<p>The centromere is essential for chromosome segregation and genome stability. It is the site of kinetochore assembly and chromosome attachment to the spindle microtubules, and it is important for chromosome movement during mitosis and meiosis. Normal human chromosomes have one centromere, but genome rearrangements that occur with instability, aging, and disease often result in chromosomes with two centromeres, called dicentrics. Nearly seventy-five years ago, Barbara McClintock demonstrated that dicentric chromosomes in plants are associated with instability through mitotic "breakage-fusion-bridge" cycles. However, human dicentrics are unusually stable due to the poorly understood phenomenon of centromere inactivation. Centromere inactivation has been primarily studied in patient-derived dicentrics, limiting the derivation of a molecular pathway. Key centromere and kinetochore proteins are not present at inactive centromeres, but beyond these observations, the process of centromere inactivation is unclear. Epigenetic and sequence-dependent factors are known to contribute to centromere specification, but requirements for centromere assembly, maintenance, and suppression remain obscure. The aims of this research were to (1) determine the mechanism(s) by which de novo dicentric chromosomes are stabilized, (2) ascertain the factors influencing the involvement of specific chromosomes in de novo fusions, and (3) establish the epigenomic, temporal, and mechanistic basis of centromere inactivation. To uncover the mechanistic foundations of these processes, we developed in vitro cell culture systems to study the formation and stabilization of de novo dicentrics. We demonstrate that transient disruption of human telomere structure non-randomly produces dicentric fusions involving acrocentric chromosomes. This finding is notable since the most prevalent rearrangement in humans involves the acrocentrics and is called Robertsonian translocation (ROB). In some cases, centromere inactivation occurs by an apparently epigenetic mechanism. In other dicentrics, the size of the centromeric DNA array is reduced compared to the same array before dicentric formation. Many functional dicentrics persist for months after formation. Our results indicate that dicentric human chromosomes undergo alternative fates after formation across a broad temporal window. During transient telomere disruption, we observed a dramatic change in nucleolar appearance. Nucleolar proteins did not coalesce into condensed structures, but appeared dispersed throughout the nucleus. This surprising alteration in nucleolar organization and nuclear architecture suggests remodeling of the nucleolus and subsequent effects on nucleolar-associated chromosomes, such as the acrocentrics, could contribute to the high incidence of ROB formation. Further studies and development of additional cell culture systems will allow us to evaluate current models of centromere assembly and disassembly and the importance of chromatin organization to centromere function and genome architecture.</p> / Dissertation

Here I describe the construction and characterization of a new generation of human artificial chromosome that contains an array of DNA sequences that can be used to manipulate the chromosome in vivo and possibly in vitro. This HAC was originated in human fibrosarcoma HT1080 cells from a synthetic alphoid DNA containing an array of TetOperator sequences, cloned in a BAC-based vector. This synthetic ά-satellite DNA formed HACs that were stably maintained throughtout replication and segregation in HT1080 cells. However, I succeeded to also transfer and manipulate the alphoidtetO HAC into a HeLa-based hybrid cell line. The synthetic alphoidtetO HAC chromatin was similar to the chromatin at endogenous centromeric alphoid DNA. Importantly, the DNA sequences embedded in the synthetic HAC were accessible to targeting TetR-fused constructs in vivo. The alphoidtetO HAC could be successfully targeted with a number of TetR:fusion proteins without affecting its chromatin structure, kinetochore assembly and mitotic behaviour. However, the targeting of a transcriptional activator (tTA) inactivated the HAC synthetic alphoidtetO DNA in a fraction of transfected cells. Surprisingly, the targeting of the transcriptional repressor tTS, co-repressor KAP1 or the heterochromatin-associated protein HPIά severely inactivated the synthetic alphoidtetO kinetochore . In fact, upon targeting several inner and outer kinetochore proteins were delocalized from the alphoidtetO sequences. The dissociation of kinetochore proteins CENP-H and CENP-C appeared to precede that of CENP-A. The alphoidtetO HAC lacking inner kinetochore protein complexes showed mitotic defects including misalignment at the metaphase plate and defective anaphase segregation, ultimately being included in tiny DAPI-positive nano-nuclei in the cytoplasm. The transcriptional repressor tTS repressed the low levels of transcription from the alphoidtetO sequences. In addition, targeting of transcriptional repressors altered the HAC chromatin towards a more “closed”, heterochromatic conformation, as seen from the changes in histone tail modifications. Interestingly, the targeting of the histone methyltransferase EZH2 to the alphoidteto HAC showed a much milder inactivating activity compared to KAP1. Based on these results, I propose that the formation of HPI-type of heterochromatin or accumulation of HPIά to the centromeric regions could disrupt the association of constitutive kinetochore proteins to the underlying sequences. Centromeric alphoid sequences lacking a functional kinetochore structure then also loose the centromere-specific histone H3 variant CENP-A becoming definitively inactive. Alternatively, a basal transcriptional activity from centromeric sequences might be required for centromere functionality.

