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Li Q, Button-Simons KA, Sievert MAC, Chahoud E, Foster GF, Meis K, Ferdig MT, Milenković T. Enhancing Gene Co-Expression Network Inference for the Malaria Parasite Plasmodium falciparum. Genes (Basel) 2024; 15:685. [PMID: 38927622 PMCID: PMC11202799 DOI: 10.3390/genes15060685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Malaria results in more than 550,000 deaths each year due to drug resistance in the most lethal Plasmodium (P.) species P. falciparum. A full P. falciparum genome was published in 2002, yet 44.6% of its genes have unknown functions. Improving the functional annotation of genes is important for identifying drug targets and understanding the evolution of drug resistance. RESULTS Genes function by interacting with one another. So, analyzing gene co-expression networks can enhance functional annotations and prioritize genes for wet lab validation. Earlier efforts to build gene co-expression networks in P. falciparum have been limited to a single network inference method or gaining biological understanding for only a single gene and its interacting partners. Here, we explore multiple inference methods and aim to systematically predict functional annotations for all P. falciparum genes. We evaluate each inferred network based on how well it predicts existing gene-Gene Ontology (GO) term annotations using network clustering and leave-one-out crossvalidation. We assess overlaps of the different networks' edges (gene co-expression relationships), as well as predicted functional knowledge. The networks' edges are overall complementary: 47-85% of all edges are unique to each network. In terms of the accuracy of predicting gene functional annotations, all networks yielded relatively high precision (as high as 87% for the network inferred using mutual information), but the highest recall reached was below 15%. All networks having low recall means that none of them capture a large amount of all existing gene-GO term annotations. In fact, their annotation predictions are highly complementary, with the largest pairwise overlap of only 27%. We provide ranked lists of inferred gene-gene interactions and predicted gene-GO term annotations for future use and wet lab validation by the malaria community. CONCLUSIONS The different networks seem to capture different aspects of the P. falciparum biology in terms of both inferred interactions and predicted gene functional annotations. Thus, relying on a single network inference method should be avoided when possible. SUPPLEMENTARY DATA Attached.
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Affiliation(s)
- Qi Li
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
| | - Katrina A. Button-Simons
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mackenzie A. C. Sievert
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Elias Chahoud
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Department of Preprofessional Studies, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Gabriel F. Foster
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Kaitlynn Meis
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael T. Ferdig
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Tijana Milenković
- Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
- Lucy Family Institute for Data & Society, University of Notre Dame, Notre Dame, IN 46556, USA (M.T.F.)
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Fehér A. A Common Molecular Signature Indicates the Pre-Meristematic State of Plant Calli. Int J Mol Sci 2023; 24:13122. [PMID: 37685925 PMCID: PMC10488067 DOI: 10.3390/ijms241713122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
In response to different degrees of mechanical injury, certain plant cells re-enter the division cycle to provide cells for tissue replenishment, tissue rejoining, de novo organ formation, and/or wound healing. The intermediate tissue formed by the dividing cells is called a callus. Callus formation can also be induced artificially in vitro by wounding and/or hormone (auxin and cytokinin) treatments. The callus tissue can be maintained in culture, providing starting material for de novo organ or embryo regeneration and thus serving as the basis for many plant biotechnology applications. Due to the biotechnological importance of callus cultures and the scientific interest in the developmental flexibility of somatic plant cells, the initial molecular steps of callus formation have been studied in detail. It was revealed that callus initiation can follow various ways, depending on the organ from which it develops and the inducer, but they converge on a seemingly identical tissue. It is not known, however, if callus is indeed a special tissue with a defined gene expression signature, whether it is a malformed meristem, or a mass of so-called "undifferentiated" cells, as is mostly believed. In this paper, I review the various mechanisms of plant regeneration that may converge on callus initiation. I discuss the role of plant hormones in the detour of callus formation from normal development. Finally, I compare various Arabidopsis gene expression datasets obtained a few days, two weeks, or several years after callus induction and identify 21 genes, including genes of key transcription factors controlling cell division and differentiation in meristematic regions, which were upregulated in all investigated callus samples. I summarize the information available on all 21 genes that point to the pre-meristematic nature of callus tissues underlying their wide regeneration potential.
