Genomic analysis of heat-shock factor targets in Drosophila

Promoter ChIP-chip analysis in mouse testis reveals Y chromosome occupancy by HSF2

The mammalian Y chromosome is essential for spermatogenesis, which is characterized by sperm cell differentiation and chromatin condensation for acquisition of correct shape of the sperm. Deletions of the male-specific region of the mouse Y chromosome long arm (MSYq), harboring multiple copies of a few genes, lead to sperm head defects and impaired fertility. Using chromatin immunoprecipitation on promoter microarray (ChIP-chip) on mouse testis, we found a striking in vivo MSYq occupancy by heat shock factor 2 (HSF2), a transcription factor involved in spermatogenesis. HSF2 was also found to regulate the transcription of MSYq resident genes, whose transcriptional regulation has been unknown. Importantly, disruption of Hsf2 caused a similar phenotype as the 2/3 deletion of MSYq, i.e., altered expression of the multicopy genes and increased mild sperm head abnormalities. Consequently, aberrant levels of chromatin packing proteins and more frequent DNA fragmentation were detected, implying that HSF2 is required for correct chromatin organization in the sperm. Our findings define a physiological role for HSF2 in the regulation of MSYq resident genes and the quality of sperm.

CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex

Insulator or enhancer-blocking elements are proposed to play an important role in the regulation of transcription by preventing inappropriate enhancer/promoter interaction. The zinc-finger protein CTCF is well studied in vertebrates as an enhancer blocking factor, but Drosophila CTCF has only been characterised recently. To date only one endogenous binding location for CTCF has been identified in the Drosophila genome, the Fab-8 insulator in the Abdominal-B locus in the Bithorax complex (BX-C). We carried out chromatin immunopurification coupled with genomic microarray analysis to identify CTCF binding sites within representative regions of the Drosophila genome, including the 3-Mb Adh region, the BX-C, and the Antennapedia complex. Location of in vivo CTCF binding within these regions enabled us to construct a robust CTCF binding-site consensus sequence. CTCF binding sites identified in the BX-C map precisely to the known insulator elements Mcp, Fab-6, and Fab-8. Other CTCF binding sites correlate with boundaries of regulatory domains allowing us to locate three additional presumptive insulator elements; “Fab-2,” “Fab-3,” and “Fab-4.” With the exception of Fab-7, our data indicate that CTCF is directly associated with all known or predicted insulators in the BX-C, suggesting that the functioning of these insulators involves a common CTCF-dependent mechanism. Comparison of the locations of the CTCF sites with characterised Polycomb target sites and histone modification provides support for the domain model of BX-C regulation.

There is still much to learn about the organisation of regulatory elements that control where, when, and how much individual genes in the genome are transcribed. Several types of regulatory element have been identified; some, such as enhancers, act over large genomic distances. This creates a problem: how do such long-range elements only regulate their appropriate target genes? Insulator elements have been proposed to act as barriers within the genome, confining the effects of long-range regulatory elements. Here we have mapped the locations of one insulator-binding protein, CTCF, in several regions of the Drosophila genome. In particular, we have focussed on the Hox gene cluster in the Bithorax complex; a region whose regulation has been extensively characterised. Previous investigations have identified independent regulatory domains that control the expression of Bithorax complex genes in different segments of the fly, however the molecular nature of the domain boundaries is unclear. Our major result is that we find CTCF binding sites precisely located at the boundaries of these regulatory domains, giving a common molecular basis for these boundaries. This provides a clear example of the link between the positioning of insulators and the organisation of gene regulation in the Drosophila genome.

Epigenetic blocking of an enhancer region controls irradiation-induced proapoptotic gene expression in Drosophila embryos

Drosophila embryos are highly sensitive to gamma-ray-induced apoptosis at early but not later, more differentiated stages during development. Two proapoptotic genes, reaper and hid, are upregulated rapidly following irradiation. However, in post-stage-12 embryos, in which most cells have begun differentiation, neither proapoptotic gene can be induced by high doses of irradiation. Our study indicates that the sensitive-to-resistant transition is due to epigenetic blocking of the irradiation-responsive enhancer region (IRER), which is located upstream of reaper but is also required for the induction of hid in response to irradiation. This IRER, but not the transcribed regions of reaper/hid, becomes enriched for trimethylated H3K27/H3K9 and forms a heterochromatin-like structure during the sensitive-to-resistant transition. The functions of histone-modifying enzymes Hdac1(rpd3) and Su(var)3-9 and PcG proteins Su(z)12 and Polycomb are required for this process. Thus, direct epigenetic regulation of two proapoptotic genes controls cellular sensitivity to cytotoxic stimuli.

Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila

An analysis of Drosophila Su(Hw) binding allowed the identification of new, isolated, binding sites, and the construction of a new binding site consensus. Together with gene expression data, this supports a role for Su(Hw) in maintaining a constant genomic architecture.