Le complexe cohésine maintient associées les chromatides sœurs depuis la réplication jusqu’à leur ségrégation en mitose. Une question majeure est de comprendre comment la cohésion est établie lors de la phase S. Chez les mammifères et S. pombe, les cohésines sont associées de manière labile aux chromosomes pré-réplicatifs et l’établissement de la cohésion en phase S s’accompagne de la stabilisation de l’association des cohésines aux chromosomes. L’objectif de ce travail est de comprendre comment la dynamique des cohésines est régulée et comment son inhibition créée la cohésion.En G1 les cohésines associées aux chromosomes s’échangent avec le pool soluble et leur dissociation dépend de Pds5 et Wapl. La première partie de ce travail présente les résultats d’un crible génétique visant à identifier de nouveaux régulateurs de la dynamique des cohésines.L’établissement de la cohésion nécessite l’acétyltransférase Eso1 mais pas en contexte Δwpl1, indiquant que la seule mais essentielle fonction d’Eso1 est de s’opposer à celle de Wapl. L’acétylation de Smc3 par Eso1 contribue mais n’est pas suffisante pour contrecarrer Wapl, suggérant l’existence d’un autre événement dépendant d’Eso1. En G1, Pds5 agit avec Wapl pour dissocier les cohésines des chromosomes mais après la phase S, Pds5 est requise pour leur maintien sur les chromosomes et pour la cohésion à long terme. Pds5 co-localise avec la fraction stable de cohésines mais pas Wapl. Nous suggérons un modèle dans lequel la cohésion est créée par deux événements d’acétylation couplés à la progression de la fourche de réplication conduisant à l’éviction de Wapl des cohésines destinées à produire la cohésion. / Following DNA replication, sister chromatids are connected by cohesin to ensure their correct segregation during mitosis. How cohesion is created is still enigmatic. The cohesin subunit Smc3 becomes acetylated by ECO1, a conserved acetyl-transferase, and this change is required for cohesion. As in mammals, fission yeast cohesin is not stably bound to G1 chromosomes but a fraction becomes stable when cohesion is made. The aim of this work was to understand how cohesin dynamics is regulated and how the change in cohesin dynamics creates cohesion.In G1 chromatin bound cohesin exchange with the soluble pool and the unloading reaction relies in part on Wapl. The first part of this study reports on the identification of G1/S factors as new candidate regulators of cohesin dynamics.Following S phase a stable cohesin fraction is made. The acetyl-transferase Eso1 is not required for this reaction when the wpl1 gene is deleted. Yet, it is in wild-type cells, showing that the sole but essential Eso1 function is counteracting Wapl. Eso1 acetylates the cohesin sub-unit Smc3. This renders cohesin less sensitive to Wapl but does not confer the stable binding mode, suggesting the existence of a second Eso1-dependent event. The cohesin sub-unit Pds5 act together with Wapl to promote cohesin removal from G1 chromosomes but after S phase Pds5 is essential for cohesin retention on chromosomes and long term cohesion. Pds5 co-localizes with the stable cohesin fraction whereas Wapl does not. We suggest a model in which cohesion establishment is made by two acetylation events coupled to fork progression leading to Wapl eviction while keeping Pds5 on cohesin complexes intended to make cohesion.

