Orientador: José Fernando Garcia / Banca: Marcos Vinicius Gualberto Barbosa da Silva / Banca: Gisele Zoccal Mingoti / Banca: Guilherme de Paula Nogueira / Banca: Fabiano Antonio Cadioli / Resumo: RESUMO - Uma das questões mais interessantes que poderiam ser elucidadas empregando a análise de metilação em todo o genoma é como ela afeta a regulação da temperatura corporal em animais domésticos. A resposta a esta questão torna-se imperativa, particularmente no caso de bovinos de leite e corte, uma vez que as raças modernas mais populares descendem de ancestral comum, que derivou em duas subespécies (Bos taurus e Bos indicus) as quais respondem aos estímulos ambientais de formas opostas (raças de zonas temperadas ou adaptadas a regiões tropicais, respectivamente). Mapas de metilação do DNA genômico foram originados usando a técnica de RRBS à partir de células nucleadas do sangue de um grupo de bovinos Angus e Nelore puros, expostos ao estresse ambiental condicionado pelo calor. Os dados de metilação distribuídos ao longo dos cromossomos bovinos puderam ser representados graficamente, enfatizando padrão altamente homogêneo entre as amostras analisadas e a robustez do método. A cobertura de sequenciamento empregada foi suficientemente profunda (em todos os casos superior a 20 vezes o tamanho do genoma), permitindo concluir sobre a ocorrência de eventos de metilação do DNA possivelmente associados a alterações fisiológicas causadas pelo estresse térmico. A análise da metilação do DNA revelou 4.662 janelas metiladas diferencialmente (cada uma com 1.000 pares de bases), sendo a maioria (2.695) relacionada a diferenças entre as raças e não diretamente à resposta ao estresse tér... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: ABSTRACT - One of the most interesting questions that could be solved using genome-wide methylation analysis is how it affects the regulation of body temperature in domestic animals. The answer to this question becomes imperative, particularly in the case of dairy and beef cattle, since modern breeds more frequently descended from a common ancestor, derived in two subspecies (Bos taurus and Bos indicus), which respond to environmental stimuli of different forms (breeds of temperate zones and adapted to tropical regions, respectively). Genomic maps were originated using RRBS DNA methylation data from nucleated blood cells of a group of pure Angus and Nelore cattle exposed to environmental heat strees. Methylation data distributed along the bovine chromosomes could be represented graphically, emphasizing a highly homogeneous pattern between the analyzed samples and the robustness of the method. The sequencing coverage used was sufficiently deep (in all cases higher than 20 times the genome size) leading to the identification of DNA methylation events possibly associated with physiological changes caused by heat stress. The DNA methylation analysis showed a total of 4,662 differentially methylated windows (each with 1,000 base pairs), most of them (2,695) related to differences between breeds and not to the response to heat stress. Analysis of the 214 common windows (comprising 103 genes) revealed epigenetic signals related to the heat stress response and recovery, which were ma... (Complete abstract click electronic access below) / Doutor

Cancer is a complex, heterogeneous disease and associated with a pluralism of distinct molecular events occurring on multiple layers of cell activity. It is a disease of genomic regulation driven by genetic and epigenetic mechanisms. Consideration of these regulatory levels is inevitable for understanding cancer genesis and progression. Improved high-throughput techniques developed in the last decades enable a highly resolved view on these mechanisms but at the same time the technologies produce an incredible amount of molecular data. Hence it needs advances in computational methods to master the data. In this thesis we demonstrate how to cope with high-dimensional data to characterize molecular aspects of cancer. The main aim of this thesis is to develop and to apply bioinformatics methods to unravel molecular mechanisms, with special focus on gene expression and epigenetics, underlying cancer. Therefore, we selected two cancer entities, B-cell lymphoma and glioblastoma, for a more detailed, exemplary study. Bioinformatics methods dealing with molecular cancer data have to tackle tasks like data integration, dimension reduction, data compression and proper visualization. One effective method that fulfills the mentioned tasks