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Affiliation(s)
- Attila Fehér
- Institute of Plant Biology, Biological Research Centre, 62 Temesvári Körút, 6726 Szeged, Hungary; or
- Department of Plant Biology, University of Szeged, 52 Közép Fasor, 6726 Szeged, Hungary
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Natukunda MI, Mantilla-Perez MB, Graham MA, Liu P, Salas-Fernandez MG. Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing. BMC Genomics 2022; 23:95. [PMID: 35114939 PMCID: PMC8812014 DOI: 10.1186/s12864-021-08251-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/10/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Leaf angle is an important plant architecture trait, affecting plant density, light interception efficiency, photosynthetic rate, and yield. The "smart canopy" model proposes more vertical leaves in the top plant layers and more horizontal leaves in the lower canopy, maximizing conversion efficiency and photosynthesis. Sorghum leaf arrangement is opposite to that proposed in the "smart canopy" model, indicating the need for improvement. Although leaf angle quantitative trait loci (QTL) have been previously reported, only the Dwarf3 (Dw3) auxin transporter gene, colocalizing with a major-effect QTL on chromosome 7, has been validated. Additionally, the genetic architecture of leaf angle across canopy layers remains to be elucidated. RESULTS This study characterized the canopy-layer specific transcriptome of five sorghum genotypes using RNA sequencing. A set of 284 differentially expressed genes for at least one layer comparison (FDR < 0.05) co-localized with 69 leaf angle QTL and were consistently identified across genotypes. These genes are involved in transmembrane transport, hormone regulation, oxidation-reduction process, response to stimuli, lipid metabolism, and photosynthesis. The most relevant eleven candidate genes for layer-specific angle modification include those homologous to genes controlling leaf angle in rice and maize or genes associated with cell size/expansion, shape, and cell number. CONCLUSIONS Considering the predicted functions of candidate genes, their potential undesirable pleiotropic effects should be further investigated across tissues and developmental stages. Future validation of proposed candidates and exploitation through genetic engineering or gene editing strategies targeted to collar cells will bring researchers closer to the realization of a "smart canopy" sorghum.
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Affiliation(s)
| | - Maria B Mantilla-Perez
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Present address: Bayer Crop Science, Chesterfield, MO, USA
| | - Michelle A Graham
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Corn Insects and Crop Genetics Research, USDA-ARS, Ames, IA, 50011, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, 50011, USA
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Defective cytokinin signaling reprograms lipid and flavonoid gene-to-metabolite networks to mitigate high salinity in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2105021118. [PMID: 34815339 PMCID: PMC8640937 DOI: 10.1073/pnas.2105021118] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Cytokinin (CK) in plants regulates both developmental processes and adaptation to environmental stresses. Arabidopsis histidine phosphotransfer ahp2,3,5 and type-B Arabidopsis response regulator arr1,10,12 triple mutants are almost completely defective in CK signaling, and the ahp2,3,5 mutant was reported to be salt tolerant. Here, we demonstrate that the arr1,10,12 mutant is also more tolerant to salt stress than wild-type (WT) plants. A comprehensive metabolite profiling coupled with transcriptome analysis of the ahp2,3,5 and arr1,10,12 mutants was conducted to elucidate the salt tolerance mechanisms mediated by CK signaling. Numerous primary (e.g., sugars, amino acids, and lipids) and secondary (e.g., flavonoids and sterols) metabolites accumulated in these mutants under nonsaline and saline conditions, suggesting that both prestress and poststress accumulations of stress-related metabolites contribute to improved salt tolerance in CK-signaling mutants. Specifically, the levels of sugars (e.g., trehalose and galactinol), amino acids (e.g., branched-chain amino acids and γ-aminobutyric acid), anthocyanins, sterols, and unsaturated triacylglycerols were higher in the mutant plants than in WT plants. Notably, the reprograming of flavonoid and lipid pools was highly coordinated and concomitant with the changes in transcriptional levels, indicating that these metabolic pathways are transcriptionally regulated by CK signaling. The discovery of the regulatory role of CK signaling on membrane lipid reprogramming provides a greater understanding of CK-mediated salt tolerance in plants. This knowledge will contribute to the development of salt-tolerant crops with the ability to withstand salinity as a key driver to ensure global food security in the era of climate crisis.
