Center for Genome Regulation

A FONDAP Center of Excellence

"Exploring the Genomic Landscape of Chile"

2019 Publications

ISI Papers


Morales RA, Allende ML. 2019. Peripheral Macrophages Promote Tissue Regeneration in Zebrafish by Fine-tuning the Inflammatory Response. Front. Immunol. 10:253. doi: 10.3389/fimmu.2019.00253.

Young RM, Hawkins TA, Cavodeassi F, Stickney HL, Schwarz Q, Lawrence LM, Wierzbicki C, Cheng BYL, Luo J, Ambrosio E, Klosner A, Sealy IM, Rowell J, Trivedi C, Bianco I, Allende ML, Busch- Nentwich EM, Gestri G, Wilson SM. 2019. Compensatory growth renders Tcf7l1a dispensable for eye formation despite its requirement in eye field specification. Elife. 8. pii: e40093. doi: 10.7554/eLife.40093.

Del Pozo T, Miranda S, Latorre M, Olivares F, Pavez L, Gutiérrez R, Maldonado J, Hinrichsen P, Defilippi BG, Orellana A, Gonzalez M. 2019. Comparative transcriptome profiling in a segregating peach population with contrasting juiciness phenotypes. J Agric Food Chem. doi: 10.1021/acs.jafc.8b05177. 

Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT. 2019. Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. Nat Protoc. 14(3):639-702. doi: 10.1038/s41596-018-0098-2.

Fernández-Gómez B, Maldonado J, Mandakovic D, Gaete A, Gutiérrez RA, Maass A, Cambiazo V, González M. 2019. Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils. Sci Rep. 2019 Jan 31;9(1):1042. doi: 10.1038/s41598-018-37776-0.

Díaz FP, Latorre C, Carrasco-Puga G, Wood JR, Wilmshurst JM, Soto DC, Cole TL, Gutiérrez RA. 2019. Multiscale climate change impacts on plant diversity in the Atacama Desert. Glob Chang Biol. 25: 1733-1745. doi: 10.1111/gcb.14583.

Bustos BI, Pérez-Palma E, Buch S, Azócar L, Riveras E, Ugarte GD, Toliat M, Nürnberg P, Lieb W, Franke A, Hinz S, Burmeister G, von Schönfels W, Schafmayer C, Völzke H, Völker U, Homuth G, Lerch MM, Santos JL, Puschel K, Bambs C, Roa JC, Gutiérrez RA, Hampe J, De Ferrari GV, Miquel JF. 2019. Variants in ABCG8 and TRAF3 genes confer risk for gallstone disease in admixed Latinos with Mapuche Native American ancestry. Sci Rep. 9(1):772. doi: 10.1038/s41598-018-35852-z.

Brooks MD, Cirrone J, Pasquino AV, Swift J, Alvarez JM, Mittal S, Juang CL, Varala K, Gutiérrez RA, Krouk G, Shasha D, Coruzzi GM (2019). Network Walking charts transcriptional pathways for dynamic nitrogen signaling using validated and predicted genome-wide interactions. Nature Comm. 10(1):1569. doi: 10.1038/s41467-019-09522-1.

Maza F, Maldonado J, Vásquez-Dean J, Mandakovic D, Gaete A, Cambiazo V, González M. 2019. Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability. Front Bioeng Biotechnol. 7:10. doi: 10.3389/fbioe.2019.00010.

Vergara-Pulgar C, Rothkegel K, González-Agüero M, Pedreschi R, Campos-Vargas R, Defilippi BG, Meneses C. 2019. De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development. BMC Genomics. 20(1):108. doi: 10.1186/s12864-019-5486-7.

Anguita-Salinas C, Sánchez M, Morales RA, Ceci ML, Rojas-Benítez D, Allende ML. 2019. Cellular dynamics during spinal cord regeneration in larval zebrafish. Dev. Neurosci. 7:1-11. doi: 10.1159/000500185.

