The Anopheles gambiae complex is comprised of the most important vectors of malaria in Sub-Saharan Africa. Most current control methods involve the use of chemicals that help to limit potential contact with these mosquitoes. However, these control methods still have risks that include insect resistance, environmental toxicity, human health, as well as animal health. In order to develop new strategies that either produce novel targeted insecticides or transgenic mosquitoes that can replace current mosquito populations, it is important to acquire as much biological information about the vector as possible. The reduction in cost and speed of high-throughput sequencing has brought forth many new sequenced genomes that can provide a wealth of information about individual populations as well as their respective evolutionary histories. However, in order to fully understand a genome, these sequences must be assembled properly. One of the largest challenges toward fully assembling a genome is the abundance of repetitive sequences. These sequences, typically part of gene poor regions known as heterochromatin, are generally left as unassembled scaffolds that are neglected in many genomic studies. Heterochromatin is a biologically important chromatin state that has roles in gene regulation and genome stability. Exclusion of these chromatin domains from experimental assays can provide an incomplete picture in regards to organismal biology. A lack of information regarding heterochromatin, even in An. gambiae, necessitates further understanding and characterization of this chromatin type that can provide valuable information about the mosquito's biology. Heterochromatin is organized differently amongst different species. Some species with compact genomes, like Drosophila melanogaster, exhibit rigid organization of heterochromatin, with repetitive elements being confined to peri-centromeric and sub-telomeric regions of the chromosome. Larger genomes such as Aedes aegypti, have a much less structured heterochromatin pattern, with repetitive elements being dispersed across the genome. However, An. gambiae's genome is more intermediate in size as well as transposable element content. These factors may have an impact in controlling how heterochromatin is organized within the An. gambiae genome. Does An. gambiae compensate for the increased genome size by expanding past the peri-centromeric heterochromatin into new intercalary compartments? In An. gambiae, heterochromatin had yet to be identified separately from euchromatin. Morphologically, some regions of An. gambiae chromosomes exhibited characteristics similar to transcriptionally active puffs or peri-centromeric heterochromatin. We characterize these regions, as well as the rest of the genomic landscape, by using morphological and genetic features to identify various chromatin types. Peri-centromeric heterochromatin and new regions of intercalary heterochromatin were identified. Genomic coordinates representing the transition from euchromatin to heterochromatin were also identified. By finding these heterochromatin-euchromatin boundaries, various genetic features could be assigned to either heterochromatin or euchromatin. Critical genes associated with heterochromatin formation and basic genomic functions were identified. These data help to better understand features that are associated with the different environments created by chromatin compaction. This study also looks at the Piwi-interacting RNA (piRNA) pathway and its role in An. gambiae. The piRNA pathway is associated with transposable element (TE) suppression in many species, where clusters of vestigial TEs provide some of the RNA necessary for the pathway to function. These clusters are primarily associated with heterochromatin in Drosophila melanogaster. We identify piRNA clusters in An. gambiae and see a similar shift from primarily peri-centromeric compartmentalization toward the presence of intercalary regions located within the euchromatin. Transposable elements are maintained in secondary heterochromatin regions that exhibit similar morphology and features to peri-centromeric heterochromatin. The piRNA pathway also has implications in gene regulation, germline development, and anti-viral immunity. Three candidate genes associated with spermatogenesis and embryogenesis have been identified. These genes showed piRNA enrichment, and upon further analysis show up-regulation after a blood meal is taken. These genes could potentially prove useful in vector control as targets of transgenic experiments. Heterochromatin is an important, yet neglected aspect of the genome. These studies attempt to provide data to stimulate the study of heterochromatin through characterization of heterochromatin-related genomic features. / Ph. D.