is self organizing map (SOM) machine learning, a technique to ‘organize’ complex, multivariate data. We present an analytic framework based on SOMs that aims at characterizing single-omics landscapes, here either regarding genome wide expression or methylation, to describe the heterogeneity of cancer on the molecular level. Molecular data of each sample is presented in terms of ‘individual’ maps, which enable their evaluation by visual inspection. The portrayal method also realizes comprehensive downstream analysis tasks such as marker selection and clustering of co-regulated features into modules, stratification of cases into subtypes, knowledge discovery, function mining and pathway analysis. Further, we describe how to detect and to correct outlier samples. In a novel combining approach all these analytic tasks of the single-omics SOM are embedded in a workflow to integratively analyze gene expression and DNA methylation data of unmatched patient cohorts. We showed that this approach provides detailed insights into the transcriptome and methylome landscapes of cancer. Furthermore, we developed a new inter-omics method based on SOM machine learning for the combined analysis of gene expression and DNA methylation data obtained from the same patient cohort. The method allows the visual inspection of the data landscapes of each sample on a personalized and class-related level, where the relative contribution of each of both data entities can be tuned either to focus on expression or methylation landscapes or on a combination of both. Using the single-omics SOM approach, we studied molecular subtypes of B-cell lymphoma based on gene expression data. The method disentangles tumor heterogeneity and provides suited markers for the cancer subtypes. We proposed a refined subtyping of B-cell lymphoma into four subtypes, rather than a previously assumed three-group classification. In a second application of the single-omics SOM we studied a gene expression data set concerning glioblastoma for which we confirmed an established four-subtype classification. Our results suggested a similar gene activation pattern as observed in the lymphoma study characterized by an antagonistic switching between transcriptional modes related to immune response and cell division. Our integrative study on a larger lymphoma cohort comprising additional subtypes confirmed previous results about the role of stemness genes during development and maturation of B-cells. Their dysfunctions in lymphoma are governed by widespread epigenetic effects altering the promoter methylation of the involved genes, their activity status as moderated by histone modifications, and also by chromatin remodeling. We identified subtype-specific signatures that associate with epigenetic effects such as remodeling from transcriptionally inactive into active chromatin states, differential promoter methylation, and the enrichment of targets of transcription factors such as EZH2 and SUZ12. While studying the transcription of epigenetic modifiers in lymphoma and healthy controls, we found that the expression levels of nearly all modifiers are strongly disturbed in lymphoma and concluded that the epigenetic machinery is highly deregulated. Our results suggested that Burkitt’s lymphoma and diffuse large B-cell lymphoma differ by an imbal-ance of repressive and poised promoters, which is associated with an imbalance of the activity of histone- and DNA-modifying enzymes. Our inter-omics method was applied to a high-grade glioblastomas. Their expression and methylation landscapes were segmented into modes of co-expressed and co-methylated genes, which reflect underlying regulatory modes of cell activity. We found antagonistic methylation and gene expression changes between the IDH1 mutated and IDH1 wild type subtypes, which affect predominantly poised and repressed chromatin states. Therefore we assume that these effects deregulate developmental processes either by their blockage or by aberrant activation. Our methods presented in this thesis enable a holistic view on high-dimensional molecular data collected in large-scale cancer studies. The examples chosen illustrate the mutual dependence of regulatory effects on genetic, epigenetic and transcriptomic levels. Our finding revealed that epigenetic deregulation in cancer must go beyond simple schemes using only a few modes of regulation. By applying the tools and methods described above to large-scale cancer cohorts we could confirm and supplement previous findings about underlying cancer biology.

