Transcriptional Regulation by CHIP/LDB Complexes

Abstract

It is increasingly clear that transcription factors play versatile roles in turning genes “on” or “off” depending on cellular context via the various transcription complexes they form. This poses a major challenge in unraveling combinatorial transcription complex codes. Here we use the powerful genetics of Drosophila combined with microarray and bioinformatics analyses to tackle this challenge. The nuclear adaptor CHIP/LDB is a major developmental regulator capable of forming tissue-specific transcription complexes with various types of transcription factors and cofactors, making it a valuable model to study the intricacies of gene regulation. To date only few CHIP/LDB complexes target genes have been identified, and possible tissue-dependent crosstalk between these complexes has not been rigorously explored. SSDP proteins protect CHIP/LDB complexes from proteasome dependent degradation and are rate-limiting cofactors for these complexes. By using mutations in SSDP, we identified 189 down-stream targets of CHIP/LDB and show that these genes are enriched for the binding sites of APTEROUS (AP) and PANNIER (PNR), two well studied transcription factors associated with CHIP/LDB complexes. We performed extensive genetic screens and identified target genes that genetically interact with components of CHIP/LDB complexes in directing the development of the wings (28 genes) and thoracic bristles (23 genes). Moreover, by in vivo RNAi silencing we uncovered novel roles for two of the target genes, xbp1 and Gs-alpha, in early development of these structures. Taken together, our results suggest that loss of SSDP disrupts the normal balance between the CHIP-AP and the CHIP-PNR transcription complexes, resulting in down-regulation of CHIP-AP target genes and the concomitant up-regulation of CHIP-PNR target genes. Understanding the combinatorial nature of transcription complexes as presented here is crucial to the study of transcription regulation of gene batteries required for development.

Author Summary

Different cell types in multi-cellular organisms are determined by the repertoire of genes active in each cell. This repertoire, or transcriptome, is established by the coordinated activity of transcription factors and cofactors that form modular transcription complexes. The modular nature of transcription complexes complicates our understanding of how transcription factors shape the transcriptome. CHIP/LDB transcription complexes direct formation of various cell types including blood and nerve cells. CHIP/LDB malfunction leads to developmental defects and cancer. The function of these complexes depends critically on the docking of specific transcription factors and co-factors at a specific time and in a specific cell type, making them outstanding models for intricate transcriptional regulation. Here we demonstrate that loss of SSDP, a key regulatory component of CHIP/LDB transcription complexes, alters transcription of a large group of genes. We used bioinformatics tools and genetic tests to examine the function of additional components of CHIP/LDB transcription complexes and their target genes during the development of specific organs. We demonstrate how differences in the availability of transcription factors in different cells can affect the function and composition of CHIP/LDB transcription complexes.