Maintenance of an intact genome and proper regulation of the genes within are crucial aspects for life. The work of this dissertation has implicated the Drosophila condensin II complex in both processes. Condensin II's ability to reconfigure chromosomes into spatially separated and discrete units is necessary to ensure proper meiotic segregation. When this "individualization" activity fails in a condensin II mutant, chromosomes remain entangled, and either cosegregate or become lost during cell division. This leads to the creation of aneuploid sperm. We have also implicated condensin II as a factor necessary to individualize interphase somatic chromosomes from one another. This is relevant in Drosophila because the association of homologous chromosomes is thought to facilitate gene regulation activity in trans. We speculate that condensin II individualization spatially distances aligned chromosomes from one another and prevents this trans-communication between allelic loci. This is supported first by an increase of homologous chromosome pairing in a condensin II mutant background. Secondly, loss of condensin II leads to elevated production from alleles that are known to depend on pairing for transcriptional activation. These meiotic and interphase condensin II roles support its necessity to Drosophila genome integrity and transcriptional regulation. Given the conservation of condensin from bacteria to humans, it is likely that equivalent or related roles exist in a variety of species.

Com a idéia de identificar proteínas envolvidas no processo de enovelamento das proteínas sintetizadas na glândula salivar de Rhynchosciara americana, no início deste projeto adotou-se como estratégia o seqüenciamento de uma biblioteca de cDNA. Esta biblioteca foi construída utilizando-se glândulas salivares de Rhynchosciara americana do período de seu desenvolvimento onde tem início a síntese de seu casulo. Mensagens de proteínas envolvidas no processo de enovelamento, transporte e proteólise foram isoladas, alguns exemplos são hsc70, hsp83, hip, hop, dnaJ, trap1 e prolil isomerase, sec61α/β, sec23, peptidase de sinal, rab7, partícula reconhecedora de sinal (srp), enzima conjugadora de ubiquitina e complexo regulatório proteassomo 26, cop 1 e ubiquitina ligase. A identificação destes genes permitiu o isolamento de clones genômicos através de triagem em banco de fagos e caracterização dos genes hsc70 e hsp83 para verificação de sua organização em Rhynchosciara americana. A expressão dos seus respectivos mRNAs foi avaliada em vários períodos do último estágio larval. A localização por hibridização in situ mostrou que estes genes estão localizados em regiões dos cromossomos politênicos próximas a dois pufes de DNA, C3 e C8. O estudo dos níveis de expressão das proteínas codificadas pelos genes hsc70 e hsp83 mostrou a diferença de comportamento destes genes sob condições de estresse térmico e que a expressão destas proteínas deve ser regulada pelo período de desenvolvimento das larvas de Rhynchosciara americana. Quando evidenciada por imunofluorescência a proteína Hsc70 mostra localização predominantemente no citoplasma. / With the idea of identify some of these proteins involved in the folding process of the proteins synthesized on the Rhynchosciara salivary gland, this project started adopting the shotgun cDNA sequencing strategy. This cDNA library was constructed utilizing salivary glands of Rhynchosciara americana at a developmental period where the cocoon construction begins. Messengers of important proteins involved in the folding, transport and proteolysis process were isolated, some examples are hsc70, hsp83, hip, hop, sec61 α/β, sec23, signal peptidase, rab7, signal recognition particle (srp), ubiquitin conjugating enzyme e 26 proteasome regulatory complex, cop 1 and ubiquitin ligase. Identification of these genes allowed the screening of genomic clones from a phage library; hsc70 and hsp83 characterization was carried out to verify the arrangement of these genes on genome of Rhynchosciara americana. The study of these genes will contribute with phylogenetic information about the specie. The mRNA expression of these genes was analyzed during several periods of the last larval developmental stage. In situ localization showed that these genes are located in polytene chromosomes regions near two DNAs puffs, C3 and C8. The expression levels of the proteins codified by genes hsc70 and hsp83 showed different behaviors of these genes under heat stress conditions and mainly, that the regulation of the proteins Hsc70 and Hsp83 can be related to the period of development of the larvae of Rhynchosciara americana. When revealed by immunofluorescence, Hsc70 protein shows localization predominantly on the cytoplasm.

