Center for Genome Regulation

A FONDAP Center of Excellence

"Exploring the Genomic Landscape of Chile"

2015 Publications

1.     Mandakovic D, Cabrera P, Pulgar R, Maldonado J, Aravena P, Latorre M, Cambiazo V, González M. 2015. Complete genome sequence of Microbacterium sp. CGR1, bacterium tolerant to wide abiotic conditions isolated from the Atacama Desert. J Biotechnol. 2015 Dec 20;216:149-50. 3.180

     2.     Palacios-García I, Lara-Vásquez A, Montiel JF, Díaz-Veliz G, Sepúlveda H, Utreras E, Montecino M, González-Billault C, Aboitiz F. 2015. Prenatal Stress Decreases the Density of Cajal-Retzius Neurons, downregulates Reelin Expression and Induces Adult Behavioral Impairments in Rats. PLoS One 10, e0117680. 3.702

     3.     Canovas J, Berndt FA, Sepulveda H, Aguilar R, Veloso F, Montecino M, Oliva C, Maass JC, Sierralta J, Kukuljan M. 2015. The specification of cortical subcerebral projection neurons depends on the direct repression of TBR1 by CTIP1. Journal of Neuroscience. 35,7552-7564. 7.348

     4.     Montecino M, Stein GS, Zaidi SK, Aguilar R. 2015. Multiple Levels of Epigenetic Control for Bone Biology and Pathology. Bone doi: 10.1016/j.bone.2015.03.013. 4.312

     5.     Vidal EA, Alvarez JM, Moyano TC, Gutierrez RA. 2015. Transcriptional networks in the nitrate response of Arabidopsis Thaliana. Current opinion in Plant Biology 27:125-32. 9.203

     6.     Arguello G, Balboa E, Arrese M, Zanlungo S. 2015. Recent insights on the role of cholesterol in non-alcoholic fatty liver disease. Biochimica et Biophysica Acta. 1852,1765-1778. 4.969

     7.     Loira N, Zhukova A, Sherman DJ. 2015. Pantograph: A Template-based Method for Genome-scale Metabolic Model Reconstruction. Journal of Bioinformatics and Computational Biology. 13,19. 0.783

     8.     Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J Brookes, Gabriele Bucci, Iwan Buetti, Sarah Burge, Cédric Cabau, Joseph W Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J Cutts, Erik Dassi, Alex Di Genova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon Forbes, Robert C Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M Garcia-Manteiga, David Goodstein, Kristian Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dong-Jin Han, Byung Woo Han, Todd Harris, Jayson Harshbarger, Robert K Hastings, Richard D Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Lio, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jerome Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, Francois Moreews, Ibounyamine Nabihoudine, Nelson Ndegwa, Céline Noirot, Cristian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M Staines, Delphine Steinbach, Kevin Stone, Elia Stupka, Jon W Teague, Abu Z Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, Arek Kasprzyk. Nucleic Acids Res. 2015 Jul 1;43(W1):W589-98. 8.867

     9.     Zhao M, Andrieu-Soler C, Kowalczuk L, Paz Cortés M, Berdugo M, Dernigoghossian M, Halili F, Jeanny JC, Goldenberg B, Savoldelli M, El Sanharawi M, Naud MC, van Ijcken W, Pescini-Gobert R, Martinet D, Maass A, Wijnholds J, Crisanti P, Rivolta C, Behar-Cohen F. 2015. A New CRB1 Rat Mutation Links Müller Glial Cells to Retinal Telangiectasia. The Journal of Neuroscience. 35, 6093-6106. 7.348

     10.     Pulgar R, Hödar C, Travisany D, Zuñiga A, Domínguez C, Maass A, González M, Cambiazo V. 2015. Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system. BMC-Genomics. 16:495. 4.360

     11.     Blanco-Herrera F, Moreno AA, Tapia R, Reyes F, Araya M, D'Alessio C, Parodi A, Orellana A. 2015. The UDP-glucose: glycoprotein glucosyltransferase (UGGT), a key enzyme in ER quality control, plays a significant role in plant growth as well as biotic and abiotic stress in Arabidopsis thaliana. BMC Plant Biology 15,12. 4.714

     12.     Parra-Rojas J, Moreno AA, Mitina I, Orellana A. 2015. The dynamic of the splicing of bZIP60 and the proteins encoded by the spliced and unspliced mRNAs reveals some unique features during the activation of UPR in Arabidopsis thaliana. PLoS One 10, e0122936. 3.702

     13.     Ejsmentewicz T, Balic I, Sanhueza D, Barria R, Meneses C, Orellana A, Prieto H, Defilippi BG, Campos-Vargas R. 2015. Comparative study of two table grape varieties with contrasting texture during cold storage. Molecules 20, 3667-3680. 2.791

     14.     Henriquez-Valencia C, Moreno A, Sandoval-Ibañez O, Mitina I, Blanco-Herrera F, Cifuentes-Esquivel N, Orellana A. 2015. bZIP17 and bZIP60 regulate the expression of BiP3 and other salt stress responsive genes in a UPR-independent manner in Arabidopsis thaliana. Journal of Cellular Biochemistry. 116,1638-1645. 3.173

