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The correct number of chromosomes is important for the maintenance of healthy cells and organisms. Maintenance of a correct chromosome number depends on the accurate distribution of chromosomes to the daughter cells during cell division, and errors in chromosome segregation result in abnormal chromosome numbers, or aneuploidy. Aneuploidy is typically associated with deleterious effects on organismal and cellular fitness; however, aneuploidy has also been associated with enhanced cellular growth in certain contexts, such as cancer. Another type of deviation from the normal chromosome number can occur when entire sets of chromosomes are added to the normal (diploid) chromosome number, resulting in polyploidy. Whereas polyploidy is found in certain normal tissues and organisms, tetraploidy (four sets of chromosomes) is associated with a number of precancerous lesions and is believed to promote aneuploidy and tumorigenesis. While it is clear that chromosome mis-segregation causes aneuploidy, the effect of aneuploidy on chromosome segregation is less clear. Similarly, it is unclear whether and how tetraploidy may affect chromosome segregation. The work described here shows that aneuploidy can cause chromosome mis-segregation and induces chromosome-specific phenotypic effects. In contrast, tetraploidy does not per se induce chromosome mis-segregation, but enables the accumulation of aneuploidy thanks to a "genetic buffer" effect that allows tetraploid cells to tolerate aneuploidy better than diploid cells. / Ph. D.

Tetraploidy – the presence of four copies of the haploid chromosome complement – is common in cancer. There is evidence that ~40% of tumors pass through a tetraploid stage at some point during their development, and tetraploid cells injected in mice are more tumorigenic than their diploid counterparts. However, the reason for this increased tumorigenicity of tetraploid cells is not well established. Most routes by which cells may become tetraploid also confer cells with double the number of centrosomes, the small membraneless organelle that organizes the cell's microtubule cytoskeleton and mitotic spindle apparatus. Centrosome number homeostasis is crucial for health, and recent studies have shown inducing extra centrosomes in cells can induce tumor formation in mice. This has led some researchers to propose that the extra centrosomes that arise together with tetraploidy may be the reason that tetraploid cells are more tumorigenic. However, several anecdotal reports have found that tetraploid clones generated and grown in vitro appear to lose their extra centrosomes. Here, I investigate the population dynamics of the loss of extra centrosomes in newly formed tetraploid cells generated via cytokinesis failure. I uncover the mechanism driving the process and build a mathematical model that captures the experimentally observed dynamics. Next, I investigate karyotypic heterogeneity in newly formed tetraploid cells and their counterparts that are grown for 12 days under standard culture conditions and find that karyotypic heterogeneity has increased after 12 days of growth after tetraploidization. The day 12 'evolved' population with increased heterogeneity formed larger colonies in soft agar than newly formed tetraploid cells or diploid parental precursors and karyotype analysis of the largest soft agar colonies revealed recurrent aneuploidies shared by a subset of colonies. Finally, I investigate the effects of different culture conditions - meant to mimic various conditions in the tumor microenvironment - on the evolution of centrosome and chromosome number in newly formed tetraploid cells and identify a small subset of conditions that altered centrosome homeostasis or the fitness of tetraploid cells. / Doctor of Philosophy / The genetic information in cancer cells is often drastically altered compared to normal cells in the body. As one important example of this, the number and structure of chromosomes - the DNA structures