Suppressor of Hairy-wing [Su(Hw)] is a twelve zinc-finger (ZF), DNA binding transcription factor. Su(Hw) has been well characterized as critical component of the gypsy insulator complex, required for the enhancer blocking and the barrier activity of the insulator. In addition to gypsy, Su(Hw) localizes to ~3,000 binding sites in the Drosophila genome, with association to a subset of sites required for female germline development. Loss of Su(Hw) results in activation of a developmental checkpoint and apoptosis at mid- oogenesis, with a critical role during oogenesis in down-regulation of neural genes. Studies of Su(Hw) function have identified transcriptional activator, repressor and insulator roles at distinct binding sites. Current investigations aim to understand the factors that dictate the regulatory output of Su(Hw) at individual sites in the Drosophila genome, with a focus on the ZF domain. A genetic screen was completed to generate novel mutations in su(Hw). After screening more than 8,000 mutagenized chromosomes, we identified four new su(Hw) alleles, including two deletion mutations and two amino acid substitutions disrupting individual ZFs (ZF4 and ZF8). Studies of the ZF4 mutant, Su(Hw)M4M393, revealed that Su(Hw) requires this ZF for female fertility, but notgypsy insulator function. To achieve a comprehensive understanding of the Su(Hw) ZF domain, we generated Su(Hw) mutant proteins carrying disruptions in individual ZFs. Analyses utilizing these proteins have defined the requirement for each ZF in DNA association in vitro. To complement extant ZF alleles, Su(Hw) ZF mutants were expressed in vivo. Analyses of these mutants established how each ZF contributes to SBS occupancy, gypsy insulator function and female fertility. Gene expression and ChIP analyses suggest that some Su(Hw) ZFs may execute roles apart from direct DNA recognition. Genome-wide binding analyses of Su(Hw)M4M393, combined with previous studies, found that the SBS binding motif contains three DNA sequence cores (termed upstream, central and downstream). Analyses of these sequence cores in combination with Su(Hw) ZF mutants have outlined which ZFs associate with each core. Interestingly, the class containing all three sequence cores represents high occupancy SBSs that are enriched for protein factors from functional classes including transcriptional repression, nucleosome remodeling and DNA replication. The class containing the upstream and central core correlates with insulator function, while the class containing the central and downstream cores correlates with activation or repression of Su(Hw) target genes. Finally, in vitro studies of Su(Hw) ZF mutants revealed a DNA bound conformation distinct from wild type Su(Hw). Su(Hw) is a versatile transcription factor able to act as an insulator, activator and repressor. Analyses of SBSs with these functions suggest that DNA sequence, ZF usage, protein partnership and Su(Hw) conformation, combine to dictate regulatory output. Together, these studies provide insight into how discrete ZFs contribute to the roles of a multifunctional, polydactyl transcription factor.

The Drosophila Suppressor of Hairy-wing [Su(Hw)] protein is a multi-zinc finger DNA binding factor required for the gypsy insulator function. At the gypsy element, Su(Hw) recruits partners Centrosomal Protein of 190 kD (CP190) and Modifier of mdg4 67.2 kD isoform (Mod67.2), which facilitate the enhancer blocking and barrier functions of the insulator. Our genome-wide studies have identified thousands of endogenous non-gypsy Su(Hw) binding sites (SBSs) in Drosophila genome, constitutively occupied throughout development. Yet, only a third of SBSs associate with CP190 and Mod67.2, suggesting that the endogenous function of Su(Hw) may not necessarily involve formation of a gypsy-like chromatin insulator. To understand the function of endogenous SBSs, we investigated the requirement for Su(Hw) during female germline development. To this end, we performed genome-wide transcriptional analyses in su(Hw) mutant ovaries coupled with the genome-wide definition of ovary SBSs. We identified 49 direct targets of Su(Hw) regulation in the ovary, with 80% of these genes showing increased RNA accumulation when Su(Hw) is lost. Derepressed Su(Hw) targets are normally highly expressed in central nervous system, suggesting that Su(Hw) has a critical role in silencing neural genes in the non-neural tissues. We find that a single upregulated target gene is largely responsible for the female sterility of the su(Hw) mutants. This gene encodes an elav family factor RNA binding protein 9 (Rbp9), and Su(Hw)-mediated repression of Rbp9 is required at a specific stage of germline development. Decreasing the levels of Rbp9 restores female fertility of su(Hw) null mutants. Further, we demonstrate that Su(Hw) is required for transcriptional activation of pointed, gene involved in eggshell patterning during late embryogenesis. Importantly, both CP190 and Mod67.2 are dispensable for Rbp9 regulation, indicating that mechanism of Rbp9 repression is independent of the insulator function of Su(Hw). Our studies extend the known transcriptional activities of Su(Hw), indicating that it can function as an insulator, activator and repressor, the latter function being essential for oogenesis. These findings highlight that insulator proteins are versatile transcriptional regulators, suggesting that tissue specific contributions to transcription result from direct regulation of individual genes.

