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

Abstract

Epigenetic patterns of histone modifications contribute to the maintenance of tissue-specific gene expression. Here, we show that such modifications also accompany the specification of cell identities by the NF-κB transcription factor Dorsal in the precellular Drosophila embryo. We provide evidence that the maternal pioneer factor, Zelda, is responsible for establishing poised RNA polymerase at Dorsal target genes before Dorsal-mediated zygotic activation. At the onset of cell specification, Dorsal recruits the CBP/p300 coactivator to the regulatory regions of defined target genes in the presumptive neuroectoderm, resulting in their histone acetylation and transcriptional activation. These genes are inactive in the mesoderm due to transcriptional quenching by the Snail repressor, which precludes recruitment of CBP and prevents histone acetylation. By contrast, inactivation of the same enhancers in the dorsal ectoderm is associated with Polycomb-repressed H3K27me3 chromatin. Thus, the Dorsal morphogen gradient produces three distinct histone signatures including two modes of transcriptional repression, active repression (hypoacetylation), and inactivity (H3K27me3). Whereas histone hypoacetylation is associated with a poised polymerase, H3K27me3 displaces polymerase from chromatin. Our results link different modes of RNA polymerase regulation to separate epigenetic patterns and demonstrate that developmental determinants orchestrate differential chromatin states, providing new insights into the link between epigenetics and developmental patterning.eneration of many specialized cell types from an identical DNA sequence is a remarkable property of genomes in multicellular organisms. Cell fate is specified by transcription factors through the initiation of differential gene expression patterns, but maintenance of cell-type-specific gene expression programs often relies on epigenetic mechanisms (reviewd in ref. 1). Epigenetic events such as Polycomb-mediated repression are therefore important for maintenance of specific cell identities and have been implicated in human disease (reviewed in refs. 2 and 3), but how differences in epigenetic information between cell types arise is poorly understood.The repressive nature of chromatin limits access of proteins to DNA. Pioneer factors facilitate chromatin opening, allowing additional proteins to bind DNA (reviewed in ref. 4). In the Drosophila embryo, zygotic genome activation occurs with the help of Zelda (5), a transcription factor with many features of a pioneer factor. Zelda associates with target genes before their activation (6, 7) and increases chromatin accessibility (8-11). Zelda facilitates DNA binding of other transcription factors, including Dorsal, a Rel-family transcription factor related to mammalian NF-κB (9).Formation of the three germ layers, mesoderm, neuroectoderm, and dorsal ectoderm, in Drosophila embryos involves establishment of differential gene expression patterns by the Dorsal morphogen (reviewed in refs. 12 and 13) (Fig. 1A). Dorsal forms an intr...

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning

“…Although the gd 7 , Toll rm9/rm10 , and Toll 10B embryos still have heterogeneous gene expression profiles, nevertheless there are clear differences in chromatin state and overall gene expression between them (Boija and Mannervik, 2016;Koenecke et al, 2016;Stathopoulos et al, 2002;Zeitlinger et al, 2007). We expanded on previous studies by identifying putative enhancers specific to neuroectoderm in addition to dorsal ectoderm and mesoderm.…”

“…Maternal effect mutations in the Toll signalling pathway lead to embryos that lack the usual patterning of the DV axis (Stein and Stevens, 2014). These embryos have long been used as a system to study the specification of mesoderm (Toll 10B ), neuroectoderm (Toll rm9/rm10 ), and dorsal ectoderm (gd 7 ) cell fates and the regulation of tissue-specific gene expression (Boija and Mannervik, 2016;Koenecke et al, 2016;Koenecke et al, 2017;Stathopoulos et al, 2002;Zeitlinger et al, 2007). However, these embryos are still under the influence of anterior-posterior patterning signals and do not show completely uniform cell identities (Stathopoulos et al, 2002).…”

“…1A). These embryos provide an excellent model system to study tissue-specific regulation during development, which has led to the discovery of key transcription factors, regulatory elements, and processes required for embryo patterning (Boija and Mannervik, 2016;Hong et al, 2008;Koenecke et al, 2016;Koenecke et al, 2017;Stathopoulos et al, 2002;Zeitlinger et al, 2007). High levels of nuclear Dl on the ventral side of the embryo produce mesoderm (ME, yellow), intermediate levels produce neuroectoderm (NE, pink), while nuclei without Dl will produce dorsal ectoderm (DE, blue).…”

Role of co-repressor genomic landscapes in shaping the Notch response

“…Similar features have been noted for Groucho [ 6 ] , a key partner of Hairless, and for another class of repressors/co-repressors [ 5 ] . Likewise, Dorsal repressed enhancers exhibited some active chromatin marks (H3K4me1) although these were found to be hypoacetylated compared to their active counterparts [ 52 , 53 ] . It is proposed these repressive factors contribute to polymerase pausing [ 6 , 52 ] rather than more long-term silencing [ 53 ] , so that gene transcription would be kept in check until/unless conditions change and RNA polymerase is released.…”

“…Likewise, Dorsal repressed enhancers exhibited some active chromatin marks (H3K4me1) although these were found to be hypoacetylated compared to their active counterparts [ 52 , 53 ] . It is proposed these repressive factors contribute to polymerase pausing [ 6 , 52 ] rather than more long-term silencing [ 53 ] , so that gene transcription would be kept in check until/unless conditions change and RNA polymerase is released. Another suggestion is that modulation by repressors enables a fine regulatory control over transcriptional output from a given target gene so that it can be graded over range of values.…”