Background

Insulator elements are proposed to play a key role in the organization of the regulatory architecture of the genome. In Drosophila, one of the best studied is the gypsy retrotransposon insulator, which is bound by the Suppressor of Hairy-wing (Su [Hw]) transcriptional regulator. Immunolocalization studies suggest that there are several hundred Su(Hw) sites in the genome, but few of these endogenous Su(Hw) binding sites have been identified.

Results

We used chromatin immunopurification with genomic microarray analysis to identify in vivo Su(Hw) binding sites across the 3 megabase Adh region. We find 60 sites, and these enabled the construction of a robust new Su(Hw) binding site consensus. In contrast to the gypsy insulator, which contains tightly clustered Su(Hw) binding sites, endogenous sites generally occur as isolated sites. These endogenous sites have three key features. In contrast to most analyses of DNA-binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Examination of occupancy in different tissues and developmental stages reveals that most Su(Hw) sites, if not all, are constitutively occupied, and these isolated Su(Hw) sites are generally highly conserved. Analysis of transcript levels in su(Hw) mutants indicate widespread and general changes in gene expression. Importantly, the vast majority of genes with altered expression are not associated with clustering of Su(Hw) binding sites, emphasizing the functional relevance of isolated sites.

Conclusion

Taken together, our in vivo binding and gene expression data support a role for the Su(Hw) protein in maintaining a constant genomic architecture.

Transcriptional activation by GAGA factor is through its direct interaction with dmTAF3

The GAGA factor (GAF), encoded by the Trithorax like gene (Trl) is a multifunctional protein involved in gene activation, Polycomb-dependent repression, chromatin remodeling and is a component of chromatin domain boundaries. Although first isolated as transcriptional activator of the Drosophila homeotic gene Ultrabithorax (Ubx), the molecular basis of this GAF activity is unknown. Here we show that dmTAF3 (also known as BIP2 and dTAF(II)155), a component of TFIID, interacts directly with GAF. We generated mutations in dmTAF3 and show that, in Trl mutant background, they affect transcription of Ubx leading to enhancement of Ubx phenotype. These results reveal that the gene activation pathway involving GAF is through its direct interaction with dmTAF3.

New candidate genes for heat resistance in Drosophila melanogaster are regulated by HSF

The cellular heat stress response is well studied in Drosophila in respect to the role of heat shock proteins (Hsp). Hsps are molecular chaperones, highly expressed during and after exposure to numerous stress types. Hsps are all regulated by a common transcription factor, the heat shock factor (HSF), and it is known that HSF is controlling other, so far uncharacterised, heat-responsive genes. In this study, we investigate whether novel candidate genes for heat resistance, identified by microarray experiments, are regulated by HSF. The microarray experiments recently identified several strongly upregulated genes in response to a short, non-lethal heat treatment in Drosophila melanogaster. To test whether or not a subset of these genes are HSF-induced, we studied 11 currently unannotated genes using quantitative polymerase chain reaction on HSF mutant flies with a non-functional HSF at elevated temperatures. We found indication of HSF regulation in most of the studied genes, suggesting a role of these unknown genes in heat tolerance. Surprisingly, some of the genes seemed to be upregulated independent of HSF function. The high induction in response to heat, which mimics the expression profile of Hsps, implies a role in the cellular heat response of these genes as well.

ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos

This protocol describes a method to detect in vivo associations between proteins and DNA in developing Drosophila embryos. It combines formaldehyde crosslinking and immunoprecipitation of protein-bound sequences with genome-wide analysis using microarrays. After crosslinking, nuclei are enriched using differential centrifugation and the chromatin is sheared by sonication. Antibodies specifically recognizing wild-type protein or, alternatively, a genetically encoded epitope tag are used to enrich for specifically bound DNA sequences. After purification and polymerase chain reaction-based amplification, the samples are fluorescently labeled and hybridized to genomic tiling microarrays. This protocol has been successfully used to study different tissue-specific transcription factors, and is generally applicable to in vivo analysis of any DNA-binding proteins in Drosophila embryos. The full protocol, including the collection of embryos and the collection of raw microarray data, can be completed within 10 days.

Heat shock factor 1 is a powerful multifaceted modifier of carcinogenesis

Heat shock factor 1 (HSF1) is the master regulator of the heat shock response in eukaryotes, a very highly conserved protective mechanism. HSF1 function increases survival under a great many pathophysiological conditions. How it might be involved in malignancy remains largely unexplored. We report that eliminating HSF1 protects mice from tumors induced by mutations of the RAS oncogene or a hot spot mutation in the tumor suppressor p53. In cell culture, HSF1 supports malignant transformation by orchestrating a network of core cellular functions including proliferation, survival, protein synthesis, and glucose metabolism. The striking effects of HSF1 on oncogenic transformation are not limited to mouse systems or tumor initiation; human cancer lines of diverse origins show much greater dependence on HSF1 function to maintain proliferation and survival than their nontransformed counterparts. While it enhances organismal survival and longevity under most circumstances, HSF1 has the opposite effect in supporting the lethal phenomenon of cancer.