<p><a>Prostate cancer is the second leading cause of cancer death among men in the United States. The androgen receptor (AR) antagonist enzalutamide is an FDA-approved drug for treatment of patients with late-stage prostate cancer and is currently under clinical study for early-stage prostate cancer treatment.</a> After a short positive response period to enzalutamide, tumors will develop drug resistance. In these studies, we uncovered that NOTCH signaling and DNA methylation are a deregulated in enzalutamide-resistant cells. <i>NOTCH2</i> and<i> c-MYC </i><a>gene expression<i> </i>positively correlated with <i>AR </i>expression in samples from patients with hormone refractory disease in which AR expression levels correspond to those typically observed in enzalutamide-resistance</a>. The expression of Notch signaling components was upregulated in enzalutamide-resistant cells suggesting the activation of the pathway. Inhibition of this pathway <i>in vitro</i> and <i>in vivo</i> promoted an increase in the sensitivity to enzalutamide with an impact on AR expression. On the other hand, DNMT activity and DNMT3B expression were upregulated in resistant lines. Enzalutamide induced the expression of DNMT3A and DNMT3B in prostate cancer cells with a potential role for p53 and pRB in this process. The overexpression of DNMT3B3, a DNMT3B variant, promoted an enzalutamide-resistant phenotype in C4-2 cells. DNA methylation inhibition, using low-concentration decitabine, and <i>DNMT3B</i> knockdown induced a re-sensitization of resistant prostate cancer cells and tumors to enzalutamide. Decitabine treatment in enzalutamide-resistant induced a decrease in the expression of AR-V7 and changes in genes from the apoptosis, DNA repair and mRNA splicing pathways. Decitabine plus enzalutamide treatment of 22RV1 xenografts induced a decrease in tumor weight, KI-67 and AR-V7 expression and an increase in Cleaved-Caspase3 levels. All the above suggest that Notch signaling and DNA methylation pathways are deregulated after enzalutamide resistance onset, and targeting these pathways restores the sensitivity to enzalutamide.<b><u></u></b></p>

DNA methylation is a crucial, abundant mechanism of gene regulation in vertebrates. It is less prevalent in many other metazoan organisms and completely absent in some key model species, such as D. melanogaster and C. elegans. In this thesis we report on a comprehensive study of the pres- ence and absence of DNA methyltransferases (DNMTs) in 138 Ecdysozoa covering Arthropoda, Nematoda, Priapulida, Onychophora, and Tardigrada. We observe that loss of individual DNMTs independently occured multiple times across ecdysozoan phyla. In several cases, this resulted in a loss of DNA methylation. In vertebrates, however, there is no single species known which lost DNA methylation. Actually, DNA methylation was greatly expanded after the 1R/2R whole genome duplication (WGD) and became a genome-wide phe- nomena. In our study of vertebrates we are not looking for losses of DNA methyltransferases and DNA methylation but are rather interested in the gain of additional DNA methyltransferase genes. In vertebrates there were a number of WGD. Most vertebrates only underwent two WGD but in the teleost lineage a third round of WGD occured and in some groups, e.g. Salmoniformes and some Cypriniformes even a forth WGD occured. The Carp-specific WGD (4R) is one of the most recent vertebrate WGD and is estimated to have occured 12.4 mya. We performed the most comprehen- sive analysis of the evolution of DNA methyltransferases after vertebrate whole-genome duplications (WGD) so far. We were able to show that the conservation of duplicated DNMT3 genes in Salmoniformes is more diverse than previously believed. We were also able to identify DNA methyltrans- ferases in Cypriniformes which have, due to their recent WGD, quite com- plex genomes. Our results show that the patterns of retained and lost DNA methyltransferases after a forth round of WGD differ between Cypriniformes and Salmoniformes. We also proposed a new nomenclature for teleost DNMT genes which correctly represents the orthology of DNMT genes for all teleost species. Next to these purely computational projects we collaborated with the Aluru lab to investigate the effects of different disturbances on zebrafish DNA methylation. One disturbance is the inactivation of DNMT3aa and DNMT3ab as single knockouts as well as a double knockout. This was the first double knockout of DNMT genes in zebrafish which was ever generated. It allows us to study the subfunctionalization of the two DNMT3a genes their effect on genome-wide DNA methylation. Given our results we hypothesize that DNMT3aa and DNMT3ab can compensate for each other to a high de- gree. DNMT3a genes have likely been subfuntionalized but their loss can be compensated by DNMT3b genes. This compensation by DNMT3b genes works well enough that no notable phenotype can be observed in double knockout zebrafish but a difference is notable on the epigenome level. The second disturbance we studied is the exposure