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Van den Broeck L, Gordon M, Inzé D, Williams C, Sozzani R. Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling. Front Genet 2020; 11:457. [PMID: 32547596 PMCID: PMC7270862 DOI: 10.3389/fgene.2020.00457] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/14/2020] [Indexed: 12/26/2022] Open
Abstract
Plant responses to environmental and intrinsic signals are tightly controlled by multiple transcription factors (TFs). These TFs and their regulatory connections form gene regulatory networks (GRNs), which provide a blueprint of the transcriptional regulations underlying plant development and environmental responses. This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs. Additionally, this review describes network inference techniques that leverage gene expression data to predict regulatory interactions. These computational and experimental methodologies yield complex networks that can identify new regulatory interactions, driving novel hypotheses. Biological properties that contribute to the complexity of GRNs are also described in this review. These include network topology, network size, transient binding of TFs to DNA, and competition between multiple upstream regulators. Finally, this review highlights the potential of machine learning approaches to leverage gene expression data to predict phenotypic outputs.
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Affiliation(s)
- Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Max Gordon
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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6
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DeMers LC, Redekar NR, Kachroo A, Tolin SA, Li S, Saghai Maroof MA. A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virus. PLoS One 2020; 15:e0231658. [PMID: 32315334 DOI: 10.1371/journal.pgen.0231658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/29/2020] [Indexed: 05/28/2023] Open
Abstract
Resistance genes are an effective means for disease control in plants. They predominantly function by inducing a hypersensitive reaction, which results in localized cell death restricting pathogen spread. Some resistance genes elicit an atypical response, termed extreme resistance, where resistance is not associated with a hypersensitive reaction and its standard defense responses. Unlike hypersensitive reaction, the molecular regulatory mechanism(s) underlying extreme resistance is largely unexplored. One of the few known, naturally occurring, instances of extreme resistance is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent Soybean mosaic virus strains. To discern the regulatory mechanism underlying Rsv3-mediated extreme resistance, we generated a gene regulatory network using transcriptomic data from time course comparisons of Soybean mosaic virus-G7-inoculated resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. Our results show Rsv3 begins mounting a defense by 6 hpi via a complex phytohormone network, where abscisic acid, cytokinin, jasmonic acid, and salicylic acid pathways are suppressed. We identified putative regulatory interactions between transcription factors and genes in phytohormone regulatory pathways, which is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. One such transcription factor identified as a putative transcriptional regulator was MYC2 encoded by Glyma.07G051500. Known as a master regulator of abscisic acid and jasmonic acid signaling, MYC2 specifically recognizes the G-box motif ("CACGTG"), which was significantly enriched in our data among differentially expressed genes implicated in abscisic acid- and jasmonic acid-related activities. This suggests an important role for Glyma.07G051500 in abscisic acid- and jasmonic acid-derived defense signaling in Rsv3. Resultantly, the findings from our network offer insights into genes and biological pathways underlying the molecular defense mechanism of Rsv3-mediated extreme resistance against Soybean mosaic virus. The computational pipeline used to reconstruct the gene regulatory network in this study is freely available at https://github.com/LiLabAtVT/rsv3-network.
