Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos

Abstract

CBP and the related p300 protein are widely used transcriptional co-activators in metazoans that interact with multiple transcription factors. Whether CBP/p300 occupies the genome equally with all factors or preferentially binds together with some factors is not known. We therefore compared Drosophila melanogaster CBP (nejire) ChIP–seq peaks with regions bound by 40 different transcription factors in early embryos, and we found high co-occupancy with the Rel-family protein Dorsal. Dorsal is required for CBP occupancy in the embryo, but only at regions where few other factors are present. CBP peaks in mutant embryos lacking nuclear Dorsal are best correlated with TGF-ß/Dpp-signaling and Smad-protein binding. Differences in CBP occupancy in mutant embryos reflect gene expression changes genome-wide, but CBP also occupies some non-expressed genes. The presence of CBP at silent genes does not result in histone acetylation. We find that Polycomb-repressed H3K27me3 chromatin does not preclude CBP binding, but restricts histone acetylation at CBP-bound genomic sites. We conclude that CBP occupancy in Drosophila embryos preferentially overlaps factors controlling dorso-ventral patterning and that CBP binds silent genes without causing histone hyperacetylation.

Initiation of diverse epigenetic states during nuclear programming of the Drosophila body plan

“…The following antibodies were used for histone modifications: H3 (Abcam, ab1791); H3K4me3 (Millipore, 07-473); H3K9me3 (Abcam, ab8898); H3K18ac (Abcam, ab1191); H3K27ac (Abcam, ab4729); H3K27me3 (Abcam, ab6002); basal transcription machinery, Rpb3 (gift from John Lis, Cornell University, Ithaca, NY); 8WG16 (Abcam, ab817); PolII S5 (Abcam, ab5131); TBP (Robert Tjian, University of California, Berkeley); transcription factor, Dorsal (Christos Samakovlis, Stockholm University, Stockholm); and chromatin regulators, CBP (described in ref. 24) and Polycomb (Yuri Schwartz, Umeå University, Umeå, Sweden).…”

“…Dorsal and the CBP/p300 coactivator (nejire) preferentially co-occupy genomic DNA genomewide, genetically interact, and bind each other in vitro and in vivo (23,24). Interestingly, ChIP of the CBP coactivator showed high occupancy of the brk and sog enhancers in the neuroectoderm, but only occupancy at background levels in the mesoderm (P < 0.05, Fig.…”

Drosophilapoised enhancers are generated during tissue patterning with the help of repression

“…In gastrulation defective (gd) mutant embryos gd 7 , Dl is not activated, resulting in uniformly high signaling activity of the fly BMP2/4 ortholog Decapentaplegic (Dpp) but below wildtype maximum levels (see Ashe and Levine 1999) and the specification of dorsal ectodermal fate in the entire embryo. These mutants have frequently been used in the past because they allow the analysis of patterning across the Dl activity gradient (e.g., Stathopoulos et al 2002;Zeitlinger et al 2007;Holmqvist et al 2012) and have helped DV patterning become one of the beststudied gene regulatory networks in development. The DV patterning system also illustrates another important principle of pattern formation, the widespread use and requirement of sequence-specific transcriptional repressors.…”

Structure-Function Analysis of the Drosophila melanogaster Caudal Transcription Factor Provides Insights into Core Promoter-preferential Activation

“…A, CBP and Bicoid occupancy at the gt locus in WT embryos. ChIP-sequencing peaks for CBP (73) and ChIP-chip peaks for Bicoid (82) in 2-4-h old WT embryos are shown for the gt locus. Occupancy is plotted as log 2 -fold enrichment over input.…”