of zebrafish to the toxic chemi- cal PCB126. We detected a moderate level of DNA methylation changes and a much larger effect on gene expression. Similar to previous reports we find little correlation between DNA methylation and gene expression changes. Therefore, while PCB126 exposure has a negative effect on DNA methyla- tion it is likely that other gene regulatory mechanisms play a role as well, possibly even a greater one. How do genes evolve and how are genes regulated are two of the main questions of modern molecular biology. In this thesis we have tried to shed more light on both questions. we have broadly expanded the phylogenetic range of species with a manually curated set of DNA methyltransferases. We have done this for ecdysozoan species which have lost all DNA methylating enzymes as well as for teleost fish which acquired more than ten copies of the, originally, two genes. We were also able to generate new insight into the subfunctionalization of the DNA methylation machinery in zebrafish and how it reacts to environmental effects.:1 Introduction 1.1 Biological introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1.2 Detecting DNA methylation . . . . . . . . . . . . . . . . . . . . . . . . 7 2 Evolution of DNA methylation across Ecdysozoa 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 2.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 3 Evolution of DNA methyltransferases after vertebrate whole genome duplications 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 3.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 3.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 3.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 4 The effect of DNMT3aa and DNMT3ab knockout on DNA methyla- tion in zebrafish 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 4.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 4.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58 4.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64 5 Role of DNA methylation in altered testis gene expression patterns in adult zebrafish exposed to Pentachlorobiphenyl 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 5.2 Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 5.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 5.4 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 6 Conclusions 6.1 Evolution of DNA methylation across Ecdysozoa . . . . . . . . . . . . . 95 6.2 Evolution of DNA methyltransferases after vertebrate whole genome duplications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 6.3 Role of DNA methylation in altered testis gene expression patterns in adult zebrafish (Danio rerio) exposed to Pentachlorobiphenyl (PCB 126). . . 107 6.4 Knockout of DNMT3aa and DNMT3ab in zebrafish (Danio rerio) . . . . . . 108 Bibliography 119

<p>RNA-directed DNA methylation (RdDM) is a process by which epigenetic silencing is maintained at the boundary between genes and flanking transposable elements. In maize, RdDM is dependent on <i>Mediator of Paramutation 1 (Mop1</i>), a putative RNA dependent RNA polymerase. Here I show that although RdDM is essential for the maintenance of DNA methylation of a silenced <i>MuDR</i> transposon in maize, a loss of that methylation does not result in a restoration of activity of that element. Instead, heritable maintenance of silencing is maintained by histone modifications. At one terminal inverted repeat (TIR) of the element, heritable silencing is mediated via H3K9 and H3K27 dimethylation, even in the absence of DNA methylation. At the second TIR, heritable silencing is mediated by H3K27 trimethylation, a mark normally associated with somatically inherited gene silencing. I find that a brief exposure of high temperature in a <i>mop1</i> mutant rapidly reverses both of these modifications in conjunction with a loss of transcriptional silencing. These reversals are heritable, even in <i>mop1</i> wild type progeny in which methylation is restored at both TIRs. These observations suggest that DNA methylation is neither necessary to maintain silencing, nor is it sufficient to initiate silencing once it has been reversed. To leverage the specificity of our observations made at bench, I also performed a transcriptome analysis in <i>mop1</i> mutants under heat. I found that a substantial number of genes as well as a subset of TEs are reactivated in <i>mop1</i> mutants under heat, which is consistent with the effects I observed on <i>MuDR</i>. Interestingly, I found that <i>mop1</i>-specific reactivation of TEs is closely correlated with changes in expression of nearby genes, most of which are involved in metabolic transportation and sensing. This suggests that one function of <i>MOP1</i> is to prevent inappropriate expression of genes in this pathway when they are close to TEs. Taken together, my work will provide an opportunity to better understand the causes and consequences of TE silencing and reactivation, as well as the effects of TEs on gene regulation under stress conditions.</p>