     15.     Quiroz N, Rivas N, del Pozo T, Suazo M, González M, Latorre M. 2015. Transcriptional activation of glutathione pathways and role of glucose homeostasis during copper imbalance. Biometals. 28,321-328. 3.068

     16.     Acuña M, Martínez P, Moraga C, Moraga M, Hunter B, Nuernberg P, Gutierrez R, González M, Schuchman E, Santos JL, Miquel JF, Mabe P, Zanlungo S. Epidemiological, Clinical and Biochemical Characterization of the A359D SMPD1 Mutation Causing Niemann-Pick Disease Type B. European Journal of Human Genetics. doi:10.1038/ ejhg.2015.89. 3.939

     17.     Latorre M, Low M, Garate E, Reyes-Jara A, Murray B, Cambiazo V, González M. 2015. Interplay between copper and zinc homeostasis through the transcriptional regulator Zur in Enterococcus faecalis. Metallomics. doi: 10.1039/ C5MT00043B. 3.980

     18.     Tallino S, Duffy M, Ralle M, Cortés MP, Latorre M, Burkhead JL. 2015. Nutrigenomics analysis reveals that copper deficiency and dietary sucrose up-regulate inflammation, fibrosis and lipogenic pathways in a mature rat model of nonalcoholic fatty liver disease. Journal of Nutritional Biochemistry. 26(10):996-1006. 3.989

     19.     Bernal C, Araya C, Palma V, Bronfman M. 2015. PPARβ/δ and PPARγ contribute to maintain undifferentiated phenotype in mouse adult neural precursor cells from the subventricular zone. Frontiers in Cellular Neuroscience. 9(78):1-12. 4.289

     20.     Botelho J, Smith-Paredes D, Soto-Acuña S, Mpodozis J, Palma V, Vargas AO. 2015. Skeletal plasticity under embryonic muscular activity underlies the development and evolution of the perching digit of birds. Scientific Reports. 5:9840. 5.597

     21.     Palma V, Pitossi FJ, Rehen SK, Touriño C, Velasco I. 2015. Stem cell research in Latin America: update, challenges and opportunities in a priority research area. Regenerative Medicine. 10:785-798. 3.639

     22.     Alvarez M, Reynaert N, Chávez MN, Aedo G, Araya F, Hopfner U, Fernández J, Allende ML, Egaña JT. 2015. Generation of Viable Plant-Vertebrate Chimeras. PLoS One. 10,e0130295. 3.702

     23.     Schenck TL, Hopfner U, Chávez MN, Machens HG, Somlai-Schweiger I, Giunta RE, Bohne AV, Nickelsen J, Allende ML, Egaña JT. 2015. Photosynthetic biomaterials: a pathway towards autotrophic tissue engineering. Acta Biomaterialia. 15,39-47. 6.589

     24.     Cotoras DD, Allende ML. 2015. Was the tailbud the ancestral centre where the fin developmental program evolved in chordates? Contributions Zoology 84(4): 317-328. 1.671

     25.     Rojas A, Aguilar R, Henriquez B, Lian JB, Stein JL, Stein GS, van Wijnen AJ, van Zundert B, Allende ML, Montecino M. 2015. Epigenetic Control of the Bone-master Runx2 Gene During Osteoblast-lineage Commitment by the Histone Demethylase JARID1B/KDM5B. J Biol Chem 290(47): 28329-42. 4.693

     26.     Pulgar R, Travisany D, Zuñiga A, Maass A, Cambiazo V. 2015. Complete genome sequence of Piscirickettsia salmonis LF-89 (ATCC VR-1361) a major pathogen of farmed salmonid fish. J Biotechnol. 212:30-1. 3.180

     27.     Blanco-Herrera F, Moreno AA, Tapia R, Reyes F, Araya M, D'Alessio C, Parodi A, Orellana A. The UDP-glucose: glycoprotein glucosyltransferase (UGGT), a key enzyme in ER quality control, plays a significant role in plant growth as well as biotic and abiotic stress in Arabidopsis thaliana. BMC Plant Biol. 2015 May 28;15:127. doi: 10.1186/s12870-015-0525-2. 4.714

     28.     Riveras E, Alvarez JM, Vidal EA, Oses C, Vega A, Gutiérrez RA. The Calcium Ion Is a Second Messenger in the Nitrate Signaling Pathway of Arabidopsis. Plant Physiol. 2015 Oct;169(2):1397-404. doi: 10.1104/pp.15.00961. Epub 2015 Aug 24. 8.030

     29.     Caroline Müller, Kacilda Naomi Kuki, Daniel Teixeira Pinheiro, Laíse Rosado de Souza, Advânio Inácio Siqueira Silva, Marcelo Ehlers Loureiro, Marco Antonio Oliva, Andréa Miyasaka Almeida. 2015. Differential physiological responses in rice upon exposure to excess distinct iron forms. Plant and Soil 391:123-138. 3.528

