Publications by authors named "Tomás Moyano"

18 Publications

  • Page 1 of 1

c-Abl regulates a synaptic plasticity-related transcriptional program involved in memory and learning.

Prog Neurobiol 2021 Oct 18;205:102122. Epub 2021 Jul 18.

Department of Cell & Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago de Chile, Chile; Centre for Aging and Regeneration (CARE-UC), Chile. Electronic address:

Memory consolidation requires activation of a gene expression program that allows de novo protein synthesis. But the molecular mechanisms that favour or restrict that program are poorly understood. The kinase c-Abl can modulate gene expression through transcription factors and chromatin modifiers. Here, we show that c-Abl ablation in the brain improves learning acquisition and memory consolidation in mice. Its absence also affects gene expression profiles in the mouse hippocampus. We found that genes involved in synaptic plasticity and actin cytoskeleton dynamics, such as Arp2 and Thorase, are up-regulated at the mRNA and protein levels in trained c-Abl KO mice and by a chemical-LTP stimulus. Trained c-Abl KO mice also show that dendritic spines are larger than in wild-type mice and present at a higher density. These results indicate that c-Abl kinase is an important part of the mechanism that limits or restricts signalling of relevant gene programs involved in morphological and functional spine changes upon neuronal stimulation.
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http://dx.doi.org/10.1016/j.pneurobio.2021.102122DOI Listing
October 2021

Genomic Footprinting Analyses from DNase-seq Data to Construct Gene Regulatory Networks.

Methods Mol Biol 2021 ;2328:25-46

ANID-Millennium Science Initiative Program- Millenium Institute for Integrative Biology (iBio), Santiago, Chile.

Chromatin accessibility is directly linked with transcription in eukaryotes. Accessible regions associated with regulatory proteins are highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion, followed by high-throughput DNA sequencing (DNase-seq). The single-base-pair resolution digestion patterns from DNase-seq allows identifying transcription factor (TF) footprints of local DNA protection that predict TF-DNA binding. The identification of differential footprinting between two conditions allows mapping relevant TF regulatory interactions. Here, we provide step-by-step instructions to build gene regulatory networks from DNase-seq data. Our pipeline includes steps for DHSs calling, identification of differential TF footprints between treatment and control conditions, and construction of gene regulatory networks. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be adapted to work with DNase-seq data from any organism with a sequenced genome.
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http://dx.doi.org/10.1007/978-1-0716-1534-8_3DOI Listing
August 2021

Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters.

Plant Physiol 2021 Feb 5. Epub 2021 Feb 5.

BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France.

In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.
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http://dx.doi.org/10.1093/plphys/kiab047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8154064PMC
February 2021

TGA class II transcription factors are essential to restrict oxidative stress in response to UV-B stress in Arabidopsis.

J Exp Bot 2021 02;72(5):1891-1905

Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.

Plants possess a robust metabolic network for sensing and controlling reactive oxygen species (ROS) levels upon stress conditions. Evidence shown here supports a role for TGA class II transcription factors as critical regulators of genes controlling ROS levels in the tolerance response to UV-B stress in Arabidopsis. First, tga256 mutant plants showed reduced capacity to scavenge H2O2 and restrict oxidative damage in response to UV-B, and also to methylviologen-induced photooxidative stress. The TGA2 transgene (tga256/TGA2 plants) complemented these phenotypes. Second, RNAseq followed by clustering and Gene Ontology term analyses indicate that TGA2/5/6 positively control the UV-B-induced expression of a group of genes with oxidoreductase, glutathione transferase, and glucosyltransferase activities, such as members of the glutathione S-transferase Tau subfamily (GSTU), which encodes peroxide-scavenging enzymes. Accordingly, increased glutathione peroxidase activity triggered by UV-B was impaired in tga256 mutants. Third, the function of TGA2/5/6 as transcriptional activators of GSTU genes in the UV-B response was confirmed for GSTU7, GSTU8, and GSTU25, using quantitative reverse transcription-PCR and ChIP analyses. Fourth, expression of the GSTU7 transgene complemented the UV-B-susceptible phenotype of tga256 mutant plants. Together, this evidence indicates that TGA2/5/6 factors are key regulators of the antioxidant/detoxifying response to an abiotic stress such as UV-B light overexposure.
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http://dx.doi.org/10.1093/jxb/eraa534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7921300PMC
February 2021

Transcriptomic profiles reveal differences in zinc metabolism, inflammation, and tight junction proteins in duodenum from cholesterol gallstone subjects.

