DNA methylation in Dictyostelium discoideum

DNA methyltransferases of type Dnmt2 are a highly conserved protein family with enigmatic function. The aim of this work was to characterize DnmA, the Dnmt2 methyltransferase in Dictyostelium discoideum, and further to investigate its implication in DNA methylation and transcriptional gene silencing. The genome of the social amoeba Dictyostelium encodes DnmA as the sole DNA methyltransferase. The enzyme bears all ten characteristic DNA methyltransferase motifs in its catalytic domain. The DnmA mRNA was found by RT-PCR to be expressed during vegetative growth and down regulated during development. Investigations using fluorescence microscopy showed that both DnmA-myc and DnmA-GFP fusions predominantly localised to the nucleus. The function of DnmA remained initially unclear, but later experiment revealed that the enzyme is an active DNA methyltransferase responsible for all DNA (cytosine) methylation in Dictyostelium. Neither in gel retardation assays, nor by the yeast two hybrid system, clues on the functionality of DnmA could be obtained. However, immunological detection of the methylation mark with an α - 5mC antibody gave initial evidence that the DNA of Dictyostelium was methylated. Furthermore, addition of 5-aza-cytidine as demethylating agent to the Dictyostelium medium and subsequent in vitro incubation of the DNA isolated from these cells with recombinant DnmA showed that the enzyme binds slightly better to this target DNA. In order to investigate further the function of the protein, a gene knock-out for dnmA was generated. The gene was successfully disrupted by homologous recombination, the knock-out strain, however, did not show any obvious phenotype under normal laboratory conditions. To identify specific target sequences for DNA methylation, a microarray analysis was carried out. Setting a threshold of at least 1.5 fold for differences in the strength of gene expression, several such genes in the knock-out strain were chosen for further investigation. Among the up-regulated genes were the ESTs representing the gag and the RT genes respectively of the retrotransposon skipper. In addition Northern blot analysis confirmed the up-regulation of skipper in the DnmA knock-out strain. Bisufite treatment and sequencing of specific DNA stretches from skipper revealed that DnmA is responsible for methylation of mostly asymmetric cytosines. Together with skipper, DIRS-1 retrotransposon was found later also to be methylated but was not present on the microarray. Furthermore, skipper transcription was also up-regulated in strains that had genes disrupted encoding components of the RNA interference pathway. In contrast, DIRS 1 expression was not affected by a loss of DnmA but was strongly increased in the strain that had the RNA directed RNA polymerase gene rrpC disrupted. Strains generated by propagating the usual wild type Ax2 and the DnmA knock-out cells over 16 rounds in development were analyzed for transposon activity. Northern blot analysis revealed activation for skipper expression, but not for DIRS-1. A large number of siRNAs were found to be correspondent to the DIRS-1 sequence, suggesting concerted regulation of DIRS-1 expression by RNAi and DNA methylation. In contrast, no siRNAs corresponding to the standard skipper element were found. The data show that DNA methylation plays a crucial role in epigenetic gene regulation in Dictyostelium and that different, partially overlapping mechanisms control transposon silencing for skipper and DIRS-1. To elucidate the mechanism of targeting the protein to particular genes in the Dictyostelium genome, some more genes which were up-regulated in the DnmA knock-out strain were analyzed by bisulfite sequencing. The chosen genes are involved in the multidrug response in other species, but their function in Dictyostelium is uncertain. Bisulfite data showed that two of these genes were methylated at asymmetrical C-residues in the wild type, but not in DnmA knock-out cells. This suggested that DNA methylation in Dictyostelium is involved not only in transposon regulation but also in transcriptional silencing of specific genes.

Heterochromatin und epigenetische Kontrolle der Centromere in Dictyostelium discoideum