DNA methylation patterns are sex and tissue specific in many species, yet many studies useblood samples, due to its accessibility, to establish links between the DNA methylation anddifferent phenotypes. This raises the question of whether DNA methylation in blood samplesreflect the DNA methylation pattern in other tissues that are more relevant to the phenotypebeing studied. In this research, samples were collected from the brain, blood, liver and gonadof 16 house sparrow (Passer domesticus), half of them were female, while the others weremale. Reduced representation bisulfite sequencing (RRBS) was performed to get themethylation profile in each sample. The result showed a tissue specific methylation profile inthe four investigated tissues, a strong and positive correlation between 0.74 – 0.85 was foundbetween tissues, in which a weaker correlation was found between blood and other tissue. Indifferential methylation analysis, most of the differently methylated sites between sexes werefound in gonads, while the fewest was found in blood, and Z chromosome wasoverrepresented place in all four tissues where the majority of the differently methylated sitesbetween sexes were found. Comparison with the house sparrow genome annotation foundabout half of the differentially methylated sites between sexes were within genes and about 20 % of them were in the exon or coding region of a gene. The result suggested that bloodcould be useful in reflecting the general DNA methylation level in other tissues, but it was nota reliable bioindicator for further detailed study in DNA methylation pattern or in geneontology enrichment pathway analysis.

In multicellular organisms, all the cells are genetically identical but turn genes on or off at the right time to promote differentiation into specific cell types. The regulation of higher-order chromatin structure is essential for genome-wide reprogramming and for tissue-specific patterns of gene expression. The complexity of the genome is regulated by epigenetic mechanisms, which act at the level of DNA, histones, and nucleosomes. Epigenetic machinery is involved in many biological processes, including genomic imprinting, X-chromosome inactivation, heterochromatin formation, and transcriptional regulation, as well as DNA damage repair. In this review, we summarize the recent understanding of DNA methylation, cytosine derivatives, active and passive demethylation pathways as well as histone variants. DNA methylation is one of the well-characterized epigenetic signaling tools. Cytosine methylation of promoter regions usually represses transcription but methylation in the gene body may have a positive correlation with gene expression. The attachment of a methyl group to cytosine residue in the DNA sequence is catalyzed by enzymes of the DNA methyltransferase family. Recent studies have shown that the Ten-Eleven translocation family enzymes are involved in stepwise oxidation of 5-methylcytosine, creating new cytosine derivatives including 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine. Additionally, histone variants into nucleosomes create another strategy to regulate the structure and function of chromatin. The replacement of canonical histones with specialized histone variants regulates accessibility of DNA, and thus may affect multiple biological processes, such as replication, transcription, DNA repair, and play a role in various disorders such as cancer.

DNA methylation and histone modifications have emerged as key mechanisms in transcriptional regulation. The target of methylation-induced silencing 1 (TMS1) is a bipartite protein. Recent studies have indicated that methylation-associated silencing of TMS1 occurs in many cancers. However, whether and how TMS1 is regulated by epigenetic mechanisms in cancers remains unknown. In this study we showed that methylation of the TMS1 promoter occurred in five of six hepatocellular carcinoma (HCC) cell lines. TMS1 expression was reduced in four HCC cell lines and correlated with methylation status. Furthermore, the TMS1 promoter was completely methylated and mRNA expression was undetectable. TMS1 expression could be restored by 5-aza-2′-deoxycitidine (5-Aza-dC) (a DNA methyltransferase inhibitor) or trichostatin A (TSA) (a histone deacetylase inhibitor) alone and the promoter methylation. was partially reversible. TSA was more efficient than 5-Aza-dC in inducing TMS1 expression, and the combination of 5-Aza-dC and TSA resulted in markedly synergistic reactivation of the gene and completely reversed promoter methylation. Interestingly, TMS1 promoter methylation-associated gene silencing was accompanied by histone H3 Lysine 9 (H3K9) hypoacetylation and trimethylation. 5-Aza-dC and/or TSA also had some effect on conversion of methylated to acetylated H3K9 in restoring TMS1. This conversion was dynamic at the TMS1 promoter and a decrease in H3K9 trimethylation preceded an increase in H3K9 acetylation after 5-Aza-dC and/or TSA treatment. Our results thus suggest that epigenetic inactivation of TMS1 expression is regulated by promoter hypermethylation and H3K9 modifications in a coordinated way.