Miranda M, Egaña JT, Allende ML, Eblen-Zajjur, A. 2019. Myocardial transmembrane action potential recorded by suction electrode for ionic current studies in zebrafish. Zebrafish doi: 10.1089/zeb.2019.1753.

Latorre M, Burkhead JL, Hodar C, Arredondo M, González M, Araya M. 2019. Chronic copper treatment prevents the liver critical balance transcription response induced by acetaminophen. J Trace Elem Med Biol. 53:113-119. doi: 10.1016/j.jtemb.2019.02.007.

Gavicho Uarrota V, Fuentealba C, Hernández I, Defilippi-Bruzzone B, Meneses C, Campos-Vargas R, Lurie S, Hertog M, Carpentier S, Poblete-Echeverría C, Pedreschi R. 2019. Integration of proteomics and metabolomics data of early and middle season Hass avocados under heat treatment. Food Chem. 289:512-521. doi: 10.1016/j.foodchem.2019.03.090.

Quesille-Villalobos AM, Parra A, Maza F, Navarrete P, González M, Latorre M, Toro M, Reyes-Jara A. 2019. The Combined Effect of Cold and Copper Stresses on the Proliferation and Transcriptional Response of Listeria monocytogenes. Front Microbiol. 10:612. doi: 10.3389/fmicb.2019.00612.

Fitzpatrick C, Bendek MF, Briones M, Farfán N, Silva VA, Nardocci G, Montecino M, Boland A, Deleuze JF, Villegas J, Villota C, Silva V, Lobos-Gonzalez L, Borgna V, Barrey E, Burzio LO, Burzio VA. 2019. Mitochondrial ncRNA targeting induces cell cycle arrest and tumor growth inhibition of MDA-MB-231 breast cancer cells through reduction of key cell cycle progression factors. Cell Death Dis. 10(6):423. doi: 10.1038/s41419-019-1649-3.

Delucchi Á, Toro L, Alzamora R, Barrientos V, González M, Andaur R, León P, Villanueva F, Galindo M, Heras FL, Montecino M, Moena D, Lazcano A, Pinto V, Salas P, Reyes ML, Mericq V, Michea L. 2019. Glucocorticoids Decrease Longitudinal Bone Growth in Paediatric Kidney Transplant Recipients by Stimulating the FGF23/FGFR3 Signalling Pathway. J Bone Miner Res. 34(10):1851-1861. doi: 10.1002/jbmr.3761.

Saa PA, Cortés MP, López J, Bustos D, Maass A, Agosin E. 2019. Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies. Biotechnol J. 29:e1800734. doi: 10.1002/biot.201800734.

Parra-Rojas JP, Largo-Gosens A, Carrasco T, Celiz-Balboa J, Arenas-Morales V, Sepúlveda-Orellana P, Temple H, Sanhueza D, Reyes FC, Meneses C, Saez-Aguayo S, Orellana A. 2019. New steps in mucilage biosynthesis revealed by analysis of the transcriptome of UDP-rhamnose/UDP-galactose transporter 2 (URGT2) mutant. J Exp Bot. 70(19):5071-5088. pii: erz262. doi: 10.1093/jxb/erz262.

Falter-Braun P, Brady S, Gutiérrez RA, Coruzzi GM, Krouk G. 2019. iPlant Systems Biology (iPSB): An International Network Hub in the Plant Community. Mol Plant. 12(6):727-730. doi: 10.1016/j.molp.2019.05.005.

Travisany D, Ayala-Raso A, Di Genova A, Monsalve L, Bernales M, Martínez JP, González-Agüero M, Defilippi B, Cherian S, Maass A, Fuentes L. 2019. RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus Heritage) revealed several candidate genes involved in fruit development and ripening. Scientia Horticulturae 254, 26-34.