Com a idéia de identificar proteínas envolvidas no processo de enovelamento das proteínas sintetizadas na glândula salivar de Rhynchosciara americana, no início deste projeto adotou-se como estratégia o seqüenciamento de uma biblioteca de cDNA. Esta biblioteca foi construída utilizando-se glândulas salivares de Rhynchosciara americana do período de seu desenvolvimento onde tem início a síntese de seu casulo. Mensagens de proteínas envolvidas no processo de enovelamento, transporte e proteólise foram isoladas, alguns exemplos são hsc70, hsp83, hip, hop, dnaJ, trap1 e prolil isomerase, sec61α/β, sec23, peptidase de sinal, rab7, partícula reconhecedora de sinal (srp), enzima conjugadora de ubiquitina e complexo regulatório proteassomo 26, cop 1 e ubiquitina ligase. A identificação destes genes permitiu o isolamento de clones genômicos através de triagem em banco de fagos e caracterização dos genes hsc70 e hsp83 para verificação de sua organização em Rhynchosciara americana. A expressão dos seus respectivos mRNAs foi avaliada em vários períodos do último estágio larval. A localização por hibridização in situ mostrou que estes genes estão localizados em regiões dos cromossomos politênicos próximas a dois pufes de DNA, C3 e C8. O estudo dos níveis de expressão das proteínas codificadas pelos genes hsc70 e hsp83 mostrou a diferença de comportamento destes genes sob condições de estresse térmico e que a expressão destas proteínas deve ser regulada pelo período de desenvolvimento das larvas de Rhynchosciara americana. Quando evidenciada por imunofluorescência a proteína Hsc70 mostra localização predominantemente no citoplasma. / With the idea of identify some of these proteins involved in the folding process of the proteins synthesized on the Rhynchosciara salivary gland, this project started adopting the shotgun cDNA sequencing strategy. This cDNA library was constructed utilizing salivary glands of Rhynchosciara americana at a developmental period where the cocoon construction begins. Messengers of important proteins involved in the folding, transport and proteolysis process were isolated, some examples are hsc70, hsp83, hip, hop, sec61 α/β, sec23, signal peptidase, rab7, signal recognition particle (srp), ubiquitin conjugating enzyme e 26 proteasome regulatory complex, cop 1 and ubiquitin ligase. Identification of these genes allowed the screening of genomic clones from a phage library; hsc70 and hsp83 characterization was carried out to verify the arrangement of these genes on genome of Rhynchosciara americana. The study of these genes will contribute with phylogenetic information about the specie. The mRNA expression of these genes was analyzed during several periods of the last larval developmental stage. In situ localization showed that these genes are located in polytene chromosomes regions near two DNAs puffs, C3 and C8. The expression levels of the proteins codified by genes hsc70 and hsp83 showed different behaviors of these genes under heat stress conditions and mainly, that the regulation of the proteins Hsc70 and Hsp83 can be related to the period of development of the larvae of Rhynchosciara americana. When revealed by immunofluorescence, Hsc70 protein shows localization predominantly on the cytoplasm.

Polytäne Chromosomen von Drosophila sind in eine Abfolge von Banden und Interbanden unterschiedlichen Kompaktionsgrades gegliedert. Das Protein Z4 ist notwendig, um dieses Muster aufrecht zu erhalten (Eggert et al., 2004). Durch Koimmunpräzipitation mit Z4 wurde in unserer Arbeitsgruppe ein Chromodomänen Protein identifiziert, das von uns als Chriz bezeichnet wurde (Gortchakov et al., 2005). In meiner Arbeit testete ich die Interaktion zwischen den vollständigen Proteinen Chriz und Z4. Ich konnte dabei zeigen, dass beide Proteine in vivo direkt miteinander interagieren. Die kartierten Interaktionsdomänen am N-Terminus von Z4 und am C-Terminus von Chriz sind hinreichend für die wechselseitige Interaktion beider Proteine. Chriz ist wie Z4 in vielen Interbanden polytäner Interphasechromosomen gebunden. Die überexpression verschiedener Domänen von Chriz zeigte, dass sowohl der N- als auch der C-Terminus von Chriz für die Interbandenbindung von Chriz ausreichend sind. Der Chriz C-Terminus ist dar Über hinaus notwendig, um das überleben von Tieren mit einer Chriz Null Mutation bis in das larvale Stadium zu