DNA translocases are molecular motors that use energy from nucleotide triphosphate (NTP) hydrolysis to move along, pump, remodel or clear DNA. Unlike helicases, double-stranded DNA (dsDNA) translocases do not unwind DNA; their action has no net product apart from inducing supercoils as a result of groove-tracking, which has hampered their characterisation. Many dsDNA translocases appear to have biased directionality. However, the inherent symmetry of dsDNA requires that translocase activity is regulated by specific sequences or through modulation by interaction partners. FtsK is a highly conserved bacterial cell-division protein, localised to the dividing septum, that coordinates chromosome segregation with cytokinesis. It is responsible for the resolution of chromosome dimers by activating the tyrosine recombinases XerCD bound to the 28bp chromosomal site dif. The C-terminal domain of FtsK (FtsKC) is a dsDNA translocase (speed ~5 kb/s, stall force ~60 pN) most closely related to superfamily 4 helicases and is active as a hexameric ring. A winged-helix subdomain at the C-terminus of FtsKC, FtsKgamma, binds to specific 8 bp sequences, KOPS, that are polarised in the bacterial chromosome from the origin to towards dif. FtsKgamma also interacts with XerD, activating it for catalysis. Studies of FtsK translocation have differed over whether KOPS act as a loading or a reversal sequence for FtsK. In Chapter 2, I use a continuous ensemble assay for dsDNA translocation to show that FtsK initiates rapidly at KOPS, with loading dependent on FtsKgamma. Translocation requires moderately cooperative ATP binding, while ATP hydrolysis has a more relaxed cooperativity. I have determined the ATP coupling efficiency of translocation to be ~1.6 bp/ATP, in line with theoretical estimates. Though FtsK probably strips most proteins from DNA, I show in Chapter 3 that FtsK stops translocating when it encounters XerCD bound to dif. The interaction is most likely a specific down-regulation, but surprisingly does not depend on FtsKgamma or on the catalytic or synaptic activity of XerCD. In Chapter 4, I show some preliminary structural data of FtsKC bound to dsDNA, with the aim of determining the first high resolution structure of a ring dsDNA translocase bound to nucleic acid.

Following their dispersal out of Africa, humans colonised all continents of the world save one, Antarctica. Whilst Europe was initially peopled soon after this exodus, paleoclimatic, archaeological, and historical evidence suggest that successive waves and migrations of people have contributed to the population resident in Europe today. I therefore examined the impact of past events on the European population through the analysis of DNA sampled both from contemporary Europeans, and from worldwide populations pertinent to its history. I genotyped and analysed data from the Y chromosomes of over 2,000 haplogroup R-M269 European men from over 30 different populations and, in combination with comparable datasets gathered from the literature, show that there it is not possible to assign a date to the origin of this lineage in Europe, and thus that any conclusion as to the ancient or recent spread of this lineage in Europe is unfounded. I also show that commonly used Y chromosome lineage dating techniques based on STR variation are biased by the markers used and conclusions based on such dates should be viewed with a large amount of caution. I next use genome-wide SNP data from 1,550 individuals from 95 worldwide populations to explore the population structure of Europe and present an analysis of the detailed structure of Europe in a novel analytical framework using ChromoPainter and fineSTRUCTURE. Admixture analysis based this data reveals distinct genomic inputs to peripheral European populations, from North Africa, Sub-Saharan Africa, the Middle East, and East Asia, and provides dates for this admixture within the last 1,000 years that correspond to the emergence and decline of empires and kingdoms in these regions of Europe. This novel analysis highlights the importance of recent historical events on European population structure, but also suggests a degree of ancient structure across European populations. Taken together, these analyses demonstrate the substantial effects of both ancient and recent migrations and mixture on the contemporary genetic structure of Europe.