Mendez KN, Hoare A, Soto C, Bugueño I, Olivera M, Meneses C, Pérez-Donoso JM, Castro-Nallar E, Bravo D. 2019. Variability in Genomic and Virulent Properties of Porphyromonas gingivalis Strains Isolated From Healthy and Severe Chronic Periodontitis Individuals. Front Cell Infect Microbiol. 9:246. doi: 10.3389/fcimb.2019.00246.

Orellana-Saez M, Pacheco N, Costa JI, Mendez KN, Miossec MJ, Meneses C, Castro-Nallar E, Marcoleta AE, Poblete-Castro I. 2019. In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential. Front Microbiol. 10:1154. doi: 10.3389/fmicb.2019.01154.

Cáceres G, López ME, Cádiz MI, Yoshida GM, Jedlicki AM, Palma-Véjares R, Travisany D, Díaz-Domínguez D, Maass A, Lhorente JP, Soto J, Salas D, Yáñez JM. 2019. Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia (Oreochromis niloticus L.). G3 (Bethesda). doi: 10.1534/g3.119.400297. 

Alvarez JM, Moyano TC, Zhang T, Gras DE, Herrera FJ, Araus V, O'Brien JA, Carrillo L, Medina J, Vicente-Carbajosa J, Jiang J, Gutiérrez RA. 2019. Local changes in chromatin accessibility and transcriptional networks underlying the nitrate response in Arabidopsis roots. Mol Plant. 2019 Sep 14. pii: S1674-2052(19)30291-6. doi: 10.1016/j.molp.2019.09.002.

Pérez-Palma E, Bustos BI, Lal D, Buch S, Azocar L, Toliat MR, Lieb W, Franke A, Hinz S, Burmeister G, von Shönfels W, Schafmayer C, Ahnert P, Völzke H, Völker U, Homuth G, Lerch MM, Puschel K, Gutiérrez RA, Hampe J, Nürnberg P, Francisco Miquel J, De Ferrari GV.  2019. Copy number variants in lipid metabolism genes are associated with gallstones disease in men. Eur J Hum Genet. 2019 Sep 4. doi: 10.1038/s41431-019-0501-7.

Young R, Ewan K, Ferrer V, Allende ML, Godovac-Zimmermann J, Dale T, Wilson SW. 2019. Developmentally regulated tcf7l2 splice variants mediate transcriptional repressor functions during eye formation. ELife 8:e51447 DOI: 10.7554/eLife.51447.

Rojas-Benítez D, Allende ML. 2019. Elongator subunit 3 (Elp3) is required for zebrafish trunk development. Int. J. Mol. Sci. 21(3). doi: 10.3390/ijms21030925.

Fehrmann-Cartes K, Coronado M, Hernandez A, Allende ML, Feijoo CG. 2019. Anti-inflammatory effects of Aloe vera on soy meal-induced intestinal inflammation in zebrafish. Fish and Shellfish Immunology doi: 10.1016/j.fsi.2019.10.075.

Ortiz-Severín J, Travisany D, Maass A, Chávez FP, Cambiazo V. 2019. Piscirickettsia salmonis Cryptic Plasmids: Source of Mobile DNA and Virulence Factors. Pathogens. 8(4). pii: E269. doi: 10.3390/pathogens8040269.

Naulin PA, Armijo G, Vega A, Tamayo KP, Gras DE, de la Cruz J, Gutiérrez RA.  2019. Nitrate Induction of Primary Root Growth Requires Cytokinin Signaling in Arabidopsis thaliana. Plant Cell Physiol. pii: pcz199. doi: 10.1093/pcp/pcz199.

Vega A, O'Brien JA, Benková E, Gutiérrez RA. 2019. Nitrate and hormonal signaling crosstalk for plant growth and development. Curr Opin Plant Biol. 52:155-163. doi: 10.1016/j.pbi.2019.10.001.

Pedreschi R, Uarrota V, Fuentealba C, Alvaro JE, Olmedo P, Defilippi BG, Meneses C, Campos-Vargas R. 2019. Primary Metabolism in Avocado Fruit. Front Plant Sci. 10:795. doi: 10.3389/fpls.2019.00795.