X-linked QTL for knockdown resistance to high temperature in Drosophila melanogaster

Knockdown Resistance to High Temperature (KRHT) is an adaptive trait of thermotolerance in insects. An interval mapping was performed on chromosome X of Drosophila melanogaster to search for quantitative trait loci (QTL) affecting KRHT. A backcross population was obtained from two lines that dramatically differ for KRHT. Microsatellites were used as markers. Composite interval mapping identified a large-effect QTL in the region of band 10 where putative candidate genes map. To further test for this QTL a set of recombinant (but non-inbred) lines was obtained from backcrosses between the parental lines used for the interval mapping. Recombinant line analysis confirmed that one QTL is targeted by band 10. We identify and discuss candidate loci contained within our QTL region.

Heat shock factors at a crossroad between stress and development

Organisms must be able to sense and respond rapidly to changes in their environment in order to maintain homeostasis and survive. Induction of heat shock proteins (Hsps) is a common cellular defense mechanism for promoting survival in response to various stress stimuli. Heat shock factors (HSFs) are transcriptional regulators of Hsps, which function as molecular chaperones in protecting cells against proteotoxic damage. Mammals have three different HSFs that have been considered functionally distinct: HSF1 is essential for the heat shock response and is also required for developmental processes, whereas HSF2 and HSF4 are important for differentiation and development. Specifically, HSF2 is involved in corticogenesis and spermatogenesis, and HSF4 is needed for maintenance of sensory organs, such as the lens and the olfactory epithelium. Recent evidence, however, suggests a functional interplay between HSF1 and HSF2 in the regulation of Hsp expression under stress conditions. In lens formation, HSF1 and HSF4 have been shown to have opposite effects on gene expression. In this chapter, we present the different roles of the mammalian HSFs as regulators of cellular stress and developmental processes. We highlight the interaction between different HSFs and discuss the discoveries of novel target genes in addition to the classical Hsps.

A core transcriptional network for early mesoderm development in Drosophila melanogaster

Embryogenesis is controlled by large gene-regulatory networks, which generate spatially and temporally refined patterns of gene expression. Here, we report the characteristics of the regulatory network orchestrating early mesodermal development in the fruitfly Drosophila, where the transcription factor Twist is both necessary and sufficient to drive development. Through the integration of chromatin immunoprecipitation followed by microarray analysis (ChIP-on-chip) experiments during discrete time periods with computational approaches, we identified >2000 Twist-bound cis-regulatory modules (CRMs) and almost 500 direct target genes. Unexpectedly, Twist regulates an almost complete cassette of genes required for cell proliferation in addition to genes essential for morophogenesis and cell migration. Twist targets almost 25% of all annotated Drosophila transcription factors, which may represent the entire set of regulators necessary for the early development of this system. By combining in vivo binding data from Twist, Mef2, Tinman, and Dorsal we have constructed an initial transcriptional network of early mesoderm development. The network topology reveals extensive combinatorial binding, feed-forward regulation, and complex logical outputs as prevalent features. In addition to binary activation and repression, we suggest that Twist binds to almost all mesodermal CRMs to provide the competence to integrate inputs from more specialized transcription factors.

A cDNA microarray analysis of the response to heat stress in hepatopancreas tissue of the porcelain crab Petrolisthes cinctipes

Intertidal zone organisms experience thermal stress during periods of low tide, and much work has shown that induction of heat shock proteins and ubiquitination occurs in response to this stress. However, less is known of other cellular pathways that are regulated following thermal stress in these organisms. Here, we used a functional genomics approach to identify genes that were up- and downregulated following heat stress in the intertidal porcelain crab, Petrolisthes cinctipes using custom cDNA microarrays made from 13,824 cloned P. cinctipes ESTs representing 6717 unique consensus sequences. Statistically significant differences in gene expression between heat stressed and control groups were determined with R/maanova. Genes upregulated following heat stress were involved with protein folding, protein degradation, protein synthesis and gluconeogenesis, suggesting that heat stress accelerated protein turnover. Genes downregulated following heat stress were involved with detoxification, oxygen transport, oxidative phosphorylation, and lipid metabolism, suggesting that the animals were avoiding the generation of reactive oxygen species. ESTs matching hypothetical proteins and ESTs that had no GenBank match were also found to have been both upregulated and downregulated following heat stress, suggesting that novel genes may be involved in the heat stress response.