that hold the genetic information - is often abnormal in cancer cells. Abnormal chromosome number is closely linked with cancer development, but the details of why this leads to more cancer are not clear. One important kind of chromosome number change is when a cell undergoes incomplete cell division, and the resulting cell acquires double the number of chromosomes compared to a normal cell (known as tetraploidy). Tetraploidy occurs in close to 40% of cancers and is linked with the most aggressive cases. The abnormal cell divisions that cause tetraploidy also lead to other cellular changes. One important change is that tetraploid cells also acquire double the number of the structures that organizes cell division (centrosomes). The centrosome organizes the mitotic spindle, the major apparatus that is responsible for equally distributing chromosomes to two daughter cells during the cell division process. Extra centrosomes in cells are closely linked with cancer and can lead to additionally chromosome number changes. Researchers have believed that the extra centrosomes that are acquired with doubled chromosome number may be the major reason that tetraploid cells are linked to more aggressive cancer. However, recent studies have suggested that tetraploid cells may lose their extra centrosomes, calling into question the details of the relationship between tetraploidy and tumor formation. Here, I use human cells grown in culture to understand how extra centrosomes are lost from tetraploid cells. I find that extra centrosomes in newly formed tetraploid cells promote abnormal 'multipolar' cell divisions, in which chromosomes are segregated unevenly to three or more partitions. Such divisions are often fatal to daughter cells. In some cases, the extra centrosomes can cluster to form bipolar spindles that segregate chromosomes into two equal partitions (as is normal). When forming bipolar spindles, extra centrosomes can cluster asymmetrically (three centrosomes at one pole, one at the other) or symmetrically (two centrosomes at each pole). Tetraploid cells with a normal number of centrosomes emerge when extra centrosomes cluster asymmetrically in a bipolar spindle, yielding one tetraploid daughter cell with a normal number of centrosomes. Such cells have a fitness advantage over cells with extra centrosomes, which over time are very likely to undergo fatal multipolar divisions. Thus, cells with a normal centrosome number 'take over' the population. Next, I investigate the cancer-like properties of tetraploid cells without their extra centrosomes and find that they display increased tumor-like behavior even in the absence of extra centrosomes. Finally, I investigate whether changing the conditions in which cells are grown (in ways meant to mimic different conditions that may be experienced in the body) affects whether tetraploid cells lose their extra centrosomes. We identify a small number of conditions that do influence loss of extra centrosomes. Together, these studies illuminate important details of the relationship between tetraploidy and tumor formation. This work lays the foundation to further explore and understand the relative roles of tetraploidy, extra centrosomes, and tissue environment in cancer.

Chan, Ka Ying. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references (leaves 133-150). / Abstract also in Chinese. / ABSTRACT --- p.i / 摘要 --- p.iii / ACKNOWLEDGEMENTS --- p.iv / CONTRIBUTORS --- p.vi / TABLE OF CONTENTS --- p.vii / LIST OF TABLES --- p.x / LIST OF FIGURES --- p.xi / LIST OF ABBREVIATIONS --- p.xiii / Chapter SECTION I: --- BACKGROUND --- p.1 / Chapter CHAPTER 1: --- PRENATAL DIAGNOSIS OF FETAL TRISOMY 21 --- p.2 / Chapter 1.1 --- Down syndrome --- p.2 / Chapter 1.2 --- Current methods of prenatal diagnosis of fetal trisomy 21 --- p.3 / Chapter 1.2.1 --- Non-invasive procedures --- p.3 / Chapter 1.2.2 --- Invasive procedures --- p.5 / Chapter 1.3 --- Alternative methods for the prenatal diagnosis of fetal trisomy 21 --- p.7 / Chapter CHAPTER 2: --- CELL-FREE