Chromosomal clustering of genes in trithorax (trx) mutant larvae

We have performed a systematic examination of genome-wide expression profiles using microarrays to reconstruct a global picture of the trx regulatory gene network in D. melanogaster. Using computational analysis of the microarray data, we have identified 25 clusters of genes potentially regulated by trx, most of them being located in the arm L of chromosome 3. Functional analysis revealed that most clusters are enriched in structural proteins involved in cuticle formation, which are preferently expressed in salivary glands. The same organization in clusters was observed in the transcriptomes of four independent experiments, being a distinctive feature of the regulatory networks of trx and other chromatin regulators (ASH2, NURF, Pc, ASH1). We have also identified many of these clusters in D. simulans, D. yakuba, D. pseudoobscura and partially in A. gambiae. Keywords: loss of function analysis Total RNA from w1118;+;+ larvae was pooled and used as a common reference in four microarrays against w1118;+;trxE3/trxB11 total RNA coming from two different extractions to take biological differences into account. Two amplifications from w1118;+;+ and one from each w1118;+;trxE3/trxB11 replicate were performed with the Amino-Allyl Messageamp II aRNA Amplification Kit (Ambion, Inc) to obtain amplified RNA (aRNA). The two arrays from each replicate pair were hybridized with the same amplified RNA from sample and common reference but with dyes (Cy3 and Cy5 from Amersham, Inc) swapped to take dye-bias into account.