Heterochromatin Protein 1 (HP1) is an evolutionarily conserved protein required for formation of a higher-order chromatin structures and epigenetic gene silencing. The objective of the present work was to functionally characterise HP1-like proteins in Dictyostelium discoideum, and to investigate their function in heterochromatin formation and transcriptional gene silencing. The Dictyostelium genome encodes three HP1-like proteins (hcpA, hcpB, hcpC), from which only two, hcpA and hcpB, but not hcpC were found to be expressed during vegetative growth and under developmental conditions. Therefore, hcpC, albeit no obvious pseudogene, was excluded from this study. Both HcpA and HcpB show the characteristic conserved domain structure of HP1 proteins, consisting of an N-terminal chromo domain and a C-terminal chromo shadow domain, which are separated by a hinge. Both proteins show all biochemical activities characteristic for HP1 proteins, such as homo- and heterodimerisation in vitro and in vivo, and DNA binding activtity. HcpA furthermore seems to bind to K9-methylated histone H3 in vitro. The proteins thus appear to be structurally and functionally conserved in Dictyostelium. The proteins display largely identical subnuclear distribution in several minor foci and concentration in one major cluster at the nuclear periphery. The localisation of this cluster adjacent to the nucleus-associated centrosome and its mitotic behaviour strongly suggest that it represents centromeric heterochromatin. Furthermore, it is characterised by histone H3 lysine-9 dimethylation (H3K9me2), which is another hallmark of Dictyostelium heterochromatin. Therefore, one important aspect of the work was to characterise the so-far largely unknown structural organisation of centromeric heterochromatin. The Dictyostelium homologue of inner centromere protein INCENP (DdINCENP), co-localized with both HcpA and H3K9me2 during metaphase, providing further evidence that H3K9me2 and HcpA/B localisation represent centromeric heterochromatin. Chromatin immunoprecipitation (ChIP) showed that two types of high-copy number retrotransposons (DIRS-1 and skipper), which form large irregular arrays at the chromosome ends, which are thought to contain the Dictyostelium centromeres, are characterised by H3K9me2. Neither overexpression of full-length HcpA or HcpB, nor deletion of single Hcp isoforms resulted in changes in retrotransposon transcript levels. However, overexpression of a C-terminally truncated HcpA protein, assumed to display a dominant negative effect, lead to an increase in skipper retrotransposon transcript levels. Furthermore, overexpression of this protein lead to severe growth defects in axenic suspension culture and reduced cell viability. In order to elucidate the proteins functions in centromeric heterochromatin formation, gene knock-outs for both hcpA and hcpB were generated. Both genes could be successfully targeted and disrupted by homologous recombination. Surprisingly, the degree of functional redundancy of the two isoforms was, although not unexpected, very high. Both single knock-out mutants did not show any obvious phenotypes under standard laboratory conditions and only deletion of hcpA resulted in subtle growth phenotypes when grown at low temperature. All attempts to generate a double null mutant failed. However, both endogenous genes could be disrupted in cells in which a rescue construct that ectopically expressed one of the isoforms either with N-terminal 6xHis- or GFP-tag had been introduced. The data imply that the presence of at least one Hcp isoform is essential in Dictyostelium. The lethality of the hcpA/hcpB double mutant thus greatly hampered functional analysis of the two genes. However, the experiment provided genetic evidence that the GFP-HcpA fusion protein, because of its ability to compensate the loss of the endogenous HcpA protein, was a functional protein. The proteins displayed quantitative differences in dimerisation behaviour, which are conferred by the slightly different hinge and chromo shadow domains at the C-termini. Dimerisation preferences in increasing order were HcpA-HcpA << HcpA-HcpB << HcpB-HcpB. Overexpression of GFP-HcpA or a chimeric protein containing the HcpA C-terminus (GFP-HcpBNAC), but not overexpression of GFP-HcpB or GFP-HcpANBC, lead to increased frequencies of anaphase bridges in late mitotic cells, which are thought to be caused by telomere-telomere fusions. Chromatin targeting of the two proteins is achieved by at least two distinct mechanisms. The N-terminal chromo domain and hinge of the proteins are required for targeting to centromeric heterochromatin, while the C-terminal portion encoding the CSD is required for targeting to several other chromatin regions at the nuclear periphery that are characterised by H3K9me2. Targeting to centromeric heterochromatin likely involves direct binding to DNA. The Dictyostelium genome encodes for all subunits of the origin recognition complex (ORC), which is a possible upstream component of HP1 targeting to chromatin. Overexpression of GFP-tagged OrcB, the Dictyostelium Orc2 homologue, showed a distinct nuclear localisation that partially overlapped with the HcpA distribution. Furthermore, GFP-OrcB localized to the centrosome during the entire cell cycle, indicating an involvement in centrosome function. DnmA is the sole DNA methyltransferase in Dictyostelium required for all DNA(cytosine-)methylation. To test for its in vivo activity, two different cell lines were established that ectopically expressed DnmA-myc or DnmA-GFP. It was assumed that overexpression of these proteins might cause an increase in the 5-methyl-cytosine(5-mC)-levels in the genomic DNA due to genomic hypermethylation. Although DnmA-GFP showed preferential localisation in the nucleus, no changes in the 5-mC-levels in the genomic DNA could be detected by capillary electrophoresis.