gewährleisten. Tiere mit induziertem Chriz RNAi knock down zeigten eine verringerte DNA Kondensation polytäner Chromosomen. Die Ähnlichkeit des chromosomalen Phänotyps von Z4 und Chriz Mutationen legt nahe, dass beide Proteine in einem gemeinsamen Komplex in Interbanden vorkommen. Unter Ausnutzung von Chriz RNAi bzw. Z4 RNAi konnte ich zeigen, dass die chromosomale Bindung von Z4 von Chriz abhängt. Weiterhin sind die Proteinkinase Jil-1 und an Serin 10 phosphoryliertes H3 (H3pS10), beides Marker für dekondensiertes Chromatin, in Chriz RNAi Tieren verringert. Aus meinen Daten schliesse ich, dass Chriz/Z4/Jil-1 in einem gemeinsamen Komplex an Interbanden gebunden sind. Chriz ist dabei fundamental wichtig für die zielgerichtete Bindung und Stabilität des Komplexes. Der Komplex selbst ist erforderlich, um die lokale Chromatinstruktur aufrecht zu erthalten. / Drosophila polytene chromosomes are compacted into a series of bands and interbands. Z4 is a protein to keep this pattern, since Z4 mutant larvae show a decompaction of chromosomes and a loss of banding pattern (Eggert et al., 2004). By coimmuno-precipitation, we identified a chromodomain protein, which we named Chriz, for chromodomain protein interacting with Z4 (Gortchakov et al., 2005). In my PhD thesis, I tested the interactions between the full length proteins and different fragments of Chriz and Z4 which showed that Chriz could directly interact with Z4 in vivo. The interaction domains were mapped and it was determined that the N terminus of Z4 and the C terminus of Chriz are sufficient for mutual interaction. GST pull down confirmed these data and more precisely localized the interaction domains. Chriz, like Z4, is present in many interbands of interphase polytene chromosomes. The overexpression of different domains of Chriz demonstrated that both the N and C terminus are sufficient for targeting of Chriz to interbands. The C terminus was shown to be sufficient for rescue of Chriz null mutations into larva stage. Chriz full length proteins, with site directed mutations within the chromodomain, could still partially rescue the null mutant. Chriz RNAi knock down resulted in a loss of structure of polytene chromosome. The similar chromosomal phenotype of Z4 and Chriz indicate that they cooperate in the formation of chromosomal structure. Using the Chriz RNAi, I showed that Z4 chromosomal binding is dependent on Chriz. However, by a similar assay I showed that Chriz binding did not depend on Z4. Finally, the decondensed interphase chromatin marker Jil-1, a H3S10 histone kinase, and H3pS10 are decreased in Chriz RNAi line. From these data, I conclude that Chriz/Z4/Jil-1 form an interband binding complex. Chriz is the fundamental factor for the chromosomal targeting and stabilitation of the complex that is required to maintain locally chromatin structure.

Polytäne Riesenchromosomen von Drosophila melanogaster bieten ein ideales Modellsystem für die Untersuchung der Mechanismen zur strukturellen Bildung chromosomaler Domänen. Über Manipulation und Rekonstruktion des chromosomalen Bandenmusters polytäner Chromosomen können artifiziell kondensierte als auch dekondensierte Domänen etabliert werden. Diese Eigenschaft habe ich in meiner Arbeit genutzt für die Etablierung eines experimentellen Systems zur Analyse der strukturellen Vorraussetzungen zur Bildung offener Chromatindomänen. Dafür wurde eine transgene kondensierte Chromatindomäne ektopisch innerhalb offenen Chromatins generiert. Diese kondensierte „Modellbande“ bietet einen definierten genetischen Hintergrund für die gezielte Insertion von DNA-Sequenzen unter Ausschluss variabler Positionseffekte und ermöglicht dadurch eine vergleichende Analyse dieser Sequenzen auf ihr Vermögen offenes Chromatin zu bilden. Zu diesem Zweck wurde über Sequenz-spezifische Rekombination die 61C7/8 Interbandensequenz gezielt in die „Modellbande“ eingefügt. Die zytogenetische Untersuchung dieser Insertion zeigt, dass infolge der Insertion offenes Chromatin gebildet wird, was in einer Aufsplittung der kondensierten „Modellbande“ resultiert. Molekulare Analysen weisen darauf hin, dass auch die epigenetischen Charakteristika wie z.B. die Rekrutierung typischer Proteine oder transkriptionelle Eigenschaften zur endogenen Domäne immitiert werden. Über Deletionsanalysen konnte von mir die essentielle DNA-Sequenz zur Bildung offenen