Sci Rep 2020 05 4;10(1):7448. Epub 2020 May 4.

Departamento de Gastroenterología. Facultad de Medicina. Pontificia Universidad Católica de Chile, Santiago, Chile.

Cholesterol Gallstone Disease (GSD) is a common multifactorial disorder characterized by crystallization and aggregation of biliary cholesterol in the gallbladder. The global prevalence of GSD is ~10-20% in the adult population but rises to 28% in Chile (17% among men and 30% among women). The small intestine may play a role in GSD pathogenesis, but the molecular mechanisms have not been clarified. Our aim was to identify the role of the small intestine in GSD pathogenesis. Duodenal biopsy samples were obtained from patients with GSD and healthy volunteers. GSD status was defined by abdominal ultrasonography. We performed a transcriptome study in a discovery cohort using Illumina HiSeq. 2500, and qPCR, immunohistochemistry and immunofluorescence were used to validate differentially expressed genes among additional case-control cohorts. 548 differentially expressed genes between GSD and control subjects were identified. Enriched biological processes related to cellular response to zinc, and immune and antimicrobial responses were observed in GSD patients. We validated lower transcript levels of metallothionein, NPC1L1 and tight junction genes and higher transcript levels of genes involved in immune and antimicrobial pathways in GSD patients. Interestingly, serum zinc and phytosterol to cholesterol precursor ratios were lower in GSD patients. A significant association was observed between serum zinc and phytosterol levels. Our results support a model where proximal small intestine plays a key role in GSD pathogenesis. Zinc supplementation, modulation of proximal microbiota and/or intestinal barrier may be novel targets for strategies to prevent GSD.
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http://dx.doi.org/10.1038/s41598-020-64137-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7198580PMC
May 2020

Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots.

Mol Plant 2019 12 14;12(12):1545-1560. Epub 2019 Sep 14.

Pontificia Universidad Catolica de Chile, Santiago, Chile. Electronic address:

Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO treatments. NO-modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.
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http://dx.doi.org/10.1016/j.molp.2019.09.002DOI Listing
December 2019

Whole Genome Sequence, Variant Discovery and Annotation in Mapuche-Huilliche Native South Americans.

Sci Rep 2019 02 14;9(1):2132. Epub 2019 Feb 14.

FONDAP Center for Genome Regulation, Santiago, Chile.

Whole human genome sequencing initiatives help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations, and the information of the genomic structure of Native Americans, especially those from the Southern Cone is scant. Here we present annotation and variant discovery from high-quality complete genome sequences of a cohort of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile. We found approximately 3.1 × 10 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs events. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a sample from a marginally admixed population from the Southern Cone, whose main genetic component derives from Native American ancestors. Additionally, we found that HUI genomes contain variants in genes associated with 5 of the 6 leading causes of noncommunicable diseases in Chile, which may have an impact on the risk of prevalent diseases in Chilean and Amerindian populations. Our data represents a useful resource that can contribute to population-based studies and for the design of early diagnostics or prevention tools for Native and admixed Latin American populations.
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http://dx.doi.org/10.1038/s41598-019-39391-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376018PMC
February 2019

Loop assembly: a simple and open system for recursive fabrication of DNA circuits.

New Phytol 2019 04 25;222(1):628-640. Epub 2019 Feb 25.

Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.

High-efficiency methods for DNA assembly have enabled the routine assembly of synthetic DNAs of increased size and complexity. However, these techniques require customization, elaborate vector sets or serial manipulations for the different stages of assembly. We have developed Loop assembly based on a recursive approach to DNA fabrication. The system makes use of two Type IIS restriction endonucleases and corresponding vector sets for efficient and parallel assembly of large DNA circuits. Standardized level 0 parts can be assembled into circuits containing 1, 4, 16 or more genes by looping between the two vector sets. The vectors also contain modular sites for hybrid assembly using sequence overlap methods. Loop assembly enables efficient and versatile DNA fabrication for plant transformation. We show the construction of plasmids up to 16 genes and 38 kb with high efficiency (> 80%). We have characterized Loop assembly on over 200 different DNA constructs and validated the fidelity of the method by high-throughput Illumina plasmid sequencing. Our method provides a simple generalized solution for DNA construction with standardized parts. The cloning system is provided under an OpenMTA license for unrestricted sharing and open access.
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http://dx.doi.org/10.1111/nph.15625DOI Listing
April 2019

MicroRNA Profiling and Bioinformatics Target Analysis in Dorsal Hippocampus of Chronically Stressed Rats: Relevance to Depression Pathophysiology.