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Affiliation(s)
- Lindsay C DeMers
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Neelam R Redekar
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, Virginia, United States of America
| | - Sue A Tolin
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - M A Saghai Maroof
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
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7
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DeMers LC, Redekar NR, Kachroo A, Tolin SA, Li S, Saghai Maroof MA. A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virus. PLoS One 2020; 15:e0231658. [PMID: 32315334 PMCID: PMC7173922 DOI: 10.1371/journal.pone.0231658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/29/2020] [Indexed: 01/02/2023] Open
Abstract
Resistance genes are an effective means for disease control in plants. They predominantly function by inducing a hypersensitive reaction, which results in localized cell death restricting pathogen spread. Some resistance genes elicit an atypical response, termed extreme resistance, where resistance is not associated with a hypersensitive reaction and its standard defense responses. Unlike hypersensitive reaction, the molecular regulatory mechanism(s) underlying extreme resistance is largely unexplored. One of the few known, naturally occurring, instances of extreme resistance is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent Soybean mosaic virus strains. To discern the regulatory mechanism underlying Rsv3-mediated extreme resistance, we generated a gene regulatory network using transcriptomic data from time course comparisons of Soybean mosaic virus-G7-inoculated resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. Our results show Rsv3 begins mounting a defense by 6 hpi via a complex phytohormone network, where abscisic acid, cytokinin, jasmonic acid, and salicylic acid pathways are suppressed. We identified putative regulatory interactions between transcription factors and genes in phytohormone regulatory pathways, which is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. One such transcription factor identified as a putative transcriptional regulator was MYC2 encoded by Glyma.07G051500. Known as a master regulator of abscisic acid and jasmonic acid signaling, MYC2 specifically recognizes the G-box motif ("CACGTG"), which was significantly enriched in our data among differentially expressed genes implicated in abscisic acid- and jasmonic acid-related activities. This suggests an important role for Glyma.07G051500 in abscisic acid- and jasmonic acid-derived defense signaling in Rsv3. Resultantly, the findings from our network offer insights into genes and biological pathways underlying the molecular defense mechanism of Rsv3-mediated extreme resistance against Soybean mosaic virus. The computational pipeline used to reconstruct the gene regulatory network in this study is freely available at https://github.com/LiLabAtVT/rsv3-network.
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Affiliation(s)
- Lindsay C. DeMers
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Neelam R. Redekar
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Aardra Kachroo
- Department of Plant Pathology, University of Kentucky, Lexington, Virginia, United States of America
| | - Sue A. Tolin
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - Song Li
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
| | - M. A. Saghai Maroof
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, United States of America
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Montiel G, Gaudet M, Laurans F, Rozenberg P, Simon M, Gantet P, Jay-Allemand C, Breton C. Overexpression of MADS-box Gene AGAMOUS-LIKE 12 Activates Root Development in Juglans sp. and Arabidopsis thaliana. PLANTS 2020; 9:plants9040444. [PMID: 32252382 PMCID: PMC7238194 DOI: 10.3390/plants9040444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 01/21/2023]
Abstract
Until recently, the roles of plant MADS-box genes have mainly been characterized during inflorescence and flower differentiation. In order to precise the roles of AGAMOUS-LIKE 12, one of the few MADS-box genes preferentially expressed in roots, we placed its cDNA under the control of the double 35S CaMV promoter to produce transgenic walnut tree and Arabidopsis plants. In Juglans sp., transgenic somatic embryos showed significantly higher germination rates but abnormal development of their shoot apex prevented their conversion into plants. In addition, a wide range of developmental abnormalities corresponding to ectopic root-like structures affected the transgenic lines suggesting partial reorientations of the embryonic program toward root differentiation. In Arabidopsis, AtAGL12 overexpression lead to the production of faster growing plants presenting dramatically wider and shorter root phenotypes linked to increased meristematic cell numbers within the root apex. In the upper part of the roots, abnormal cell divisions patterns within the pericycle layer generated large ectopic cell masses that did not prevent plants to grow. Taken together, our results confirm in both species that AGL12 positively regulates root meristem cell division and promotes overall root vascular tissue formation. Genetic engineering of AGL12 expression levels could be useful to modulate root architecture and development.
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Affiliation(s)
- Grégory Montiel
- INRAE Val de Loire–Orléans, UMR 0588 BioForA INRAE-ONF, 2163 avenue de la pomme de pin, CS 40001 Ardon, CEDEX 02, 45075 Orléans, France; (G.M.); (M.G.); (F.L.); (P.R.)
- Laboratoire de Biologie et Pathologie Végétales (EA 1157), 2 rue de la Houssinière, BP 92208, 44322 Nantes, France
| | - Muriel Gaudet
- INRAE Val de Loire–Orléans, UMR 0588 BioForA INRAE-ONF, 2163 avenue de la pomme de pin, CS 40001 Ardon, CEDEX 02, 45075 Orléans, France; (G.M.); (M.G.); (F.L.); (P.R.)
