TY - JOUR A1 - Garcia, Tzintzuni I. A1 - Matos, Isa A1 - Shen, Yingjia A1 - Pabuwal, Vagmita A1 - Coelho, Maria Manuela A1 - Wakamatsu, Yuko A1 - Schartl, Manfred A1 - Walter, Ronald B. T1 - Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion JF - PLOS ONE N2 - Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression. KW - RNA-SEQ data KW - copy-number alteration KW - squalius alburnoides KW - gene expression KW - medaka KW - variant detection KW - transplantation KW - genome KW - generation KW - evolution Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-116000 SN - 1932-6203 VL - 9 IS - 6 ER - TY - JOUR A1 - Reynolds, David A1 - Cliffe, Laura A1 - Förstner, Konrad U. A1 - Hon, Chung-Chau A1 - Siegel, T. Nicolai A1 - Sabatini, Robert T1 - Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei JF - Nucleic Acids Research N2 - Base J, beta-d-glucosyl-hydroxymethyluracil, is an epigenetic modification of thymine in the nuclear DNA of flagellated protozoa of the order Kinetoplastida. J is enriched at sites involved in RNA polymerase ( RNAP) II initiation and termination. Reduction of J in Leishmania tarentolae via growth in BrdU resulted in cell death and indicated a role of J in the regulation of RNAP II termination. To further explore J function in RNAP II termination among kinetoplastids and avoid indirect effects associated with BrdU toxicity and genetic deletions, we inhibited J synthesis in Leishmania major and Trypanosoma brucei using DMOG. Reduction of J in L. major resulted in genome-wide defects in transcription termination at the end of polycistronic gene clusters and the generation of antisense RNAs, without cell death. In contrast, loss of J in T. brucei did not lead to genome-wide termination defects; however, the loss of J at specific sites within polycistronic gene clusters led to altered transcription termination and increased expression of downstream genes. Thus, J regulation of RNAP II transcription termination genome-wide is restricted to Leishmania spp., while in T. brucei it regulates termination and gene expression at specific sites within polycistronic gene clusters. KW - RNA-polymerase-II KW - variant surface glycoprotein KW - SWI2/SNF2-like protein KW - messenger RNA KW - polycistronic transcription KW - DNA glycosation KW - hela cells KW - gene expression KW - genome KW - 5-bromodeoxyuridine Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-117863 VL - 42 IS - 15 ER - TY - JOUR A1 - Brehm, Klaus A1 - Koziol, Uriel T1 - On the importance of targeting parasite stem cells in anti-echinococcosis drug development T1 - De l’importance de cibler les cellules souches du parasite dans la recherche de nouveaux médicaments contre les échinococcoses JF - Parasite N2 - The life-threatening diseases alveolar and cystic echinococcoses are caused by larvae of the tapeworms Echinococcus multilocularis and E. granulosus, respectively. In both cases, intermediate hosts, such as humans, are infected by oral uptake of oncosphere larvae, followed by asexual multiplication and almost unrestricted growth of the metacestode within host organs. Besides surgery, echinococcosis treatment relies on benzimidazole-based chemotherapy, directed against parasite beta-tubulin. However, since beta-tubulins are highly similar between cestodes and humans, benzimidazoles can only be applied at parasitostatic doses and are associated with adverse side effects. Mostly aiming at identifying alternative drug targets, the nuclear genome sequences of E. multilocularis and E. granulosus have recently been characterized, revealing a large number of druggable targets that are expressed by the metacestode. Furthermore, recent cell biological investigations have demonstrated that E. multilocularis employs pluripotent stem cells, called germinative cells, which are the only parasite cells capable of proliferation and which give rise to all differentiated cells. Hence, the germinative cells are the crucial cell type mediating proliferation of E. multilocularis, and most likely also E. granulosus, within host organs and should also be responsible for parasite recurrence upon discontinuation of chemotherapy. Interestingly, recent investigations have also indicated that germinative cells might be less sensitive to chemotherapy because they express a beta-tubulin isoform with limited affinity to benzimidazoles. In this article, we briefly review the recent findings concerning Echinococcus genomics and stem cell research and propose that future research into anti-echinococcosis drugs should also focus on the parasite’s stem cell population. N2 - Les échinococcoses alvéolaire et kystique, deux maladies potentiellement mortelles, sont respectivement causées par les larves des vers plats Echinococcus multilocularis et E. granulosus. Dans les deux cas, les hôtes intermédiaires, comme l’homme, s’infectent par l’ingestion des oncosphères, suivie de la multiplication asexuée et la croissance presque illimitée du métacestode dans les organes de l’hôte. À côté de la chirurgie, le traitement des échinococcoses repose sur une chimiothérapie par les benzimidazoles, dont l’action est dirigée contre la bêta-tubuline du parasite. Cependant, comme les bêta-tubulines sont extrêmement similaires chez les cestodes et les humains, les benzimidazoles ne peuvent être utilisés qu’à des posologies parasitostatiques et sont associés à des effets secondaires indésirables. Avec l’objectif principal d’identifier des cibles pour des médicaments alternatifs, le génome nucléaire d’E. multilocularis et d’E. granulosus a été récemment séquencé, et de nombreuses cibles potentielles pour des médicaments sont exprimées par le métacestode. De plus, des études récentes de biologie cellulaire ont montré qu’E. multilocularis dispose de cellules souches multipotentes, appelées cellules germinales, qui sont les seules cellules parasitaires capables de prolifération et à l’origine de toutes les cellules différenciées. Ces cellules germinales représentent donc un type cellulaire crucial pour la prolifération d’E. multilocularis, et très vraisemblablement aussi d’E. granulosus, dans les organes de l’hôte, et vraisemblablement responsables des récurrences parasitaires à l’arrêt de la chimiothérapie. Des études récentes ont aussi indiqué que les cellules germinales pourraient être moins sensibles à la chimiothérapie car elles expriment un isoforme de la bêta-tubuline à affinité limitée vis-à-vis des benzimidazoles. Dans cet article, nous faisons une courte revue des découvertes récentes concernant la génomique d’Echinococcus et la recherche sur les cellules souches. Nous proposons que les recherches futures sur de nouveaux médicaments contre les échinococcoses se focalisent sur la population des cellules souches du parasite. KW - genome KW - chemotherapy KW - benzimidazole KW - stem cells KW - germinative cells KW - beta-tubulin Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-118030 SN - 1252-607X VL - 21 ER -