This thesis investigates patterns and mechanisms of gene expression in P. falciparum. The rapidly cycling patterns of genes during the asexual stages confounds the analysis of gene expression in culture and in patients. In order to overcome this problem, we develop statistical models to estimate the temporal progression of malaria parasites by using the observed gene expression values and known reference sets. We extend this framework to account for lineage commitment, and show that, similar to asexual development, it is also possible to recover information about parasite sexual differentiation given observed gene expression values. Using datasets from our own lab as well as those available in the literature, we establish that the patterns of expression in patients are similar to those observed in culture but in additive mixtures whose proportions can vary between patients. We then investigate epigenetic and spatial factors that are important in regulating gene expression. Using second-generation DNA sequencing, we generate genomic maps of chromatin state and chromosome interactions. These maps provide the first global view of chromosome folding and locus-specific affinities in malaria. They also highlight the importance of epigenetic modifications in imposing structure on the spatial organization of the genome. After generating an initial set of genomic maps, we apply these tools to study chromatin reconfigurations during var gene switching. We show that when the active var gene changes, reconfigurations can be seen in the local three-dimensional chromatin structure of the activated locus. Overall, our results contribute new methods for analyzing malaria microarray data, highlight the importance of lineage mixtures in patient infections, generate an atlas of spatial interactions in the nucleus at a resolution of approximately 5 kilobases, and establish a link in malaria between the spatial configuration of active loci and the local chromatin environment.

The genes of the human β-globin locus are located on chromosome 11 in the order of their expression during development: 5' ε, γ, β 3'. During development, silencing of the 5' gene occurs with activation of the immediate 3' gene. This process occurs twice and is termed hemoglobin switching. The exact mechanism(s) of this process have not been fully described. Herein, we describe a role for DNA methylation and methyl binding domain protein 2 in the transcriptional regulation of the human embryonic and fetal beta type globin genes. Adult mice containing the entire human β-globin locus as a yeast artificial chromosome (βYAC) express very low levels of the fetal γ-globin gene. However, treatment of adult βYAC transgenic mice with the DNA methyltransferase inhibitor, 5-azacytidine, induces a >10-fold increase γ-globin mRNA levels. In addition, βYAC transgenic mice null for methyl binding domain protein 2 (MBD2) express a similar level of γ-globin mRNA. DNA methylation and MBD2 appear to induce γ-globin expression via the same pathway(s), as treatment of MBD2 null βYAC transgenic mice do not show an additive boost in γ-globin expression. MBD2 does not bind to the γ-globin promoter region in vivo indicating MBD2 mediated transcriptional silencing does not occur by recruitment of transcriptional repression complexes to the γ-globin gene promoter. Additionally, these transgenic mice contain only the 5' portion of the β-globin locus through the ε-globin, and do not express the ε-globin genes as adults. However, treatment with 5-azacytidine or loss of MBD2 induces expression of the ε-globin gene in adult transgenic mice. A similar induction of ε-globin is seen in βYAC transgenic mice under the same conditions. The level of expression of the ε-globin gene is much lower than the γ-globin gene, indicating the powerful effect of the cis elements mediating transcriptional repression of the ε-globin gene. These studies indicate DNA methylation and MBD2 contribute to the transcriptional repression of the human embryonic and fetal β-type globin genes. Additionally, MBD2 has been identified as a potential target for the therapeutic induction of fetal hemoglobin for the treatment of hemoglobinopathies.

While age-related sex chromosomal aneuploidy is a well-characterized phenomenon, the relationship between autosomal loss and age remains unclear. The emergence of the specific and highly sensitive fluorescence in situ hybridization (FISH) technology has enabled investigators to study interphase cells, thereby overcoming problems inherent with the study of metaphase spreads for acquired aneuploidy assessment. Despite all the advantages of this technique, there are some limitations that could be misleading when scoring interphase autosomal aneuploidy. In this study we show that sex chromosomal hypoploidy is correlated with age. By using a twin study design, we evaluated Y chromosome hypoploidy frequencies and found that loss of the Y chromosome is likely to be a multifactorial phenotype, being influenced by both genetic and environmental factors. An analysis of acquired aneuploidy frequencies for 13 autosomes in men showed that only one autosome, chromosome 3, had an age-related increase in acquired aberrations levels. Using a multi-probe study design, we determined that an apparent loss of fluorescent signal(s) could result from the coincident positioning (overlaying) of the repeat sequences targeted by the probes (due to either somatic homolog pairing or aggregation of the heterochromatic regions). Therefore, caution should be taken when performing autosomal FISH analysis to avoid overestimation of autosomal aneuploidy in uncultured leukocytes.