Dettleff P, Hormazabal E, Aedo J, Fuentes M, Meneses C, Molina A, Valdes JA. 2019. Identification and Evaluation of Long Noncoding RNAs in Response to Handling Stress in Red Cusk-Eel (Genypterus chilensis) via RNA-seq. Mar Biotechnol (NY). doi: 10.1007/s10126-019-09934-6.

Ortiz J, Soto J, Fuentes A, Herrera H, Meneses C, Arriagada C. 2019. The Endophytic Fungus Chaetomium cupreum Regulates Expression of Genes Involved in the Tolerance to Metals and Plant Growth Promotion in Eucalyptus globulus Roots. Microorganisms. 7(11). pii: E490. doi: 10.3390/microorganisms7110490.

González P, Dettleff P, Valenzuela C, Estrada JM, Valdés JA, Meneses C, Molina A. 2019. Evaluating the genetic structure of wild and commercial red cusk-eel (Genypterus chilensis) populations through the development of novel microsatellite markers from a reference transcriptome. Mol Biol Rep. 46(6):5875-5882. doi: 10.1007/s11033-019-05021-0.

Aedo JE, Zuloaga R, Bastías-Molina M, Meneses C, Boltaña S, Molina A, Valdés JA. 2019. Early transcriptomic responses associated with the membrane-initiated action of cortisol in the skeletal muscle of rainbow trout (Oncorhynchus mykiss). Physiol Genomics. 51(11):596-606. doi: 10.1152/physiolgenomics.00042.2019.

De Ferrari G, Pérez-Palma E, Bustos B, Lal D, Buch S, Azocar L, Toliat M, Lieb W, Franke A, Hinz S, Burmeister G, von Shönfels W, Schafmayer C, Ahnert P, Völzke H, Voelker U, Homuth G, Lerch M, Puschel K, Gutiérrez RA, Hampe J, Nürnberg P, and Miquel JF. 2019. Copy number variants in lipid metabolism genes are associated with gallstones disease in men. Eur. J Human Genet. In press.

Cruz N, Méndez T, Ramos P, Urbina D, Vega A, Gutiérrez RA, Moya-León MA, Herrera R. 2019. Induction of PrMADS10 on the lower side of bent pine tree stems: potential role in modifying plant cell wall properties and wood anatomy. Sci Rep. 9(1):18981. doi: 10.1038/s41598-019-55276-7.

Zuñiga A, Aravena P, Pulgar RE, Dante Travisany D,  Ortiz-Severín J,  Chávez FP,  Maass A,  Gonzalez M,  Cambiazo V. 2019. Transcriptomic changes of Piscirickettsia salmonis during intracellular growth in a salmon macrophage-like cell line. Front. Cell. Infect. Microbiol.  doi: 10.3389/fcimb.2019.00426

Edwards S, Blosveld F, Bellaiche Y, Lennon-Dumenil AM, Glavic A. 2020. Trpml controls actomyosin contractility and couples migration to phagocytosis in fly macrophages. Journal of Cell Biology. e201905228. https://doi.org/10.1083/jcb.201905228

Wood JR, Díaz FP, Latorre C, Wilmshurst JM, Burge OR, Gutiérrez RA. 2019. Ancient parasite DNA from late Quaternary Atacama Desert rodent middens. Quat. Sci Rev. 226:106031.   https://doi.org/10.1016/j.quascirev.2019.106031.

Moena D, Merino P, Lian JB, Stein GS, Stein JL, Montecino M. 2019. Switches in histone modifications epigenetically control vitamin D3-dependent transcriptional upregulation of the CYP24A1 gene in osteoblastic cells. J Cell Physiol. doi: 10.1002/jcp.29420.

Moena D, Nardocci G, Acevedo E, Lian J, Stein G, Stein J, Montecino M. 2020. Ezh2-dependent H3K27me3 modification dynamically regulates vitamin D3-dependent epigenetic control of CYP24A1 gene expression in osteoblastic cells. J Cell Physiol. doi: 10.1002/jcp.29428.