- National Research Council (CNR), Institute of Research on Terrestrial Ecosystems (IRET), Via G. Marconi N. 2, 05010 Porano (TR), Italy
| | - Françoise Laurans
- INRAE Val de Loire–Orléans, UMR 0588 BioForA INRAE-ONF, 2163 avenue de la pomme de pin, CS 40001 Ardon, CEDEX 02, 45075 Orléans, France; (G.M.); (M.G.); (F.L.); (P.R.)
| | - Philippe Rozenberg
- INRAE Val de Loire–Orléans, UMR 0588 BioForA INRAE-ONF, 2163 avenue de la pomme de pin, CS 40001 Ardon, CEDEX 02, 45075 Orléans, France; (G.M.); (M.G.); (F.L.); (P.R.)
| | - Matthieu Simon
- Institut Jean-Pierre Bourgin, INRAE-AgroParisTech, UMR1318, Bâtiment 7, INRAE Centre de Versailles-Grignon, Route de St-Cyr, CEDEX, 78026 Versailles, France;
| | - Pascal Gantet
- Université de Montpellier, UMR DIADE, 911 avenue Agropolis, CEDEX 05, 34394 Montpellier, France;
| | - Christian Jay-Allemand
- Université de Montpellier, UMR IATE (UM, INRAE, CIRAD, SupAgro), CC024, Place Eugène Bataillon, CEDEX 05, 34095 Montpellier, France;
| | - Christian Breton
- INRAE Val de Loire–Orléans, UMR 0588 BioForA INRAE-ONF, 2163 avenue de la pomme de pin, CS 40001 Ardon, CEDEX 02, 45075 Orléans, France; (G.M.); (M.G.); (F.L.); (P.R.)
- Correspondence: ; Tel.: +33-238-41-78-71
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Monaco A, Amoroso N, Bellantuono L, Lella E, Lombardi A, Monda A, Tateo A, Bellotti R, Tangaro S. Shannon entropy approach reveals relevant genes in Alzheimer's disease. PLoS One 2019; 14:e0226190. [PMID: 31891941 PMCID: PMC6938408 DOI: 10.1371/journal.pone.0226190] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/19/2019] [Indexed: 12/18/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common type of dementia and affects millions of people worldwide. Since complex diseases are often the result of combinations of gene interactions, microarray data and gene co-expression analysis can provide tools for addressing complexity. Our study aimed to find groups of interacting genes that are relevant in the development of AD. In this perspective, we implemented a method proposed in a previous work to detect gene communities linked to AD. Our strategy combined co-expression network analysis with the study of Shannon entropy of the betweenness. We analyzed the publicly available GSE1297 dataset, achieved from the GEO database in NCBI, containing hippocampal gene expression of 9 control and 22 AD human subjects. Co-expressed genes were clustered into different communities. Two communities of interest (composed by 72 and 39 genes) were found by calculating the correlation coefficient between communities and clinical features. The detected communities resulted stable, replicated on two independent datasets and mostly enriched in pathways closely associated with neuro-degenative diseases. A comparison between our findings and other module detection techniques showed that the detected communities were more related to AD phenotype. Lastly, the hub genes within the two communities of interest were identified by means of a centrality analysis and a bootstrap procedure. The communities of the hub genes presented even stronger correlation with clinical features. These findings and further explorations on the detected genes could shed light on the genetic aspects related with physiological aspects of Alzheimer’s disease.