It has been shown that the key components of the hsp90 chaperone complex, including hsp90, p23, hsp70, hsp40, and HOP (p60), associate with telomerase; however, their specific roles in telomerase function and tumor progression have not yet been defined. HSF1, the primary mammalian heat shock protein transcription factor, may affect telomerase activity and transformation by regulating the expression of several hsp90 chaperone complex proteins in response to stress as well as regulating the transcription of hTERT, the protein subunit of telomerase.In our in vitro model of prostate cancer progression, as cells progress from immortal but non-tumorigenic (P69) to tumorigenic (M2182) and eventually metastatic (M12) capabilities, both telomerase activity and global chaperone protein levels increase. Our hypothesis is that HSF1 affects telomerase activity directly at the level of transcription and indirectly at the protein level via its regulation of proteins of the hsp90 chaperone complex. Furthermore, upregulation of HSF1 and/or members of the hsp90 chaperone complex directly contribute to prostate cell transformation and that introduction of chaperone-related genes will convert non-tumorigenic prostate cells to a tumorigenic state.We have shown that ectopic overexpression of HSF1 induces increased expression of endogenous hsp90 in P69 cells. Furthermore, telomerase activity in the overexpressing HSF1 cell lines is increased as well and is the end result of two disparate, yet ultimately cooperating pathways. However, the increased telomerase activity does not correlate with increased tumorigenicity.In conjunction with this study, we have overexpressed hTERT in the P69 cell lines and found that telomerase activity is markedly increased in the absence of chaperone upregulation. We propose that the demand for increased folding and stability of the exogenous hTERT leads to a recruitment of telomerase associated chaperone proteins, which can be measured by increased activity after immunoprecipitations and nuclear translocation of hsp90 chaperone complex proteins.Taken together, these projects indicate a significant role for HSF1 and the hsp90 chaperone complex proteins on telomerase activity, and provide evidence that each may be a viable target for therapeutic intervention.

Seven families of XX and YY homozygous Oreochromis niloticus were produced by mitotic gynogenesis from XY neofemales and their genetic status was verified by multilocus DNA fingerprinting and progeny testing. Two of these gynogenetic families and their corresponding diploid controls were used with 64 AFLP primer combinations in different levels of screening (XX/YY grand pool; XX/YY family pool; XX/YY gynogenetics and XX/XY control individuals) to search for sex-linked or sex-specific markers. Grand pool screening did not reveal any sex-linked markers. Subsequent family pool and individual level screening identified four sex-linked AFLP markers from two primer combinations, three Y-linked (OniY425, OniY382, OniY227) and one X-linked (OniX420). Two of these (OniX420, OniY425) were shown to be allelic. Single locus PCR markers were developed for all of those markers. Linkage analysis of these markers and the sex locus within the source families revealed tight linkage, with estimated map distances of 13cM, 17cM and 20cM for OniY382, OniY227 and OniX420/OniY425 respectively. However, these sex-linked AFLP markers failed to consistently identify sex in unrelated individuals. To develop an effective system for parentage analysis in normal and gynogenetic progeny, AFLPs and multiplexed polymorphic microsatellite loci were investigated. Both were found to be effective, but microsatellites were more appropriate since they are codominant and some loci showed high gene-centromere recombination rates, suitable for discriminating meiotic from mitotic gynogenetics, while AFLPs are dominant markers. Spontaneous diploidization of the maternal chromosome set (SDM) was observed in gynogenetic progeny of one XY neofemale. Maternal inheritance and ploidy status were verified by multilocus DNA fingerprinting and chromosome karyotyping. Close genetic linkage between the red gene and an autosomal sex-reversal gene(s) in gynogenetic progeny and influences of autosomal sex-reversal gene(s) producing males in a fully inbred XX clonal line were previously reported in O. niloticus. To test if the same autosomal sex-reversal locus was responsible in both cases, a series of test crosses was carried out involving XX clonal neomale(s) and homozygous red females. The results indicated the involvement of more than one autosomal sex-reversal locus, one of which is linked to red body colour.