The interaction between the coactivator dCBP and Modulo, a chromatin-associated factor, affects segmentation and melanotic tumor formation in Drosophila

Zika virus infection drives epigenetic modulation of immunity by the histone acetyltransferase CBP of Aedes aegypti

Epigenetic mechanisms are responsible for a wide range of biological phenomena in insects, controlling embryonic development, growth, aging and nutrition. Despite this, the role of epigenetics in shaping insect-pathogen interactions has received little attention. Gene expression in eukaryotes is regulated by histone acetylation/deacetylation, an epigenetic process mediated by histone acetyltransferases (HATs) and histone deacetylases (HDACs). In this study, we explored the role of the Aedes aegypti histone acetyltransferase CBP (AaCBP) after infection with Zika virus (ZIKV), focusing on the two main immune tissues, the midgut and fat body. We showed that the expression and activity of AaCBP could be positively modulated by blood meal and ZIKV infection. Nevertheless, Zika-infected mosquitoes that were silenced for AaCBP revealed a significant reduction in the acetylation of H3K27 (CBP target marker), followed by downmodulation of the expression of immune genes, higher titers of ZIKV and lower survival rates. Importantly, in Zika-infected mosquitoes that were treated with sodium butyrate, a histone deacetylase inhibitor, their capacity to fight virus infection was rescued. Our data point to a direct correlation among histone hyperacetylation by AaCBP, upregulation of antimicrobial peptide genes and increased survival of Zika-infected-A. aegypti.

Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches

During embryogenesis, organisms undergo considerable cellular remodelling requiring the combined action of thousands of proteins. In case of the well-studied model Drosophila melanogaster, transcriptomic studies, most notably from the modENCODE project, have described in detail changes in gene expression at the mRNA level across development. Although such data are clearly very useful to understand how the genome is regulated during embryogenesis, it is important to understand how changes in gene expression are reflected at the level of the proteome. In this study, we describe a combination of two quantitative label-free approaches, SWATH and data-dependent acquisition, to monitor changes in protein expression across a timecourse of D. melanogaster embryonic development. We demonstrate that both approaches provide robust and reproducible methods for the analysis of proteome changes. In a preliminary analysis of Drosophila embryogenesis, we identified several pathways, including the heat-shock response, nuclear protein import and energy production that are regulated during embryo development. In some cases changes in protein expression mirrored transcript levels across development, whereas other proteins showed signatures of post-transcriptional regulation. Taken together, our pilot study provides a solid platform for a more detailed exploration of the embryonic proteome.

A graphical model method for integrating multiple sources of genome-scale data

Making effective use of multiple data sources is a major challenge in modern bioinformatics. Genome-wide data such as measures of transcription factor binding, gene expression, and sequence conservation, which are used to identify binding regions and genes that are important to major biological processes such as development and disease, can be difficult to use together due to the different biological meanings and statistical distributions of the heterogeneous data types, but each can provide valuable information for understanding the processes under study. Here we present methods for integrating multiple data sources to gain a more complete picture of gene regulation and expression. Our goal is to identify genes and cis-regulatory regions which play specific biological roles. We describe a graphical mixture model approach for data integration, examine the effect of using different model topologies, and discuss methods for evaluating the effectiveness of the models. Model fitting is computationally efficient and produces results which have clear biological and statistical interpretations. The Hedgehog and Dorsal signaling pathways in Drosophila, which are critical in embryonic development, are used as examples.

Heterochromatin-mediated gene silencing is not affected by Drosophila CBP activity

Cyclic AMP Response Element Binding protein (CREB)-binding protein (CBP) is an acetyltransferase important for modifying histones and chromatin-associated proteins and thus affecting transcription and other DNA metabolic processes. We found that the Drosophila CBP (dCBP) is associated with the NAD(+)-dependent deacetylase, SIR2, which was originally identified as a silencing information regulator in yeast that models silenced and repeated sequence chromatin such as centric heterochromatin, telomeres, and the repeated rDNA sequences. As in yeast, Drosophila sir2 (dsir2) affects the formation and/or function of centric heterochromatin. The fact that we found dCBP in immunecomplexes with dSIR2 in vivo and found that dCBP can interact with dSIR2 directly in vitro suggested that dCBP might affect the packaging of silencing heterochromatin as well. A careful study of the dCBP mutations provides evidence that dCBP does not affect the formation and/or function of centric heterochromatin and thus may affect other dSIR2 functions.

Corepressive action of CBP on androgen receptor transactivation in pericentric heterochromatin in a Drosophila experimental model system

Ligand-bound nuclear receptors (NR) activate transcription of the target genes. This activation is coupled with histone modifications and chromatin remodeling through the function of various coregulators. However, the nature of the dependence of a NR coregulator action on the presence of the chromatin environment at the target genes is unclear. To address this issue, we have developed a modified position effect variegation experimental model system that includes an androgen-dependent reporter transgene inserted into either a pericentric heterochromatin region or a euchromatic region of Drosophila chromosome. Human androgen receptor (AR) and its constitutively active truncation mutant (AR AF-1) were transcriptionally functional in both chromosomal regions. Predictably, the level of AR-induced transactivation was lower in the pericentric heterochromatin. In genetic screening for AR AF-1 coregulators, Drosophila CREB binding protein (dCBP) was found to corepress AR transactivation at the pericentric region whereas it led to coactivation in the euchromatic area. Mutations of Sir2 acetylation sites or deletion of the CBP acetyltransferase domain abrogated dCBP corepressive action for AR at heterochromatic areas in vivo. Such a CBP corepressor function for AR was observed in the transcriptionally silent promoter of an AR target gene in cultured mammalian cells. Thus, our findings suggest that the action of NR coregulators may depend on the state of chromatin at the target loci.