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Affiliation(s)
- Alfonso Monaco
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, Italy
| | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, Italy
- Department of Physics ‘Michelangelo Merlin’, University of Bari ‘Aldo Moro’, Bari, Italy
- * E-mail:
| | - Loredana Bellantuono
- Department of Physics ‘Michelangelo Merlin’, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Eufemia Lella
- Department of Physics ‘Michelangelo Merlin’, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Angela Lombardi
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, Italy
| | - Anna Monda
- Department of Physics ‘Michelangelo Merlin’, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Andrea Tateo
- Department of Physics ‘Michelangelo Merlin’, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Roberto Bellotti
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, Italy
- Department of Physics ‘Michelangelo Merlin’, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Sabina Tangaro
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Bari, Bari, Italy
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Li Y, Liu X, Chen R, Tian J, Fan Y, Zhou X. Genome-scale mining of root-preferential genes from maize and characterization of their promoter activity. BMC PLANT BIOLOGY 2019; 19:584. [PMID: 31878892 PMCID: PMC6933907 DOI: 10.1186/s12870-019-2198-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/12/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Modification of root architecture and improvement of root resistance to stresses can increase crop productivity. Functional analyses of root-specific genes are necessary for root system improvement, and root-specific promoters enable research into the regulation of root development and genetic manipulation of root traits. Maize is an important crop species; however, little systematic mining of root-specific genes and promoters has been performed to date. RESULTS Genomic-scale mining based on microarray data sets followed by transcript detection resulted in the identification of 222 root-specific genes. Gene Ontology enrichment analyses revealed that these 222 root-specific genes were mainly involved in responses to chemical, biotic, and abiotic stresses. Of the 222 genes, 33 were verified by quantitative reverse transcription polymerase chain reaction, and 31 showed root-preferential activity. About 2 kb upstream 5 of the 31 identified root-preferential genes were cloned from the maize genome as putative promoters and named p8463, p5023, p1534, p8531 and p6629. GUS staining of transgenic maize-derived promoter-GUS constructs revealed that the five promoters drove GUS expression in a root-preferential manner. CONCLUSIONS We mined root-preferential genes and their promoters in maize and verified p8463, p5023, p1534, p8531 and p6629 as root-preferential promoters. Our research enables the identification of other tissue-specific genes and promoters in maize and other species. In addition, the five promoters may enable enhancement of target gene(s) of maize in a root-preferential manner to generate novel maize cultivars with resistance to water, fertilizer constraints, or biotic stresses.
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Affiliation(s)
- Ye Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
| | - Rumei Chen
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China
| | - Yunliu Fan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China.
| | - Xiaojin Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 ZhongGuanCun South Street, Beijing, 100081, China.
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Mercatelli D, Scalambra L, Triboli L, Ray F, Giorgi FM. Gene regulatory network inference resources: A practical overview. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194430. [PMID: 31678629 DOI: 10.1016/j.bbagrm.2019.194430] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/08/2023]
Abstract
Transcriptional regulation is a fundamental molecular mechanism involved in almost every aspect of life, from homeostasis to development, from metabolism to behavior, from reaction to stimuli to disease progression. In recent years, the concept of Gene Regulatory Networks (GRNs) has grown popular as an effective applied biology approach for describing the complex and highly dynamic set of transcriptional interactions, due to its easy-to-interpret features. Since cataloguing, predicting and understanding every GRN connection in all species and cellular contexts remains a great challenge for biology, researchers have developed numerous tools and methods to infer regulatory processes. In this review, we catalogue these methods in six major areas, based on the dominant underlying information leveraged to infer GRNs: Coexpression, Sequence Motifs, Chromatin Immunoprecipitation (ChIP), Orthology, Literature and Protein-Protein Interaction (PPI) specifically focused on transcriptional complexes. The methods described here cover a wide range of user-friendliness: from web tools that require no prior computational expertise to command line programs and algorithms for large scale GRN inferences. Each method for GRN inference described herein effectively illustrates a type of transcriptional relationship, with many methods being complementary to others. While a truly holistic approach for inferring and displaying GRNs remains one of the greatest challenges in the field of systems biology, we believe that the integration of multiple methods described herein provides an effective means with which experimental and computational biologists alike may obtain the most complete pictures of transcriptional relationships. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony.
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Affiliation(s)
- Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Laura Scalambra
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Luca Triboli
- Centre for Integrative Biology (CIBIO), University of Trento, Italy
| | - Forest Ray
- Department of Systems Biology, Columbia University Medical Center, New York, NY, United States
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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Schubert M, Colomé-Tatché M, Foijer F. Gene networks in cancer are biased by aneuploidies and sample impurities. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194444. [PMID: 31654805 DOI: 10.1016/j.bbagrm.2019.194444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/05/2019] [Accepted: 10/14/2019] [Indexed: 12/14/2022]
Abstract
Gene regulatory network inference is a standard technique for obtaining structured regulatory information from, for instance, gene expression measurements. Methods performing this task have been extensively evaluated on synthetic, and to a lesser extent real data sets. In contrast to these test evaluations, applications to gene expression data of human cancers are often limited by fewer samples and more potential regulatory links, and are biased by copy number aberrations as well as cell mixtures and sample impurities. Here, we take networks inferred from TCGA cohorts as an example to show that (1) transcription factor annotations are essential to obtain reliable networks, and (2) even for state of the art methods, we expect that between 20 and 80% of edges are caused by copy number changes and cell mixtures rather than transcription factor regulation.