Transgenic mosquitoes are beneficial for the design and implementation of various pathogen control programs. However, low and variable expression of transgenes caused by position effects is a hindrance to the characterization and effective use of transgenes in mosquito species. The use of insulator sequences to flank transgenes may have the ability to overcome position effects caused by the genomic environment surrounding the insertion site. CTCF is a multifunctional protein, conserved from humans to Drosophila. Its role as an enhancer blocker in the Drosophila bithorax complex and its proximal binding to other insulator proteins on Drosophila chromosomes makes it a good candidate for identifying insulator sequences throughout the mosquito genome that may be used to improve mosquito transgenesis. Its multi-functionality as a transcription factor and genome organizer also makes CTCF worthy of investigation for an improved understanding of the regulation of the mosquito genome. This study uses chromatin immunoprecipitation with an An. gambiae CTCF antibody followed by Illumina deep sequencing (ChIP-Seq) to identify regions of CTCF binding throughout the An. gambiae genome. A subset of the CTCF binding site peaks was validated using ChIP-PCR. Another subset of this data set, including the ChIP-PCR validated peaks, was input into the motif finding tool, AlignACE, in order to identify a CTCF binding site consensus. Four motifs were identified, none of which were found in more than 11.9% of the ChIP-Seq data set. These results lead us to conclude that An. gambiae CTCF binds to a wider variety of sequences compared to Drosophila CTCF. This work also includes a comparison of the expression profiles of the dipteran insulator proteins, Su(Hw) and CP190, with that of CTCF across multiple life stages in Ae. aegypti. The results of this study suggest the possibility of genomic colocalization, as has been recently discovered in Drosophila. The identification of CTCF binding site peaks throughout the An. gambiae genome provides a large data set of potential insulator sequences that may be used to improve mosquito transgenesis, and provide a new model for the study of CTCF function in a species with medical significance.

Drosophila HP1 and Insulator Partner Protein 1 (HIPP1) is the homologue of the human co-repressor Chromodomain Y family of proteins that repress neuronal gene expression in mammals. HIPP1 was identified by its extensive co-localization with Heterochromatin Protein 1a (HP1a) in heterochromatic regions of the genome and insulator binding proteins in euchromatic regions. The majority of HIPP1 binding to euchromatin is at binding sites for Drosophila Suppressor of Hairy-wing [Su(Hw)]. Su(Hw) is a zinc finger DNA binding protein that functions as an insulator, activator, and repressor. Transcriptional regulation by Su(Hw) is essential in the ovary and testis, where Su(Hw) functions primarily as a repressor of neuronal genes. However, the mechanism of Su(Hw) dependent repression is not clear. The focus of my thesis work has been defining the role of HIPP1 in development and its contribution to Su(Hw) function and heterochromatin formation. As part of this work, CRISPR was used to generate multiple Hipp1 null alleles and a tagged derivative of the endogenous gene (Hipp1GFP). Hipp1 null flies were found to be viable. Study of HIPP1 expression revealed it is present in most tissues and restricted to the nucleus. HIPP1 showed limited colocalization with HP1a, and tests of repression of transgenes in heterochromatin suggested that HIPP1 is not required for heterochromatin formation. Investigations of HIPP1 binding revealed that Su(Hw) is responsible for the majority of HIPP1 recruitment to euchromatin. Despite this, HIPP1 was found to be dispensable for the transcriptional and insulator functions of Su(Hw) as well as for female and male fertility. These data indicate that HIPP1 is not a critical Su(Hw) cofactor. Further studies are needed to clarify the role of HIPP1 in Drosophila development.