FETAL NUCLEIC ACIDS IN MATERNAL PLASMA --- p.13 / Chapter 2.1 --- Circulating fetal cells --- p.15 / Chapter 2.2 --- Circulating cell-free fetal nucleic acids --- p.15 / Chapter 2.3 --- Diagnostic applications of cell-free fetal nucleic acids in maternal plasma --- p.17 / Chapter 2.4 --- Digital relative chromosome dosage approach --- p.20 / Chapter 2.5 --- Validation of digital RCD approach on artificial DNA mixtures --- p.22 / Chapter SECTION II --- : MATERIALS AND METHODS --- p.25 / Chapter CHAPTER 3: --- QUANTITATIVE ANALYSIS OF NUCLEIC ACIDS --- p.26 / Chapter 3.1 --- Subject recruitment and sample collection --- p.26 / Chapter 3.2 --- Sample processing --- p.26 / Chapter 3.3 --- Nucleic acid extraction --- p.27 / Chapter 3.3.1 --- Extraction of DNA from placental tissues --- p.27 / Chapter 3.3.2 --- Extraction of DNA from maternal blood cells --- p.27 / Chapter 3.4 --- Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) --- p.28 / Chapter 3.5 --- Paralogous sequence assays optimisation workflow --- p.31 / Chapter 3.5.1 --- Monoplex paralogous sequence assays --- p.31 / Chapter 3.5.2 --- Multiplex paralogous sequence assay --- p.38 / Chapter 3.6 --- Digital PCR --- p.42 / Chapter 3.6.1 --- Principle --- p.42 / Chapter 3.6.2 --- Digital multiplex paralogous sequence assay --- p.42 / Chapter 3.7 --- Statistical analysis --- p.46 / Chapter 3.7.1 --- Disease classification of samples --- p.46 / Chapter 3.7.2 --- Poisson distribution --- p.46 / Chapter 3.7.3 --- Data analysis --- p.48 / Chapter 3.7.4 --- Sequential probability ratio test (SPRT) analysis --- p.49 / Chapter SECTION III: --- ASSAY DEVELOPMENT --- p.53 / Chapter CHAPTER 4: --- TESTING OF ASSAY SPECIFICITY WITH CORIELL CELL LINES --- p.54 / Chapter 4.1 --- Coriell cell lines --- p.54 / Chapter 4.2 --- Specificity of initial PCR primers --- p.56 / Chapter 4.2.1 --- Principle --- p.56 / Chapter 4.2.2 --- Materials and methods --- p.56 / Chapter 4.2.3 --- Results --- p.60 / Chapter 4.2.4 --- Conclusion --- p.63 / Chapter 4.3 --- Specificity of the iPLEX® Gold extension primers --- p.63 / Chapter 4.3.1 --- Principle --- p.63 / Chapter 4.3.2 --- Materials and methods --- p.64 / Chapter 4.3.3 --- Results --- p.65 / Chapter 4.4 --- Further analysis on the specificity of PV2107a initial PCR primers --- p.67 / Chapter 4.5 --- Conclusion --- p.71 / Chapter CHAPTER 5: --- ASSAY OPTIMISATION --- p.72 / Chapter 5.1 --- Introduction --- p.72 / Chapter 5.2 --- Optimisation of initial PCRs with AmpliTaq Gold® DNA polymerase followed by homogeneous MassEXTEN´DёØ (hME) assays (Sequenom) --- p.72 / Chapter 5.2.1 --- Optimisation of initial PCR reactions --- p.72 / Chapter 5.2.2 --- Principle of homogeneous MassEXTEN´DёØ assays (Sequenom)… --- p.75 / Chapter 5.2.3 --- Homogeneous MassEXTEN´DёØ assays (Sequenom) on euploid and T21 samples --- p.76 / Chapter 5.3 --- Assay selection by iPLEX® Gold single base primer extension reactions (Sequenom) --- p.82 / Chapter 5.4 --- Optimisation of multiplex PCR with AmpliTaq Gold® DNA polymerase --- p.88 / Chapter 5.5 --- Optimisation of multiplex iPLEX® Gold single base primer extension reaction --- p.93 / Chapter 5.6 --- Single molecule detection test for the multiplex paralogous sequence assays … --- p.103 / Chapter SECTION IV: --- ANALYSIS OF CLINICAL SAMPLES --- p.107 / Chapter CHAPTER 6: --- DISEASE CLASSIFICATION OF EUPLOID AND TRISOMY SAMPLES WITH MULTIPLEX PARALOGOUS SEQUENCE ASSAY --- p.108 / Chapter 6.1 --- Introduction --- p.108 / Chapter 6.2 --- Materials and methods --- p.109 / Chapter 6.2.1 --- Sample collection --- p.109 / Chapter 6.2.2 --- Experimental design --- p.110 / Chapter 6.3 --- Results --- p.111 / Chapter 6.4 --- Discussion --- p.114 / Chapter SECTION V: --- CONCLUDING REMARKS --- p.122 / Chapter CHAPTER 7: --- CONCLUSION AND FUTURE PERSPECTIVES --- p.123 / Chapter 7.1 --- Conclusion --- p.123 / Chapter 7.2 --- Future perspectives --- p.124 / Appendix 1 --- p.126 / Appendix II --- p.127 / REFERENCE --- p.133

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.

