Subtelomeric I-scei-mediated Double-strand Breaks Are Repaired By Homologous Recombination In Trypanosoma Cruzi

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Trypanosoma cruzi chromosome ends are enriched in surface protein genes and pseudogenes (e.g., trans-sialidases) surrounded by repetitive sequences. It has been proposed that the extensive sequence variability among members of these protein families could play a role in parasite infectivity and evasion of host immune response. In previous reports we showed evidence suggesting that sequences located in these regions are subjected to recombination. To support this hypothesis we introduced a double-strand break (DSB) at a specific target site in a T. cruzi subtelomeric region cloned into an artificial chromosome (pTAC). This construct was used to transfect T. cruzi epimastigotes expressing the I-SceI meganuclease. Examination of the repaired sequences showed that DNA repair occurred only through homologous recombination (HR) with endogenous subtelomeric sequences. Our findings suggest that DSBs in subtelomeric repetitive sequences followed by HR between them may contribute to increased variability in T. cruzi multigene families. © 2016 Chiurillo, Moraes Barros, Souza, Marini, Antonio, Cortez, Curto, Lorenzi, Schijman, Ramirez and da Silveira.7DEC11/51475-3, FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo11/51693-0, FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo306591/2015-4, CNPq, Conselho Nacional de Desenvolvimento Científico e TecnológicoFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Exploring Iris Colour Prediction And Ancestry Inference In Admixed Populations Of South America

New DNA-based predictive tests for physical characteristics and inference of ancestry are highly informative tools that are being increasingly used in forensic genetic analysis. Two eye colour prediction models: a Bayesian classifier - Snipper and a multinomial logistic regression (MLR) system for the Irisplex assay, have been described for the analysis of unadmixed European populations. Since multiple SNPs in combination contribute in varying degrees to eye colour predictability in Europeans, it is likely that these predictive tests will perform in different ways amongst admixed populations that have European co-ancestry, compared to unadmixed Europeans. In this study we examined 99 individuals from two admixed South American populations comparing eye colour versus ancestry in order to reveal a direct correlation of light eye colour phenotypes with European co-ancestry in admixed individuals. Additionally, eye colour prediction following six prediction models, using varying numbers of SNPs and based on Snipper and MLR, were applied to the study populations. Furthermore, patterns of eye colour prediction have been inferred for a set of publicly available admixed and globally distributed populations from the HGDP-CEPH panel and 1000 Genomes databases with a special emphasis on admixed American populations similar to those of the study samples. © 2014 Elsevier Ireland Ltd.1339Walsh, S., Liu, F., Ballantyne, K.N., Van Oven, M., Lao, O., Kayser, M., Irisplex: A sensitive DNA tool for accurate prediction of blue and brown eye colour in the absence of ancestry information (2011) Forensic Sci. Int. Genet., 5, pp. 170-180Walsh, S., Liu, F., Wollstein, A., Kovatsi, L., Ralf, A., Kosiniak-Kamysz, A., Branicki, W., Kayser, M., The HIrisplex system for simultaneous prediction of hair and eye colour from DNA (2013) Forensic Sci. Int. Genet., 7, pp. 98-115Phillips, C., Salas, A., Sánchez, J.J., Fondevila, M., Gómez-Tato, A., Alvarez-Dios, J., Calaza De Cal, M., Carracedo, Á., Inferring ancestral origin using a single multiplex assay of ancestry-informative marker SNPs (2007) Forensic Sci. Int. Genet., 1, pp. 273-280. , The SNPforID ConsortiumLao, O., Vallone, P.M., Coble, M.D., Diegoli, T.M., Van Oven, M., Van Der Gaag, K.J., Pijpe, J., Kayser, M., Evaluating self-declared ancestry of U.S. Americans with autosomal, Y-chromosomal and mitochondrial DNA (2010) Hum. Mutat., 31, pp. 1875-E1893Fondevila, M., Phillips, C., Santos, C., Freirearadas, A., Vallone, P.M., Butler, J.M., Lareu, M.V., Carracedo, Á., Revision of the SNP for ID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies (2013) Forensic Sci. Int. Genet., 7, pp. 63-74Pereira, R., Phillips, C., Pinto, N., Santos, C., Dos Santos, S.E., Amorim, A., Carracedo, Á., Gusmão, L., Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing (2012) PLoS One, 7, p. 29684Ruiz, Y., Phillips, C., Gomez-Tato, A., Alvarez-Dios, J., Casares De Cal, M., Cruz, R., Maroñas, O., Lareu, M.V., Further development of forensic eye colour predictive tests (2013) Forensic Sci. Int. Genet., 7, pp. 28-40Walsh, S., Chaitanya, L., Clarisse, L., Wirken, L., Draus-Barini, J., Kovatsi, L., Maeda, H., Kayser, M., Developmental validation of the HIrisplex system: DNA-based eye and hair colour prediction for forensic and anthropological usage (2014) Forensic Sci. Int. Genet., 9, pp. 150-161Liu, X., Harada, S., DNA isolation from mammalian samples (2013) Curr. Protoc. Mol. Biol., , Chapter 2: Unit 2.14Phillips, C., Porras-Hurtado, L., Freire-Aradas, A., Fondevila, M., Santos, C., Salas, A., Henao, J., Lareu, M.V., (2014) The PIMA SNP Panel: A Population Informative Multiplex for the Americas, , (in preparation)Liu, F., Van Duijn, K., Vingerling, J.R., Hofman, A., Uitterlinden, A.G., Janssens, A.C., Kayser, M., Eye colour and the prediction of complex phenotypes from genotypes (2009) Curr. Biol., 19, pp. 192-R193Sulem, P., Gudbjartsson, D.F., Stacey, S.N., Helgason, A., Rafnar, T., Magnusson, K.P., Manolescu, A., Stefansson, K., Genetic determinants of hair, eye and skin pigmentation in Europeans (2007) Nat. Genet., 39, pp. 1443-1452Sulem, P., Gudbjartsson, D.F., Stacey, S.N., Helgason, A., Rafnar, T., Jakobsdottir, M., Steinberg, S., Stefansson, K., Two newly identified genetic determinants of pigmentation in Europeans (2008) Nat. 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