Chromatins auf ein ~490bp großes Fragment im proximalen Bereich der 61C7/8 Sequenz kartiert werden. Dieses Fragment überlappt mit Bindungsstellen spezifischer Proteine, welche dafür bekannt sind eine Rolle in der chromosomalen Domänenbildung zu spielen wie z.B. das Chromatin-Protein Chriz, die Histon-Kinase Jil1 oder das Insulator-Protein CP190. Desweiteren überlappt es mit einer Promoterregion, welche zwischen den Genen Rev1 und Med30 lokalisiert ist. / Polytene chromosomes of Drosophila melanogaster provides an ideal model-system for the analysis of the mechanisms needed for chromosomal domain formation. Condensed as well as decondensed chromosomal domains can be formed by manipulating and reconstructing the polytene banding pattern. This possibility i ha-ve used for the establishment of an experimental system to study the structural requirements for open chromatin formation. Therefor i have generated a condensed chromatin domain at ectopic positions. This condensed „model“ domain provides a defined genetic context for the targeted insertion of sequences of interest, excluding any variable position effects. This allows comarative analysis of different sequences in order to identify the structural requirements for open chromatin formation. For this purpose the 61C7/8 interband sequence was targetly integrated into the condensed „model“ domain by site-specific recombination. Thereby i could show that the 61C7/8 interband sequence maintains the capacity to form open chromatin cognizable by the splitting of the condensed „model“ domain. Furthermore the newly formed open chromatin domain also keeps epigenetic characteristica like transcriptional activity or the recruitment of typical proteins. By deletion analysis, i have mapped the essential region needed for open chromatin formation to a ~490bp fragment located in the proximal part of the 61C7/8 interband sequence. This fragment overlaps binding sites for characteristic proteins known to be involved in chromosomal domain formation like the chromatin protein Chriz, the histone kinase Jil1 or the insulator protein CP190. Furthermore the fragment overlaps a promoter region that locates between the Rev1 and Med30 genes.

Title: The subnuclear localisation of Notch responsive genes. Candidate Name: Matthew Jones Notch signalling is a highly conserved cell-cell communication pathway with critical roles in metazoan development and mutations in Notch pathway components are implicated in many types of cancer. Notch is an excellent and well-studied model of biological signalling and gene regulation, with a single intracellular messenger, one receptor and two ligands in Drosophila. However, despite the limited number of chemical players involved, a striking number of different outcomes arise. Molecular studies have shown that Notch activates different targets in different cell types and it is well known that Notch is important for maintaining a stem cell fate in some situations and driving differentiation in others. Thus some of the factors affecting the regulation of Notch target genes are yet to be discovered. Previous studies in various organisms have found that the location of a gene within the nucleus is important for its regulation and genome reorganisation can occur following gene activation or during development. Therefore this project aimed to label individual Notch responsive loci and determine their subnuclear localisation. In order to tag loci of interest a CRISPR/Cas9 genome-editing method was established that enabled the insertion of locus tags at Notch targets, namely the well-characterized Enhancer of split locus and also dpn and Hey, two transcription factors involved in neural cell fate decisions. The ParB/Int system is a recently developed locus tagging system and is not well characterised in Drosophila. It has a number of advantages over the traditional LacO/LacI-GFP locus tagging system as it does not rely on binding site repeats for signal amplification and can label two loci simultaneously in different colours. This thesis characterised the ParB/Int system in the Drosophila salivary gland and larval L3 neuroblast. Using 3D image segmentation hundreds of nuclei were reconstructed and a volume based normalisation method was applied to determine the subnuclear localisation of several Notch targets with and without genetic manipulations of the Notch pathway.