     30.     Nuñez-Lillo, G., Cifuentes-Esquivel, A., Troggio, M., Micheletti, D., Infante, R., Campos-Vargas, R., Orellana, A., Blanco-Herrera, F., Meneses, C. 2015. Identification of candidate genes associated with mealiness and maturity date in peach [Prunus persica (L.) Batsch] using QTL analysis and deep sequencing. Tree Genetics and Genomes. 11 (4):13. 2.563

     31.     Vega A, Canessa P, Hoppe G, Retamal I, Moyano TC, Canales J, Gutierrez RA, Rubilar J. 2015. Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum.     Front Plant Sci. 6:911 3.990

     32.     Angulo J, Pino K, Echeverria-Chagas N, Marco C, Martinez-Valdebenito C, Galeno H, Villagra E, Vera L, Lagos N, Becerra N, Mora J, Bermudez A, Carcamo M, Diaz J, Miquel J F, Ferres M, Lopez-Lastra M. 2015. Association of Single-Nucleotide Polymorphisms in IL28B, but Not TNF-α, With Severity of Disease Caused by Andes Virus. Clin Infect Dis. 61:9 9.206

     33.     Latorre M, Ehrenfeld N, Cortés MP, Travisany D, Budinich M, Aravena A, González M, Bobadilla-Fazzini R, Parada P, Maass A. 2015. Global transcriptional responses of Acidithiobacillus ferrooxidans Wenelen under different sulfide minerals. Bioresource Technology. 200:29-34. 5.330

     34.     Latorre M, Quesille-Villalobos AM, Maza F, Parra A, Reyes-Jara A.     2015. Synergistic effect of copper and low temperature over Listeria monocytogenes. Biometals. 3.068

     35.     Tallino S, Duffy M, Ralle M, Cortés MP, Latorre M, Burkhead JL. 2015. Nutrigenomics analysis reveals that copper deficiency and dietary sucrose up-regulate inflammation, fibrosis and lipogenic pathways in a mature rat model of nonalcoholic fatty liver disease. J Nutr Biochem 10:996-1006. 3.989

     36.     Mandakovic D, Cabrera P, Pulgar R, Maldonado J, Aravena P, Latorre M, Cambiazo V, González M. 2015. Complete genome sequence of Microbacterium sp. CGR1, bacterium tolerant to wide abiotic conditions isolated from the Atacama Desert     J. Biotechnol.     15:30168-1. 3.180

     37.     Urra F, Pulgar R, Gutiérrez R, Hodar C, Cambiazo V, Labra A. 2015. Identification and molecular characterization of five putative toxins from the venom gland of the snake Philodryas chamissonis (Serpentes: Dipsadidae). Toxicon     108:19-31. 2.708

     38.     Varela, N., Aranguiz, A., Lizama, C., Sepulveda, H., Antonelli, M., Thaler, R., Moreno, R., Montecino, M., Stein, G. S., van Wijnen, A. J., Galindo, M. 2015. Mitotic inheritance of mRNA facilitates translational activation of the osteogenic-lineage commitment factor Runx2 in progeny of osteoblastic cells. J. Cell. Physiol. 3.751

     39.     Dudakovic, A., Camilleri, E. T., Xu, F., Riester, S. M., McGee-Lawrence, M. E., Bradley1, E. W., Paradise, C. R., Thaler, R., Lewallen, E. A., Evans, J. E., Yan, H., Hawse, J. R., Subramaniam, M., Deyle, D. R., Larson, A. N., Lewallen, D. G., Dietz, A. B., Stein, G. S., Montecino, M. A., Westendorf, J. J., van Wijnen, A. J. 2015. Bone-anabolic epigenetic effects of the histone methyltransferase Enhancer of Zeste Homolog 2. J. Biol. Chem. 290:27604-27617. 4.693

     40.     Grandy, R., Whitfield, T., Wu, H., Fitzgerald, M., VanOudenhove, J., Zaidi, S., Montecino, M., van Wijnen, A. J., Lian, J. B., Stein, J. L., Stein, G. S. 2015. Genome-wide Studies Reveal that H3K4me3 Epigenetic Modification in Bivalent Genes is Dynamically Regulated During the Pluripotent Cell Cycle and Stabilized Upon Differentiation. Mol. Cell. Biol. 36:615-627. 5.228

     41.     Bernal C, Araya C, Palma V, Bronfman M. 2015. PPARβ/δ and PPARγ maintain undifferentiated phenotypes of mouse adult neural precursor cells from the subventricular zone. Front Cell Neurosci. 18:78. 4.289

     42.     Falcón-Urrutia P, Carrasco CM, Lois P, Palma V, Roth AD. 2015. Shh Signaling through the Primary Cilium Modulates Rat Oligodendrocyte Differentiation. PLoS One. 10(7):e0133567. 3.702

     43.     Rojas-Benitez D, Thiaville PC, de Crécy-Lagard V, Glavic A. 2015. The Levels of a Universally Conserved tRNA Modification Regulate Cell Growth. J Biol Chem. 290(30):18699-707. 4.693