Selecting Relevant Genes with a Spectral Approach

Array technologies have made it possible to record simultaneously the expression pattern of thousands of genes. A fundamental problem in the analysis of gene expression data is the identification of highly relevant genes that either discriminate between phenotypic labels or are important with respect to the cellular process studied in the experiment: for example cell cycle or heat shock in yeast experiments, chemical or genetic perturbations of mammalian cell lines, and genes involved in class discovery for human tumors. In this paper we focus on the task of unsupervised gene selection. The problem of selecting a small subset of genes is particularly challenging as the datasets involved are typically characterized by a very small sample size ?? the order of few tens of tissue samples ??d by a very large feature space as the number of genes tend to be in the high thousands. We propose a model independent approach which scores candidate gene selections using spectral properties of the candidate affinity matrix. The algorithm is very straightforward to implement yet contains a number of remarkable properties which guarantee consistent sparse selections. To illustrate the value of our approach we applied our algorithm on five different datasets. The first consists of time course data from four well studied Hematopoietic cell lines (HL-60, Jurkat, NB4, and U937). The other four datasets include three well studied treatment outcomes (large cell lymphoma, childhood medulloblastomas, breast tumors) and one unpublished dataset (lymph status). We compared our approach both with other unsupervised methods (SOM,PCA,GS) and with supervised methods (SNR,RMB,RFE). The results clearly show that our approach considerably outperforms all the other unsupervised approaches in our study, is competitive with supervised methods and in some case even outperforms supervised approaches.

Variability in the Stability and Productivity of Transfected Genes in Chinese Hamster Ovary (CHO) cells

In the field of biologics production, productivity and stability of the transfected gene of interest are two very important attributes that dictate if a production process is viable. To further understand and improve these two traits, we would need to further our understanding of the factors affecting them. These would include integration site of the gene, gene copy number, cell phenotypic variation and cell environment. As these factors play different parts in the development process, they lead to variable productivity and stability of the transfected gene between clones, the well-known phenomenon of “clonal variation”. A study of this phenomenon and how the various factors contribute to it will thus shed light on strategies to improve productivity and stability in the production cell line. Of the four factors, the site of gene integration appears to be one of the most important. Hence, it is proposed that work is done on studying how different integration sites affect the productivity and stability of transfected genes in the development process. For the study to be more industrially relevant, it is proposed that the Chinese Hamster Ovary dhfr-deficient cell line, CHO-DG44, is used as the model system.

En busca de los or??genes del hombre : un recorrido did??ctico por la antropolog??a f??sica

Se trata de un CD multimedia que desarrolla de una forma did??ctica, pero sin perder el rigor cient??fico y filos??fico, una serie de materiales de antropolog??a evolutiva pensados para el Bachillerato. Se pretende que el alumnado comprenda cu??les han sido los or??genes del hombre. Para ello se desarrollan: un tema introductorio sobre c??mo entender la evoluci??n org??nica y c??mo ha ido evolucionando la idea de evoluci??n desde Arist??teles a la Teor??a Sint??tica y otro, que es propiamente el contenido del CD, sobre la evoluci??n humana desde los primates hasta el hombre moderno.

Polimorfismos de los genes P53, CYP1A1, CYP1B1, GSTM1, GSTT1 y GSTP1 en cáncer de seno familiar en una población colombiana

Se considera que la susceptibilidad al cáncer de seno es poligenética1; es necesario estudiar otros factores genéticos. Se realizó un estudio analítico de casos y controles (1:2) 120:240. Se tomó una muestra de sangre periférica, y posteriormente se realizó la extracción de ADN (PROBE) y se determinó la presencia de los polimorfismos. Se encontraron asociaciones estadísticamente significativas con el cáncer de seno para: del grupo p53 exón 4, la Arginina con un OR 1,923 IC 95% (1,117 – 3.309); del grupo p53 intrón 3 el I3wm con OR 30,887 IC 95% (3,709 – 257,209); del grupo p53 intrón 6 el I6wm con OR 2.061 IC 95% (1.059 - 4,013); del grupo CYP1B1 Val432leu, la Valina con un OR 2.273 con un IC del 95% (1.084 – 4.855); del grupo CYP1B1 Asn453se la Asparagina/Serina con un OR 1,987 con IC 95% (1.076 – 3.670). El polimorfismo gstm 1r reporta un OR 0,366 con IC 95% (0,219 – 0,613) el cual se considera como protector para cáncer de seno.

Estudio molecular de los genes cdkn1b y cited2 en mujeres con falla ovárica prematura idiopática