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Affiliation(s)
- Michael Schubert
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, the Netherlands.
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Alvarez-Buylla ER, García-Ponce B, Sánchez MDLP, Espinosa-Soto C, García-Gómez ML, Piñeyro-Nelson A, Garay-Arroyo A. MADS-box genes underground becoming mainstream: plant root developmental mechanisms. THE NEW PHYTOLOGIST 2019; 223:1143-1158. [PMID: 30883818 DOI: 10.1111/nph.15793] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/26/2019] [Indexed: 05/19/2023]
Abstract
Plant growth is largely post-embryonic and depends on meristems that are active throughout the lifespan of an individual. Developmental patterns rely on the coordinated spatio-temporal expression of different genes, and the activity of transcription factors is particularly important during most morphogenetic processes. MADS-box genes constitute a transcription factor family in eukaryotes. In Arabidopsis, their proteins participate in all major aspects of shoot development, but their role in root development is still not well characterized. In this review we synthetize current knowledge pertaining to the function of MADS-box genes highly expressed in roots: XAL1, XAL2, ANR1 and AGL21, as well as available data for other MADS-box genes expressed in this organ. The role of Trithorax group and Polycomb group complexes on MADS-box genes' epigenetic regulation is also discussed. We argue that understanding the role of MADS-box genes in root development of species with contrasting architectures is still a challenge. Finally, we propose that MADS-box genes are key components of the gene regulatory networks that underlie various gene expression patterns, each one associated with the distinct developmental fates observed in the root. In the case of XAL1 and XAL2, their role within these networks could be mediated by regulatory feedbacks with auxin.
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Affiliation(s)
- Elena R Alvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
| | - Berenice García-Ponce
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
| | - María de la Paz Sánchez
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
| | - Carlos Espinosa-Soto
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Manuel Nava 6, Zona Universitaria, San Luis Potosí, CP 78290, Mexico
| | - Mónica L García-Gómez
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
| | - Alma Piñeyro-Nelson
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana Xochimilco, Ciudad de México, 04960, Mexico
| | - Adriana Garay-Arroyo
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, 3er Circuito Exterior, Ciudad Universitaria, Coyoacán, D.F. 04510, Mexico
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Kimotho RN, Baillo EH, Zhang Z. Transcription factors involved in abiotic stress responses in Maize ( Zea mays L.) and their roles in enhanced productivity in the post genomics era. PeerJ 2019; 7:e7211. [PMID: 31328030 PMCID: PMC6622165 DOI: 10.7717/peerj.7211] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/26/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Maize (Zea mays L.) is a principal cereal crop cultivated worldwide for human food, animal feed, and more recently as a source of biofuel. However, as a direct consequence of water insufficiency and climate change, frequent occurrences of both biotic and abiotic stresses have been reported in various regions around the world, and recently, this has become a constant threat in increasing global maize yields. Plants respond to abiotic stresses by utilizing the activities of transcription factors (TFs), which are families of genes coding for specific TF proteins. TF target genes form a regulon that is involved in the repression/activation of genes associated with abiotic stress responses. Therefore, it is of utmost importance to have a systematic study on each TF family, the downstream target genes they regulate, and the specific TF genes involved in multiple abiotic stress responses in maize and other staple crops. METHOD In this review, the main TF families, the specific TF genes and their regulons that are involved in abiotic stress regulation will be briefly discussed. Great emphasis will be given on maize abiotic stress improvement throughout this review, although other examples from different plants like rice, Arabidopsis, wheat, and barley will be used. RESULTS We have described in detail the main TF families in maize that take part in abiotic stress responses together with their regulons. Furthermore, we have also briefly described the utilization of high-efficiency technologies in the study and characterization of TFs involved in the abiotic stress regulatory networks in plants with an emphasis on increasing maize production. Examples of these technologies include next-generation sequencing, microarray analysis, machine learning, and RNA-Seq. CONCLUSION In conclusion, it is expected that all the information provided in this review will in time contribute to the use of TF genes in the research, breeding, and development of new abiotic stress tolerant maize cultivars.