The task of association extraction involves identifying links between different entities. Here, we make contributions to two applications related to the biomedical field. The first application is in the domain of text mining aiming at extracting associations between methylated genes and diseases from biomedical literature. Gathering such associations can benefit disease diagnosis and treatment decisions. We developed the DDMGD database to provide a comprehensive repository of information related to genes methylated in diseases, gene expression, and disease progression. Using DEMGD, a text mining system that we developed, and with an additional post-processing, we extracted ~100,000 of such associations from free-text. The accuracy of extracted associations is 82% as estimated on 2,500 hand-curated entries. The second application is in the domain of computational toxicology that aims at identifying relationships between chemical compounds and toxicity effects. Identifying toxicity effects of chemicals is a necessary step in many processes including drug design. To extract these associations, we propose using multi-label classification (MLC) methods. These methods have not undergone comprehensive benchmarking in the domain of predictive toxicology that could help in identifying guidelines for overcoming the existing deficiencies of these methods. Therefore, we performed extensive benchmarking and analysis of ~19,000 MLC models. We demonstrated variability in the performance of these models under several conditions and determined the best performing model that achieves accuracy of 91% on an independent testing set. Finally, we propose a novel framework, LDR (learning from dense regions), for developing MLC and multi-target regression (MTR) models from datasets with missing labels. The framework is generic, so it can be applied to predict associations between samples and discrete or continuous labels. Our assessment shows that LDR performed better than the baseline approach (i.e., the binary relevance algorithm) when evaluated using four MLC and five MTR datasets. LDR achieved accuracy scores of up to 97% using testing MLC datasets, and R2 scores up to 88% for testing MTR datasets. Additionally, we developed a novel method for minority oversampling to tackle the problem of imbalanced MLC datasets. Our method improved the precision score of LDR by 10%.

Somatic cell nuclear transfer (SCNT) is a useful tool for selective breeding, conservation, and production of transgenic animals. Despite the successful cloning of several species, high rates of embryo failure following SCNT prevent the wide-scale use of the technique. Embryos produced through cloning have a higher incidence of developmental arrest, decreased developmental potential, frequent implantation failures, and increased incidence of abortion. The objective of this dissertation research was to characterize the factors that lead to SCNT failures by examining epigenetic and apoptotic pathways that can negatively influence the development of cloned preimplantation embryos. Aberrant genome reprogramming is generally considered to be a key factor in the failure of SCNT embryo development. Therefore, we used bisulfite pyrosequencing technology to compare DNA methylation patterns of several genes critical for embryonic development (POU5F1, NANOG, SOX2, and KLF4) in SCNT and in vitro fertilized (IVF) blastocyst stage embryos. The methylation profiles obtained from these experiments indicate that methylation patterns of the POU5F1 gene were undermethylated compared to IVF embryos, suggesting reprogramming did occur, but that the reduced methylation was inappropriate for the blastocyst stage. Furthermore, aberrant methylation profiles were detected for SOX2 and NANOG, suggesting that problems of genome reprogramming following SCNT can be gene-specific or localized. Because high rates of apoptosis are associated with failure of preimplantation embryos, we compared the activation of the P53-mediated apoptosis pathway in individual IVF and SCNT preimplantation embryos at multiple developmental stages. This pathway is activated in response to cell stress and genomic instability, and in response to the expression of genes associated with somatic cell reprogramming. Evidence from gene expression and immunohistochemistry analyses suggests that the P53 pathway is frequently active in SCNT embryos. Also, we detected expression of several factors known to induce apoptosis more frequently and at higher levels in SCNT embryos. Collectively, the work presented here illuminates some of the molecular consequences of incomplete or inappropriate genome reprogramming in cloned embryos. The identification of these factors may lead to interventions that target the apoptosis pathway during preimplantation development and increase SCNT success rates.