En los últimos años el aumento sustancial de la incidencia de la infertilidad humana ha convertido esta patología en un problema real de salud pública: alrededor del 15% de las parejas consultan por esta causa. Entre las causas femeninas de infertilidad, la falla ovárica prematura (FOP) es extremadamente frecuente puesto que afecta entre el 1 y el 3% de las mujeres de la población general. Múltiples etiologías de FOP se han descrito (e.g. autoinmunes, infecciosas, iatrogénicas) pero desafortunadamente en más de 80% de los casos no se conocen las causas, lo que sugiere mecanismos genéticos subyacentes. Algunas causas genéticas se han descrito, especialmente relacionadas con formas sindrómicas de la enfermedad (e.g. síndromes de Turner y BPES). En estos casos se evidencian principalmente alteraciones cromosómicas y mutaciones específicas en genes participantes en la foliculogénesis. En otros casos, la presentación de la enfermedad es aislada y se relaciona con mutaciones en genes específicos localizados en los autosomas y en el cromosoma X. Sin embargo, la complejidad genética, la baja heredabilidad y el carácter cuantitativo de los fenotipos asociados a la reproducción en los mamíferos implica que en casos fisiológicos y patológicos (hipofertilidad e infertilidad) cientos de genes participen en una red de sutil regulación. En este contexto, recientemente se han propuesto una cantidad significativa de genes candidato para la FOP. Por consiguiente el estudio de genes potencialmente candidatos en la etiología de la FOP por aproximaciones gen candidato, entre ellos CDKN1B y CITED2, es de especial interés en la comprensión de los mecanismos subyacentes de esta en enfermedad. Además, es una etapa necesaria en la búsqueda de nuevos marcadores de esta patología que permitan en un futuro mejorar el asesoramiento genético y proponer alternativas terapéuticas. Durante este trabajo de tesis nos hemos focalizado en la búsqueda de variantes en la secuencia codificante de CDKN1B y CITED2 en mujeres FOP. Nuestros resultados sugieren que estos genes son dos nuevos factores etiológicos de la enfermedad.

??Qu?? ha supuesto Edutec? : apuntes para no perder los or??genes

Resumen tomado del autor

Polimorfismos de los genes ABCB1 y CYP2C8 en pacientes sometidos a TASPE. Análisis farmacogenético del Paclitaxel en la toxicidad y movilización de progenitores hemopoyéticos

Fundamentos. La eficacia de paclitaxel junto con rhG-CSF en la movilización de progenitores hematopoyéticos, se ha probada en pacientes hematológicos. Farmacogenéticamente el paclitaxel presenta una alta variabilidad inter-individual. Los genes CYP2C8 y ABCB1 involucrados en su metabolismo y transporte podrían afectar dicha variabilidad inter-individual. Objetivo. Evaluar en una cohorte retrospectiva de pacientes sometidos a TASPE, el efecto de algunos polimorfismos de nucleótido simple (del gen CYP2C8 y del gen ABCB1) sobre la eficacia en la movilización y toxicidad hematológica inducida por del paclitaxel. Materiales y Métodos. Un grupo de 107 pacientes recibieron paclitaxel y rhG-CSF como esquema movilizador. Los polimorfismos genotipados fueron para los genes ABCB1 rs1045642 A>G, ABCB1 rs2032582 C>A, ABCB1 rs2032582 C>T, CYP2C8 rs10509681 C>T, y CYP2C8 rs11572080 A>G. Resultados. El uso de paclitaxel logró éxito movilizador en más del 80% de los pacientes con linfomas o mieloma (p=0,0021), pero no lo fue en la leucemia aguda. En pacientes con mieloma la variable G>rs1045642 del gen ABCB1 se asoció con mala movilización (p= 0,018) y mayor toxicidad hematológica (p= 0,034). El alelo C>rs10509681 del gen CYP2C8 se relacionó con mayor toxicidad en pacientes con linfoma (p= 0,045) y mieloma múltiple (p=0,042), y portadores del alelo TT en homocigosis presentaron una mayor toxicidad hematológica comparada con los portadores CC o CT (p= 0,027). Conclusión. Este estudio sugiere que los SNPs de las variables alélicas analizadas en los genes CYP2C8 y ABCB1 en algunos grupos de pacientes inciden en la capacidad movilizadora y afectan el grado de toxicidad hematológica.

Els col??legis privats de segona ensenyan??a a Mallorca : els or??gens. 'Los colegios privados de segunda ense??anza en Mallorca : los or??genes'

Resumen tomado parcialmente de la publicaci??n

Els or??gens de la Inspecci?? provincial a les Balears, una mesura politicoeducativa del liberalisme moderat. 'Los or??genes de la Inspecci??n provincial en Baleares, una medida pol??tico-educativa del liberalismo moderado

Se analiza la historia de la Inspecci??n provincial de Instrucci??n P??blica en la comunidad aut??noma de las Illes Balears, con el objetivo de aportar algunos datos nuevos sobre sus or??genes. De la investigaci??n se desprende que, a pesar de que pueda parecer contradictorio, la Inspecci??n no fue inicialmente una medida educativa de progreso o de renovaci??n pedag??gica, sino un instrumento de control y centralizaci??n potenciado desde el liberalismo moderado.

Els or??gens de l'ensenyament secundari p??blic a Menorca : de l'Escola N??utica a l'Institut Lliure de Segon Ensenyament (1855-1869). 'Los or??genes de la ense??anza secundaria p??blica en Menorca : de la Escuela N??utica al Instituto Libre de Segunda Ense??anza (1855-1869)'

Resumen tomado de la publicaci??n. El contenido de este art??culo es fruto de una revisi??n de la comunicaci??n ' ....

Genes and Cancer

Lecture slides and notes