phyllotaxis, the transition to flowering, stem development and floral organ patterning [1-3]. As part of a screen for genes that mediate the function of RPL in the processes above, we compared gene expression in inflorescence apices of wild-type (Landsberg-erecta) and the rpl-1 mutant [2]. 1. Byrne, M.E., Groover, A.T., Fontana, J.R., and Martienssen, R.A. (2003). Development 130, 3941-3950. 2. Roeder, A.H.K., Ferrandiz, C., and Yanofsky, M.F. (2003). Current Biology 13, 1630-1635. 3. Smith, H.M.S., and Hake, S. (2003). Plant Cell 15, 1717-1727. Plants were grown in a controlled environment room at 20-22 °C, 16 h light (100 µE) until they flowered and the inflorescences were around 12 cm tall. Immediately after dissecting the terminal 1-2 cm of the inflorescences (1-2 g per sample, three biological replicates each for wild-type Landsberg-erecta and rpl-1 [1]), RNA was extracted with Trizol (Sigma) and purified using QIAGEN RNAeasy columns (QIAGEN) according to the manufacturer's instructions. Probes were prepared from 10 µg total RNA using a standard Affymetrix protocol (GeneChip © 3’ IVT Express kit) and hybridised to Affymetrix AGROMONICS1 oligonucleotide arrays. Data were normalized and analyzed statistically with the affylmGUI package (http://bioinf.wehi.edu.au/affylmGUI/about.html) using LIMMA (Linear Models for MicroArray data) [2] with a chip description format (CDF) file for the AGRONOMICS1 array and TAIR10 [3]. 1. Roeder, A.H.K., Ferrandiz, C., and Yanofsky, M.F. (2003). Current Biology 13, 1630-1635. 2. Smyth, G.K. (2005). Limma: linear models for microarray data. In Bioinformatics and computational biology solutions using R and Bioconductor. (Springer), pp. 397-420. 3. Müller, M., Patrignani, A., Rehrauer, H., Gruissem, W., and Hennig, L. (2012). Plant Methods 8, 1.