O estudo de agentes que interferem no funcionamento das proteínas relacionadas com o ciclo celular é importante para a compreensão dos processos de transformação e de morte celular. Alterações de ploidia, embora presentes na maioria dos tumores humanos, não têm ainda seu papel conhecido no processo de oncogênese. A alteração do número cromossômico é conseqüência primária de erros que envolvem o fuso mitótico e o cinetócoro. Dessa maneira, drogas que agem sobre os microtúbulos são consideradas aneugênicas potenciais. O presente trabalho enfocou o estudo do mecanismo pelo qual drogas que atuam sobre microtúbulos levam ao aparecimento de células multinucleadas e o significado biológico destas. Os resultados mostraram que a vincristina induziu bloqueio em mitose das células BBnt e MDCK, com conseqüente entrada em interfase no estado multinucleado. As células multinucleadas não apresentaram sinais de morte celular por apoptose, entretanto, quando em prófase apresentaram vários centrossomos, que poderiam originar divisões celulares com fusos multipolares. Estes resultados indicam que essas linhagens celulares possuem pontos de checagem mitótico funcionais e células multinucleadas são viáveis e capazes de prosseguir no ciclo celular. A presença de mitoses com fusos multipolares é indício de que as células multinucleadas passam por divisões anormais, que progrediriam para apoptose resultando na eliminação desta população. / The study of agents that interfere in the functionality of proteins related to cell cycle is important for the understanding of the transformation and cell death processes. Although ploidy alterations are presented in the majority of human tumors, their role in oncogenic process is not understood yet. The alteration on chromosomal number is the primary consequence of errors involving the mitotic spindle and kinetocore. Thus, drugs acting on the microtubules are considered as potentially aneugenic agents. The present work aimed to study the mechanism of multinucleated cells induction by action of antimicrotubule drug and biological meaning of these cells. The results showed that vincristine induced mitotic arrest of both BBnt and MDCK cells, with consequent entrance into interphasic-multinucleated status. Multinucleated cells did not present features of cell death by apoptosis; they were still viable and able to go further in cell-cycle progression. The presence of many structures suggested microtubule enucleation, centrosomes-like were detected on treated cells and could be responsible for the multi-spindle assembling that leads the multinucleated cells to abnormal divisions. Later on, when the multinucleated cells accumulated more abnormalities they were eliminated from the cell population by apoptosis.

A instabilidade cromossômica e a aneuploidia são características associadas às células malignas. Sabe-se que essas alterações podem ser resultantes de erros em eventos durante a mitose. Com o objetivo de gerar uma população com ganho de ploidia, utilizamos dois inibidores de fases distintas da mitose. Resultando no aumento da frequência celular em G2/M, ou seja, células com 4 vezes o número de cromossomos (4C) e de células com DNA acima de 4, hipertetraploide. Quantificamos a quantidade de núcleos e demonstramos que o tratamento, especificamente, levou a uma NCI, e não a multinucleação. Ambas linhagens celulares submetidas ao tratamento apresentaram alterações morfológicas, como protrusões de membrana, indicando alterações no citoesquelto. Nas análises de mRNA e da expressão proteica, observamos alterações na regulação da actina, coincidindo com a elevação dos mRNAs de YAP/TAZ, efetores co-transcricionais da via Hippo, regulada por alterações no citoesqueleto de actina. Desde modo, propomos, que o tratamento utilizado é um método eficiente para o estudo de células aneuploides e da NCI, que o citoesqueleto de actina é modulado por esse fenótipo e requer YAP/TAZ, provavelmente para manter a sobrevivência e favorecer a proliferação celular observada após o tratamento. / Chromosomal instability and aneuploidy are characteristics associated with malignant cells. It is known that these changes may be due to errors in events during mitosis. In order to generate a population with gain of ploidy, we used two inhibitors of distinct phases of mitosis. Resulting in increasing cell frequency in G2/M, cells with 4 times the number of chromosomes (4C) and cells with DNA above 4, hypertetraploid. We quantified the number of nuclei and demonstrated that the treatment specifically led to NCI, not multinucleation. Both cell lines submitted to treatment presented morphological alterations, such as membrane protrusions, indicating changes in the cytoskeleton. In the analysis of mRNA and protein expression, we observed alterations in actin regulation, coinciding with the elevation of YAP / TAZ mRNAs, co-transcriptional effectors of the Hippo signaling pathway, regulated by changes in the actin cytoskeleton. We propose, that the treatment used is an efficient method for the study of aneuploid cells as well NCI. Also, the actin cytoskeleton is modulated by that phenotype which requires high YAP / TAZ, probably to maintain cell survival and promote cell proliferation observed.