Drosophila haematopoiesis

Like in vertebrates, Drosophila haematopoiesis occurs in two waves. It gives rise to three types of haemocytes: plasmatocytes (phagocytosis), crystal cells (melanization) and lamellocytes (encapsulation of parasites). A first population of haemocytes, specified during embryogenesis, gives rise to an invariant number of plasmatocytes and crystal cells. A second population of haemocytes is specified during larval development in a specialized haematopoietic organ, the lymph gland. All three types of haemocytes can be specified in this organ, but lamellocytes only differentiate in response to parasitism. Thus, larval in contrast to embryonic haematopoiesis can be modulated by physiological constraints. Molecular cascades controlling embryonic haematopoiesis are relatively well established and require transactivators such as GATA, FOG and Runx factors, which are also co-opted in mammalian haematopoiesis. Mechanisms involved during larval haematopoiesis are less well understood although a number of chromatin remodelling factors and signalling pathways (JAK/STAT, Toll, Hedgehog, Notch) are required. In healthy larvae a pool of progenitors is maintained within the lymph gland, under the control of a signalling centre which expresses Collier, Serrate, Antennapedia and Hedgehog, and controls haemocyte homeostasis. Its key role in haemocyte homeostasis is reminiscent of interactions described in vertebrates between haematopoietic stem cells and their microenvironment (niche).

Drosophila dCBP is involved in establishing the DNA replication checkpoint

The CBP/p300 family of proteins comprises related acetyltransferases that coactivate signal-responsive transcription. Recent evidence suggests that p300/CBP may also interact directly with complexes that mediate different aspects of DNA metabolism such as replication and repair. In this report, we show that loss of dCBP in Drosophila cells and eye discs results in a defect in the cell cycle arrest induced by stalled DNA replication. We show that dCBP and the checkpoint kinase Mei-41 can be found together in a complex and, furthermore, that dCBP has a genetic interaction with mei-41 in the response to stalled DNA replication. These observations suggest a broader role for the p300/CBP acetyltransferases in the modulation of chromatin structure and function during DNA metabolic events as well as for transcription.

Transcriptional regulation by Modulo integrates meiosis and spermatid differentiation in male germ line

Transcriptional activation in early spermatocytes involves hundreds of genes, many of which are required for meiosis and spermatid differentiation. A number of the meiotic-arrest genes have been identified as general regulators of transcription; however, the gene-specific transcription factors have remained elusive. To identify such factors, we purified the protein that specifically binds to the promoter of spermatid-differentiation gene Sdic and identified it as Modulo, the Drosophila homologue of nucleolin. Analysis of gene-expression patterns in the male sterile modulo mutant indicates that Modulo supports high expression of the meiotic-arrest genes and is essential for transcription of spermatid-differentiation genes. Expression of Modulo itself is under the control of meiotic-arrest genes and requires the DAZ/DAZL homologue Boule that is involved in the control of G(2)/M transition. Thus, regulatory interactions among Modulo, Boule, and the meiotic-arrest genes integrate meiosis and spermatid differentiation in the male germ line.

The effects of parasite-derived immune-suppressive factors on the cellular innate immune and autoimmune responses of Drosophila melanogaster

Immune-suppressive factors (ISFs) introduced into larvae of Drosophila melanogaster during infection by virulent endoparasitic wasps effectively block the innate immune response mediated by blood cells (hemocytes) but have little influence on the autoimmune response made by a tumor strain in which the blood cells manifest a similar response but instead target and destroy endogenous tissues. Quantitative hemocyte analyses indicate that ISFs interfere with the immune effector responses downstream of nonself recognition, hemocyte activation and differentiation, because these responses were manifested by tumor hosts, in which the parasitoids developed. The data suggest that once activated to encapsulate aberrant tissues, the target specificity of the autoimmune-activated hemocytes, and the genetic program underlying tumor formation, cannot be blocked by parasitoid-derived ISFs, which effectively inhibit identical hemocyte-mediated responses during parasitization.

Thicker than blood: conserved mechanisms in Drosophila and vertebrate hematopoiesis

Blood development in Drosophila melanogaster shares several interesting features with hematopoiesis in vertebrates, including spatiotemporal regulation as well as the use of similar transcriptional regulators and signaling pathways. In this review, we describe what is known about hematopoietic development in Drosophila and the various cell types generated and their functions. Additionally, the molecular genetic mechanisms of hematopoietic cell fate determination and commitment within Drosophila blood cell lineages are discussed and compared to vertebrate mechanisms.

Biological functions of the ISWI chromatin remodeling complex NURF

The nucleosome remodeling factor (NURF) is one of several ISWI-containing protein complexes that catalyze ATP-dependent nucleosome sliding and facilitate transcription of chromatin in vitro. To establish the physiological requirements of NURF, and to distinguish NURF genetically from other ISWI-containing complexes, we isolated mutations in the gene encoding the large NURF subunit, nurf301. We confirm that NURF is required for transcription activation in vivo. In animals lacking NURF301, heat-shock transcription factor binding to and transcription of the hsp70 and hsp26 genes are impaired. Additionally, we show that NURF is required for homeotic gene expression. Consistent with this, nurf301 mutants recapitulate the phenotypes of Enhancer of bithorax, a positive regulator of the Bithorax-Complex previously localized to the same genetic interval. Finally, mutants in NURF subunits exhibit neoplastic transformation of larval blood cells that causes melanotic tumors to form.