ABSTRACT Chromatin insulators are required for proper temporal and spatial expression of genes in metazoans. Insulators are thought to play an important role in the regulation of gene expression through the formation of higher-order chromatin structures. One of the best characterized insulators is the Drosophila gypsy insulator, which is located in the gypsy retrovirus. Several proteins are required for gypsy insulator function, including Su(Hw), Mod(mdg4), and CP190. In addition to the gypsy insulator, these proteins are located throughout the genome at sites which are thought to correspond to endogenous insulators. Analysis of the distribution of insulator proteins across a region of chromosome 2R in Drosophila polytene chromosomes shows that Su(Hw) is found in three structures differentially associated with insulator proteins: bands, interbands and domains of coexpressed genes. Bands are formed by condensation of chromatin within genes containing one or more Su(Hw) binding sites, while Su(Hw) sites in interbands appear to form structures normally associated with open chromatin. Bands characterized by the lack of CP190 and BEAF-32 insulator proteins are formed by clusters of coexpressed genes, and these bands correlate with the distribution of specific chromatin marks. Conservation of the band interband pattern, as well as the distribution of insulator proteins in nurse cells, suggests that this organization may represent the basic organization of interphasic chromosomes. We also show that, in addition to the gypsy insulator, sequence analysis predicts the presence of Su(Hw) binding sites within a number of transposable elements. Su(Hw) binds to predicted sites within gtwin and jockey, which possesses enhancer-blocking activity. Su(Hw) affects the tissue-specific expression of transposable elements, although this effect is unrelated to the presence of Su(Hw) binding sites within the element or control of the elements via the piRNA pathway. Additionally, the effect of Su(Hw) on transposable element expression often differs from that of Mod(mdg4). Taken together, these results suggest that insulator proteins associate specifically with, and may help to define, various levels of chromatin organization on polytene chromosomes. Also, gypsy insulator proteins may influence the expression of transposable elements in a way that does not depend on Su(Hw) binding sites within the elements themselves.

Chromatin insulators are short DNA sequences that, together with enhancers and silencers, orchestrate gene transcription through DNA-protein interactions in eukaryotic genomes. It has been proposed that insulators operate at the chromatin level by generating functionally independent higher-order chromatin domains. Insulators may maintain the integrity of such domains using two properties: blocking enhancer-promoter interactions and blocking heterochromatin spreading. The gypsy insulator of Drosophila was identified as a region of the gypsy retrovirus responsible for the production of tissue-specific mutations in many genes. The Suppressor of Hairy wing [Su(Hw)] protein contains 12 zinc fingers that specifically bind the gypsy insulator. Upon DNA binding, Su(Hw) recruits a second protein, Modifier of Mdg4 67.2 [Mod(mdg4) 67.2], and the interaction of both proteins is required for insulator function in vivo. We have found that three different arrays of gypsy retrovirus insertions in a yellow transgene result in unique yellow phenotypes, showing that the enhancer-blocking activity of the Drosophila gypsy insulators depends on the relative orientation of the gypsy retroviruses on the chromosome. We also observed from transgenic lines with gypsy retrovirus or insulator insertions that interaction of insulators may be regulated by active enhancers according to the relative positions of the insulators flanking the enhancers. Moreover, we show that gypsy insulators can positively modulate yellow activation and result in wild-type levels of expression when placed upstream of enhancers in yellow transgenes in which enhancers are placed out of context by &#;-DNA spacers and fail to reproduce the expression levels of yellow in wings and body cuticle. Our results provide evidence indicating that this phenomenon is independent of the boundary activity. Genetic analysis using mod(mdg4)67.2 mutant lines containing gypsy retrovirus insertions revealed that the gypsy insulator may be placed close to the yellow promoter region and be intimately involved in transcriptional activation and repression. Therefore, we suggest that insulators may also function by mediating long range interactions between enhancers and promoters.