Khan A, Davlieva M, Panesso D, Rincon S, Miller WR, Diaz L, Reyes J, Cruz MR, Pemberton O, Nguyen AH, Siegel SD, Planet PJ, Narechania A, Latorre M, Rios R, Singh KV, Ton-That H, Garsin DA, Tran TT, Shamoo Y, Arias CA. 2019. Antimicrobial sensing coupled with cell membrane remodeling mediates antibiotic resistance and virulence in Enterococcus faecalis. Proc Natl Acad Sci U S A. 2019 Dec 9. pii: 201916037. doi: 10.1073/pnas.1916037116.

Chavez MN, Morales RA, López-Crisosto C, Roa JC, Allende ML, Lavandero S. 2020. Autophagy activation in zebrafish heart regeneration. Sci. Rep. 10(1):2191. doi: 10.1038/s41598-020-59106-z.

Molina-Montenegro MA, Ballesteros GI, Castro-Nallar E, Meneses C, Gallardo-Cerda J, Torres-Díaz C. 2019. A first insight into the structure and function of rhizosphere microbiota in Antarctic plants using shotgun metagenomic. Polar Biol 42, 1825–1835 (2019). https://doi.org/10.1007/s00300-019-02556-7

Miranda S, Vilches P, Suazo M, Pavez L, García K, Méndez M, González M, Meisel L, Defilippi BG, Del Pozo T. 2020 Melatonin triggers metabolic and gene expression changes leading to improved quality traits of two sweet cherry cultivars during cold storage. Food Chemistry (In Press). https://doi.org/10.1016/j.foodchem.2020.126360

Pardo-Esté C, Castro-Severyn J, Krüger GI, Cabezas CE, Briones AC, Aguirre C, Morales N, Baquedano MS, Sulbaran YN, Hidalgo AA, Meneses C, Poblete-Castro I, Castro-Nallar E, Valvano MA, Saavedra CP. 2019. The Transcription Factor ArcA Modulates Salmonella's Metabolism in Response to Neutrophil Hypochlorous Acid-Mediated Stress. Front Microbiol. 10:2754. doi: 10.3389/fmicb.2019.02754.

Cortés MP, Acuña V, Travisany D, Siegel A, Maass A, Latorre M.  2020. Integration of Biological Networks for Acidithiobacillus thiooxidans Describes a Modular Gene Regulatory Organization of Bioleaching Pathways. Front Mol Biosci. 6:155. doi: 10.3389/fmolb.2019.00155. 



Non-ISI


Salazar MP, Valenzuela D, Tironi M, Gutiérrez RA (2019). The construction of a regulatory style for genetically modified crops in Chile. Tapuya: Latin American Science, Technology and Society.

Aedo G, Miranda M, Chavez MN, Allende ML, Egaña JT. 2019. A reliable preclinical model to study the impact of cigarette smoke in physiology and disease. Current Protocols in Toxicology. e78. doi: 10.1002/cptx.78.

Varas MA, Ortíz-Severín J, Marcoleta AE, Santiviago CA, Allende ML, Chávez FP. 2019. Static Immersion and Injection Methods for Live Cell Imaging of Foodborne Pathogen Infections in Zebrafish Larvae. Methods Mol Biol. 1918:183-190. doi: 10.1007/978-1-4939-9000-9_15.

Herreño AM, Ramírez AC, Chaparro VP, Fernandez MJ, Cañas A, Morantes CF, Moreno OM, Brugés RE, Mejía JA, Bustos FJ, Montecino M, Rojas AP. 2019. Role of RUNX2 transcription factor in epithelial mesenchymal transition in non-small cell lung cancer lung cancer: Epigenetic control of the RUNX2 P1 promoter. Tumour Biol. 41(5):1010428319851014. doi 10.1177/1010428319851014.