Eukaryotes have developed stringent regulatory mechanisms that control cell division and ensure proper chromosome segregation. Maintaining genome integrity is especially important during meiosis, the specialised cell division programme in the germline that generates haploid gametes. As these cells transmit genetic information to the next generation, the consequences of meiotic errors are not restricted to an organismal level, but can directly impact the fitness of the offspring. Mammals display a high degree of sexual dimorphism in meiosis with regard to the stringency of regulatory mechanisms. This manifests in a relatively high degree of maternally-derived aneuploidies due to weaker checkpoint control in females, whereas more rigorous checkpoints in males frequently perturb fertility. Mouse models of aneuploidy often exhibit complete male sterility and early germ cell arrest, preventing the study of aneuploidy during late and post-meiotic stages in males. In this thesis, we have used the trans-chromosomic mouse model, Tc1, which carries a single copy of human chromosome 21 (HsChr21) and show that, unlike other aneuploid mouse strains, the Tc1 mouse can successfully passage the exogenous human chromosome through male meiosis and generate aneuploid offspring. Our investigations have shown that the presence of the aneuploid human chromosome causes spermatogenic defects due to an arrest at the first meiotic division. Despite this impairment, we found an unexpectedly high number of aneuploid gametes in Tc1 males and the majority of males were able to produce aneuploid offspring, albeit at a lower frequency. Transmission of HsChr21 through the male germline was less efficient compared to female germline transmission, but allowed us to study the impact of male germline-associated chromatin remodelling on the transcriptional deployment of HsChr21 in the offspring. This revealed that, despite fundamentally different developmental dynamics, male- versus female-germline passage result in indistinguishable transcriptional and regulatory phenotypes. An important pathway in the male germline involves the expression of piRNAs, a class of small non-coding RNAs that are commonly found in the germline of animals where they defend cells against transposable elements. Profiling the expression of small RNAs in the Tc1 mouse showed that conserved human piRNA clusters can be successfully transcribed by the mouse piRNA machinery. In addition, we detected Tc1-specific piRNA sequences that were neither present in human nor mouse, mapping to a human-specific repeat element. In line with the previously observed activation of human-specific repeat elements in the Tc1 mouse, this suggests that novel transcripts arising from human repeats can trigger an adaptive piRNA response, thereby demonstrating the plasticity of this pathway to newly invading repeat elements. Transcriptional profiling of spermatogenic cell populations on a single-cell level allowed us to generate an atlas of gene expression over the course of spermatogenesis and dissect meiotic silencing dynamics in the presence of aneuploidy. Transcriptional silencing during meiosis occurs in response to unpaired chromosomes and, in male germ cells, affects the sex chromosomes due to their largely unpaired nature. We found that the presence of HsChr21 has no impact on the silencing of chromosome X, however, the two chromosomes display drastically different silencing patterns with HsChr21 showing a much weaker repression. Taken together, this study revealed a higher than expected tolerance for aneuploidy in the mouse male germline thus allowing the characterisation of meiotic checkpoint mechanisms, the meiotic silencing response to unpaired chromosomes as well as piRNA expression in the presence of an exogenous human chromosome.