Modulation of Decapentaplegic gradient during haltere specification in Drosophila

Suppression of wing fate and specification of haltere fate in Drosophila by Ultrabithorax is a classical example of Hox regulation of serial homology. However, the mechanism of Ultrabithorax function in specifying haltere size and shape is not well understood. Here we show that Decapentaplegic signaling, which controls wing growth and shape, is a target of Ultrabithorax function during haltere specification. The Decapentaplegic signaling is down-regulated in haltere discs due to a combination of reduced levels of the Dpp, its trapping at the A/P boundary by increased levels of its receptor Thick-vein and its inability to diffuse in the absence of Dally. Results presented here suggest a complex mechanism adopted by Ultrabithorax to modulate Decapentaplegic signaling. We discuss how this complexity may regulate the final form of the adult haltere in the fly, without compromising features such as cell survival, which is also dependent on Decapentaplegic signaling.

Zebrafish promoter microarrays identify actively transcribed embryonic genes

The development and verification of a genomic microarray for ChIP-chip analysis of zebrafish genes is described.

We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation with an antibody directed against tri-methylated lysine 4 of Histone H3, we demonstrate the feasibility of this method in zebrafish. This approach will allow investigators to determine the genomic binding locations of DNA interacting proteins during development and expedite the assembly of the genetic networks that regulate embryogenesis.

DNA microarray technologies for measuring protein-DNA interactions

DNA-binding proteins have key roles in many cellular processes, including transcriptional regulation and replication. Microarray-based technologies permit the high-throughput identification of binding sites and enable the functional roles of these binding proteins to be elucidated. In particular, microarray readout either of chromatin immunoprecipitated DNA-bound proteins (ChIP-chip) or of DNA adenine methyltransferase fusion proteins (DamID) enables the identification of in vivo genomic target sites of proteins. A complementary approach to analyse the in vitro binding of proteins directly to double-stranded DNA microarrays (protein binding microarrays; PBMs), permits rapid characterization of their DNA binding site sequence specificities. Recent advances in DNA microarray synthesis technologies have facilitated the definition of DNA-binding sites at much higher resolution and coverage, and advances in these and emerging technologies will further increase the efficiencies of these exciting new approaches.

Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival

Although HSF1 plays an important role in the cellular response to proteotoxic stressors, little is known about the structure and function of the human HSF1 signaling network under both stressed and unstressed conditions. In this study, we used a combination of chromatin immunoprecipitation microarray analysis and time course gene expression microarray analysis with and without siRNA-mediated inhibition of HSF1 to comprehensively identify genes regulated directly and indirectly by HSF1. The correlation between promoter binding and gene expression was not significant for all genes bound by HSF1, suggesting that HSF1 binding per se is not sufficient for expression. However, the correlation with promoter binding was significant for genes identified as HSF1-regulated following siRNA knockdown. Among promoters bound by HSF1 following heat shock, a gene ontology analysis showed significant enrichment only in categories related to protein folding. In contrast, analysis of the extended HSF1 signaling network following siRNA knockdown showed enrichment in a variety of categories related to protein folding, anti-apoptosis, RNA splicing, ubiquitinylation and others, highlighting a complex transcriptional program regulated directly and indirectly by HSF1.

Drosophila melanogaster: a case study of a model genomic sequence and its consequences

The sequencing and annotation of the Drosophila melanogaster genome, first published in 2000 through collaboration between Celera Genomics and the Drosophila Genome Projects, has provided a number of important contributions to genome research. By demonstrating the utility of methods such as whole-genome shotgun sequencing and genome annotation by a community "jamboree," the Drosophila genome established the precedents for the current paradigm used by most genome projects. Subsequent releases of the initial genome sequence have been improved by the Berkeley Drosophila Genome Project and annotated by FlyBase, the Drosophila community database, providing one of the highest-quality genome sequences and annotations for any organism. We discuss the impact of the growing number of genome sequences now available in the genus on current Drosophila research, and some of the biological questions that these resources will enable to be solved in the future.

Spotted-dick, a zinc-finger protein of Drosophila required for expression of Orc4 and S phase

The highly condensed chromosomes and chromosome breaks in mitotic cells of a Drosophila mutant, spotted-dick/pita, are the consequence of defects in DNA replication. Reduction of levels of Spotted-dick protein, by either RNAi or mutation, leads to the accumulation of cells that have DNA content intermediate to 2N and 4N in proliferating tissues and also compromises endoreduplication in larval salivary glands. The Spotted-dick Zinc-finger protein is present in the nuclei of cells committed to proliferation but necessary in cells undertaking S phase. We show that Spotted-dick/Pita functions as a transcription factor and that, in cultured S2 cells, it is an activator of expression of some 30 genes that include the Orc4 gene, required for initiation of DNA replication. Chromatin immunoprecipitation indicates that it associates with the genes that it activates in S2 cells together with other sites that could represent genes activated in other tissues. We discuss the role of Spotted-dick in the coordination of cellular growth and DNA replication.