Front Mol Neurosci 2018 6;11:251. Epub 2018 Aug 6.

Laboratory of Neuroplasticity and Neurogenetics, Faculty of Chemical and Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, Universidad de Chile, Santiago, Chile.

Studies conducted in rodents subjected to chronic stress and some observations in humans after psychosocial stress, have allowed to establish a link between stress and the susceptibility to many complex diseases, including mood disorders. The studies in rodents have revealed that chronic exposure to stress negatively affects synaptic plasticity by triggering changes in the production of trophic factors, subunit levels of glutamate ionotropic receptors, neuron morphology, and neurogenesis in the adult hippocampus. These modifications may account for the impairment in learning and memory processes observed in chronically stressed animals. It is plausible then, that stress modifies the interplay between signal transduction cascades and gene expression regulation in the hippocampus, therefore leading to altered neuroplasticity and functioning of neural circuits. Considering that miRNAs play an important role in post-transcriptional-regulation of gene expression and participate in several hippocampus-dependent functions; we evaluated the consequences of chronic stress on the expression of miRNAs in dorsal (anterior) portion of the hippocampus, which participates in memory formation in rodents. Here, we show that male rats exposed to daily restraint stress (2.5 h/day) during 7 and 14 days display a differential profile of miRNA levels in dorsal hippocampus and remarkably, we found that some of these miRNAs belong to the miR-379-410 cluster. We confirmed a rise in miR-92a and miR-485 levels after 14 days of stress by qPCR, an effect that was not mimicked by chronic administration of corticosterone (14 days). Our study identified the top-10 biological functions influenced by miR-92a, nine of which were shared with miR-485: Nervous system development and function, Tissue development, Behavior, Embryonic development, Organ development, Organismal development, Organismal survival, Tissue morphology, and Organ morphology. Furthermore, our study provided a landscape of potential miRNA-92a and miR-485 targets, along with relevant canonical pathways related to axonal guidance signaling and cAMP signaling, which may influence the functioning of several neuroplastic substrates in dorsal hippocampus. Additionally, the combined effect of miR-92a and miR-485 on transcription factors, along with histone-modifying enzymes, may have a functional relevance by producing changes in gene regulatory networks that modify the neuroplastic capacity of the adult dorsal hippocampus under stress.
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http://dx.doi.org/10.3389/fnmol.2018.00251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6088391PMC
August 2018

Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data.

Methods Mol Biol 2018 ;1761:275-301

Departamento de Genética Molecular y Microbiología, FONDAP Center for Genome Regulation, Millennium Institute for Integrative Systems and Synthetic Biology (MIISSB), Pontificia Universidad Católica de Chile, Santiago, Chile.

The rapid increase in the availability of transcriptomics data generated by RNA sequencing represents both a challenge and an opportunity for biologists without bioinformatics training. The challenge is handling, integrating, and interpreting these data sets. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. 1). A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression. Many examples of new hypothesis derived from network analyses can be found in the literature, spanning different organisms including plants and specific fields such as root developmental biology.In order to make the process of constructing a gene co-expression network more accessible to biologists, here we provide step-by-step instructions using published RNA-seq experimental data obtained from a public database. Similar strategies have been used in previous studies to advance root developmental biology. This guide includes basic instructions for the operation of widely used open source platforms such as Bio-Linux, R, and Cytoscape. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be easily adapted to work with RNA-seq data from any organism.
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http://dx.doi.org/10.1007/978-1-4939-7747-5_21DOI Listing
January 2019

Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism.

J Exp Bot 2016 05 25;67(10):3095-108. Epub 2016 Apr 25.

Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, C/ Profesor García González, 1, 41012-Sevilla, Spain

Nitrogen is one of the most important nutrients for plants and, in natural soils, its availability is often a major limiting factor for plant growth. Here we examine the effect of different forms of nitrogen nutrition and of photorespiration on gene expression in the model legume Lotus japonicus with the aim of identifying regulatory candidate genes co-ordinating primary nitrogen assimilation and photorespiration. The transcriptomic changes produced by the use of different nitrogen sources in leaves of L. japonicus plants combined with the transcriptomic changes produced in the same tissue by different photorespiratory conditions were examined. The results obtained provide novel information on the possible role of plastidic glutamine synthetase in the response to different nitrogen sources and in the C/N balance of L. japonicus plants. The use of gene co-expression networks establishes a clear relationship between photorespiration and primary nitrogen assimilation and identifies possible transcription factors connected to the genes of both routes.
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http://dx.doi.org/10.1093/jxb/erw170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4867901PMC
May 2016

Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum.