Ulcerative colitis is a chronic inflammatory disease that mainly affects the colon and rectum. Onset of disease is most common between the ages of 15-35 years. There is an observed increased risk of colorectal cancer associated with the disease. The risk is often described to be 2% after 10 years, 8% after 20 years and 18% after 30 years disease. Since 1977, all known patients with ulcerative colitis in the catchment area of Örnsköldsvik Hospital have been invited to attend a colonoscopic surveillance programme. At endpoint of the studies included in this thesis there were 214 patients that had attended the surveillance programme. The aims of these studies have been to evaluate the efficiency of the surveillance programme, analyse the impact of findings of DNA aneuploidy, and determine the outcome for patients that underwent limited resections instead of complete proctocolectomy. Further, we have studied the long-term outcome for patients who had an early onset of disease and analysed the expression of cytokeratin 7 and 20 in respect to findings of dysplasia, DNA aneuploidy and colorectal cancer. At the end of the studies the prevalence for ulcerative colitis was 261/100 000 and the incidence rate was 7.6/100 000/year. During the period 1977-2005, four patients died of ulcerative colitis. Nine colorectal cancers were diagnosed in eight patients, one of whom died of the cancer. Fifty-two patients had findings of dysplasia and five of these patients developed colorectal cancer. In the subgroup of patients studied (N= 147) for DNA aneuploidy, 20 were found to have specimens with DNA aneuploidy on at least one occasion. The sensitivity of aneuploidy for development of dysplasia (LGD or higher) was found to be 0.50 and the specificity 0.94. The investigation of the outcome for the patients that underwent limited resections of the colon or rectum showed that none of the patients under surveillance died of colorectal cancer or metachronous cancer in their remaining colon or rectum. A separate study concerning early onset of ulcerative colitis revealed no particular increased risk of colorectal cancer in this cohort but a fairly high incidence of primary sclerosing cholangitis was seen. In the analyses of cytokeratins it was found that 7 out of 10 patients with low-grade dysplasia and 3 of 6 with high-grade dysplasia were positive for CK7. Our results indicate a possible relationship between the expression of CK7 and CK20 and neoplastic development of colorectal mucosa in patients with ulcerative colitis. The studies on which this thesis is based, were performed on a relatively small number of patients, however the time of observation was long and, most importantly, the patients were from a well defined catchment area. We conclude that the surveillance programme has been efficient in minimising the risk of lethal colorectal cancer. Analysing DNA ploidy helps to target the patients that need more attention but the method cannot stand alone. Our study on cytokeratins points to a relationship between dysplasia and CK7 but the results are preliminary and further studies needs to be done. We have shown that it is safe to do a limited colorectal resection in respect to lethal colorectal cancer. Early onset of ulcerative colitis as a risk factor for colorectal cancer was not found in the group we have studied, which could be due to effective surveillance and/or medication. A fairly high operation rate in this group may also have contributed. The most important variable in the beneficial outcome regarding lethal colorectal cancer in these studies is, in our opinion, the outstanding compliance of the patients to the colonoscopic surveillance programme.

Stimulation or repression of gene expression by genome-wide regulatory mechanisms is an important epigenetic regulatory function which can act to efficiently regulate larger regions or specific groups of genes, for example by compensating for loss or gain of chromosome copy numbers. In Drosophila melanogaster there are two known chromosome-wide regulatory systems; the MSL complex, which mediates dosage compensation of the single male X-chromosome and POF, which stimulates expression from the heterochromatic 4th chromosome. POF also interacts with the heterochromatin inducing protein HP1a, which represses expression from the 4th chromosome but which also has been assigned stimulatory functions. In addition to these two, there is another more elusive and less well-characterized genome-wide mechanism called buffering, which can act to balance transcriptional output of aneuploidy regions of the genome (i.e. copy number variation). In my thesis, I describe the presence of a novel physical link between dosage compensation and heterochromatin; mediate by two female-specific POF binding sites, proximal to roX1 and roX2 on the X chromosome (the two non-coding RNAs in the MSL complex). These sites can also provide clues to the mechanisms behind targeting of chromosome-specific proteins. Furthermore, to clarify the conflicting reports about the function of HP1a, I have suggested a mechanism in which HP1a has adopted its function to different genomic locations and gene types. Different binding mechanisms to the promoter vs. the exon of genes allows HP1a to adopt opposite functions; at the promoter, HP1a binding opens up the chromatin structure and stimulates gene expression, whereas the binding to exons condense the chromatin and thus, represses expression. This also causes long genes to be more bound and repressed by HP1a. Moreover, I show that buffering of monosomic regions is a weak but significant response to loss of chromosomal copy numbers, and that this is mediated via a general mechanism which mainly acts on differentially expressed genes, where the effect becomes stronger for long genes. I also show that POF is the factor which compensates for copy number loss of chromosome 4.