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Chromosomal clustering of genes in trithorax (trx) mutant larvae

ABSTRACT: 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

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE8748 | GEO | 2008/09/26

SECONDARY ACCESSION(S): PRJNA105287

REPOSITORIES: GEO

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Project description:Drosophila development is a complex and dynamic process regulated, in part, by members of the Polycomb (Pc), Trithorax (Trx) and Compass chromatin modifier complexes. O-GlcNAc Transferase (OGT/SXC) is essential for Pc repression suggesting that the O-GlcNAcylation of proteins plays a key role in regulating development. OGT transfers N-acetyl-D-glucosamine (GlcNAc) onto hydroxyl groups of serine or threonine residues of key transcriptional regulators using the nutrient-derived UDP-GlcNAc as a substrate, which is dynamically removed by O-GlcNAcase (OGA). We performed ChIP-chip and microarray analysis after OGT or OGA RNAi knockdown in Drosophila S2 cells and found that O-GlcNAc was elevated genome wide particularly at genes related to mitosis and cell cycle in OGA RNAi cells, but not at sites co-occupied by Pc member Pleiohomeotic (Pho), such as the Hox and NK homeobox gene clusters. Microarray analysis suggested that altered O-GlcNAc cycling perturbed the expression of genes associated with morphogenesis and cell cycle regulation. To examine the in vivo consequences of disturbed O-GlcNAc cycling in the whole animal, we produced a null allele of oga (ogadel.1) in Drosophila. Epigenetic activators including Trx group members Trithorax (Trx), Absent small or homeotic discs 1 (Ash1) and Compass member Set1 histone methyltransferases are O-GlcNAc modified in ogadel.1 mutants. ogadel.1 mutants displayed altered expression of a distinct set of cell cycle related genes in ovaries. Our results suggest that the loss of OGA could affect epigenetic machinery by accumulating O-GlcNAc on numerous chromatin factors including Trx, Ash1 and Set1 in Drosophila. We performed affymetrix tilingarray analysis after OGT or OGA RNAi knockdown in Drosophila S2 cells to find if that O-GlcNAc was elevated genome wide particularly at genes related to mitosis and cell cycle in OGA RNAi cells, but not at sites co-occupied by Pc member Pleiohomeotic (Pho), ------------------------------- This represents the gene expression component only