Front Plant Sci 2015 4;6:911. Epub 2015 Nov 4.

Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile Santiago, Chile.

Nitrogen (N) is one of the main limiting nutrients for plant growth and crop yield. It is well documented that changes in nitrate availability, the main N source found in agricultural soils, influences a myriad of developmental programs and processes including the plant defense response. Indeed, many agronomical reports indicate that the plant N nutritional status influences their ability to respond effectively when challenged by different pathogens. However, the molecular mechanisms involved in N-modulation of plant susceptibility to pathogens are poorly characterized. In this work, we show that Solanum lycopersicum defense response to the necrotrophic fungus Botrytis cinerea is affected by plant N availability, with higher susceptibility in nitrate-limiting conditions. Global gene expression responses of tomato against B. cinerea under contrasting nitrate conditions reveals that plant primary metabolism is affected by the fungal infection regardless of N regimes. This result suggests that differential susceptibility to pathogen attack under contrasting N conditions is not only explained by a metabolic alteration. We used a systems biology approach to identify the transcriptional regulatory network implicated in plant response to the fungus infection under contrasting nitrate conditions. Interestingly, hub genes in this network are known key transcription factors involved in ethylene and jasmonic acid signaling. This result positions these hormones as key integrators of nitrate and defense against B. cinerea in tomato plants. Our results provide insights into potential crosstalk mechanisms between necrotrophic defense response and N status in plants.
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http://dx.doi.org/10.3389/fpls.2015.00911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4631835PMC
November 2015

Transcriptional networks in the nitrate response of Arabidopsis thaliana.

Curr Opin Plant Biol 2015 Oct 3;27:125-32. Epub 2015 Aug 3.

FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile. Electronic address:

Nitrogen is an essential macronutrient for plants and its availability is a key determinant of plant growth and development and crop yield. Besides their nutritional role, N nutrients and metabolites are signals that activate signaling pathways that modulate many plant processes. Because the most abundant inorganic N source for plants in agronomic soils is nitrate, much of the work to understand plant N-signaling has focused on this nutrient. Over the last years, several studies defined a comprehensive catalog of nitrate-responsive genes, involved in nitrate transport, metabolism and a variety of other processes. Despite significant progress in recent years, primarily using Arabidopsis thaliana as a model system, the molecular mechanisms by which nitrate elicits changes in transcript abundance are still not fully understood. Here we highlight recent advancements in identifying key transcription factors and transcriptional mechanisms that orchestrate the gene expression response to changes in nitrate availability in A. thaliana.
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http://dx.doi.org/10.1016/j.pbi.2015.06.010DOI Listing
October 2015

Constructing simple biological networks for understanding complex high-throughput data in plants.

Methods Mol Biol 2015 ;1284:503-26

Departamento de Genética Molecular y Microbiología, FONDAP Center for Genome Regulation, Millennium Nucleus for Plant Functional Genomics, Pontificia Universidad Católica de Chile, Santiago, Chile.

Technological advances in the last decade have enabled biologists to produce increasing amounts of information for the transcriptome, proteome, interactome, and other -omics data sets in many model organisms. A major challenge is integration and biological interpretation of these massive data sets in order to generate testable hypotheses about gene regulatory networks or molecular mechanisms that govern system behaviors. Constructing gene networks requires bioinformatics skills to adequately manage, integrate, analyze and productively use the data to generate biological insights. In this chapter, we provide detailed methods for users without prior knowledge of bioinformatics to construct gene networks and derive hypotheses that can be experimentally verified. Step-by-step instructions for acquiring, integrating, analyzing, and visualizing genome-wide data are provided for two widely used open source platforms, R and Cytoscape platforms. The examples provided are based on Arabidopsis data, but the protocols presented should be readily applicable to any organism for which similar data can be obtained.
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http://dx.doi.org/10.1007/978-1-4939-2444-8_25DOI Listing
November 2015

Nitrogen control of developmental phase transitions in Arabidopsis thaliana.

J Exp Bot 2014 Oct 16;65(19):5611-8. Epub 2014 Aug 16.

FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile

Nitrogen (N) is an essential macronutrient and a key structural component of macromolecules in plants. N nutrients and metabolites can act as signals that impact on many aspects of plant biology. The plant life cycle involves a series of developmental phase transitions that must be tightly coordinated to external and internal cues in order to ensure plant survival and reproduction. N availability is one of the factors controlling phase changes. In this review, we integrate and summarize the known effects of N over different developmental stages in plants. Substantial advances have been made in our understanding of signalling and N-responsive gene regulatory networks. We focus on the molecular mechanisms underlying N regulation of developmental transitions and the role of putative new regulators that might link N availability to pathways controlling Arabidopsis growth and development from seed germination through the plant reproductive transition.
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http://dx.doi.org/10.1093/jxb/eru326DOI Listing
October 2014

Systems analysis of transcriptome data provides new hypotheses about Arabidopsis root response to nitrate treatments.

Front Plant Sci 2014 7;5:22. Epub 2014 Feb 7.

Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Pontifical Catholic University of Chile Santiago, Chile.

Nitrogen (N) is an essential macronutrient for plant growth and development. Plants adapt to changes in N availability partly by changes in global gene expression. We integrated publicly available root microarray data under contrasting nitrate conditions to identify new genes and functions important for adaptive nitrate responses in Arabidopsis thaliana roots. Overall, more than 2000 genes exhibited changes in expression in response to nitrate treatments in Arabidopsis thaliana root organs. Global regulation of gene expression by nitrate depends largely on the experimental context. However, despite significant differences from experiment to experiment in the identity of regulated genes, there is a robust nitrate response of specific biological functions. Integrative gene network analysis uncovered relationships between nitrate-responsive genes and 11 highly co-expressed gene clusters (modules). Four of these gene network modules have robust nitrate responsive functions such as transport, signaling, and metabolism. Network analysis hypothesized G2-like transcription factors are key regulatory factors controlling transport and signaling functions. Our meta-analysis highlights the role of biological processes not studied before in the context of the nitrate response such as root hair development and provides testable hypothesis to advance our understanding of nitrate responses in plants.
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http://dx.doi.org/10.3389/fpls.2014.00022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3917222PMC
February 2014

Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots.

BMC Genomics 2013 Oct 11;14:701. Epub 2013 Oct 11.

FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Functional Genomics, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331010, Chile.

Background: Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out.

Results: In this work, we employed the Illumina high throughput sequencing technology to perform an integrated analysis of the poly-A + enriched and the small RNA fractions of the Arabidopsis thaliana root transcriptome in response to nitrate treatments. Our sequencing strategy identified new nitrate-regulated genes including 40 genes not represented in the ATH1 Affymetrix GeneChip, a novel nitrate-responsive antisense transcript and a new nitrate responsive miRNA/TARGET module consisting of a novel microRNA, miR5640 and its target, AtPPC3.

Conclusions: Sequencing of small RNAs and mRNAs uncovered new genes, and enabled us to develop new hypotheses for nitrate regulation and coordination of carbon and nitrogen metabolism.
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http://dx.doi.org/10.1186/1471-2164-14-701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906980PMC
October 2013

Systems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thaliana roots.

Proc Natl Acad Sci U S A 2013 Jul 11;110(31):12840-5. Epub 2013 Jul 11.

Fondo Nacional de Areas Prioritarias (FONDAP) Center for Genome Regulation, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 833101, Santiago, Chile.

Auxin is a key phytohormone regulating central processes in plants. Although the mechanism by which auxin triggers changes in gene expression is well understood, little is known about the specific role of the individual members of the TIR1/AFB auxin receptors, Aux/IAA repressors, and ARF transcription factors and/or molecular pathways acting downstream leading to plant responses to the environment. We previously reported a role for AFB3 in coordinating primary and lateral root growth to nitrate availability. In this work, we used an integrated genomics, bioinformatics, and molecular genetics approach to dissect regulatory networks acting downstream of AFB3 that are activated by nitrate in roots. We found that the NAC4 transcription factor is a key regulatory element controlling a nitrate-responsive network, and that nac4 mutants have altered lateral root growth but normal primary root growth in response to nitrate. This finding suggests that AFB3 is able to activate two independent pathways to control root system architecture. Our systems approach has unraveled key components of the AFB3 regulatory network leading to changes in lateral root growth in response to nitrate.
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http://dx.doi.org/10.1073/pnas.1310937110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3732920PMC
July 2013
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