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Affiliation(s)
- Roy Njoroge Kimotho
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Elamin Hafiz Baillo
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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15
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Computational methods for Gene Regulatory Networks reconstruction and analysis: A review. Artif Intell Med 2019; 95:133-145. [DOI: 10.1016/j.artmed.2018.10.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/23/2018] [Accepted: 10/23/2018] [Indexed: 01/14/2023]
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Haque S, Ahmad JS, Clark NM, Williams CM, Sozzani R. Computational prediction of gene regulatory networks in plant growth and development. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:96-105. [PMID: 30445315 DOI: 10.1016/j.pbi.2018.10.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/05/2018] [Accepted: 10/18/2018] [Indexed: 05/22/2023]
Abstract
Plants integrate a wide range of cellular, developmental, and environmental signals to regulate complex patterns of gene expression. Recent advances in genomic technologies enable differential gene expression analysis at a systems level, allowing for improved inference of the network of regulatory interactions between genes. These gene regulatory networks, or GRNs, are used to visualize the causal regulatory relationships between regulators and their downstream target genes. Accordingly, these GRNs can represent spatial, temporal, and/or environmental regulations and can identify functional genes. This review summarizes recent computational approaches applied to different types of gene expression data to infer GRNs in the context of plant growth and development. Three stages of GRN inference are described: first, data collection and analysis based on the dataset type; second, network inference application based on data availability and proposed hypotheses; and third, validation based on in silico, in vivo, and in planta methods. In addition, this review relates data collection strategies to biological questions, organizes inference algorithms based on statistical methods and data types, discusses experimental design considerations, and provides guidelines for GRN inference with an emphasis on the benefits of integrative approaches, especially when a priori information is limited. Finally, this review concludes that computational frameworks integrating large-scale heterogeneous datasets are needed for a more accurate (e.g. fewer false interactions), detailed (e.g. discrimination between direct versus indirect interactions), and comprehensive (e.g. genetic regulation under various conditions and spatial locations) inference of GRNs.
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Affiliation(s)
- Samiul Haque
- Electrical and Computer Engineering, North Carolina State University, Raleigh, USA
| | - Jabeen S Ahmad
- Plant and Microbial Biology, North Carolina State University, Raleigh, USA
| | - Natalie M Clark
- Plant and Microbial Biology, North Carolina State University, Raleigh, USA
| | - Cranos M Williams
- Electrical and Computer Engineering, North Carolina State University, Raleigh, USA.
| | - Rosangela Sozzani
- Plant and Microbial Biology, North Carolina State University, Raleigh, USA.
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17
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Herrera-Ubaldo H, Lozano-Sotomayor P, Ezquer I, Di Marzo M, Chávez Montes RA, Gómez-Felipe A, Pablo-Villa J, Diaz-Ramirez D, Ballester P, Ferrándiz C, Sagasser M, Colombo L, Marsch-Martínez N, de Folter S. New roles of NO TRANSMITTING TRACT and SEEDSTICK during medial domain development in Arabidopsis fruits. Development 2019; 146:dev.172395. [PMID: 30538100 DOI: 10.1242/dev.172395] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/03/2018] [Indexed: 01/11/2023]
Abstract
The gynoecium, the female reproductive part of the flower, is key for plant sexual reproduction. During its development, inner tissues such as the septum and the transmitting tract tissue, important for pollen germination and guidance, are formed. In Arabidopsis, several transcription factors are known to be involved in the development of these tissues. One of them is NO TRANSMITTING TRACT (NTT), essential for transmitting tract formation. We found that the NTT protein can interact with several gynoecium-related transcription factors, including several MADS-box proteins, such as SEEDSTICK (STK), known to specify ovule identity. Evidence suggests that NTT and STK control enzyme and transporter-encoding genes involved in cell wall polysaccharide and lipid distribution in gynoecial medial domain cells. The results indicate that the simultaneous loss of NTT and STK activity affects polysaccharide and lipid deposition and septum fusion, and delays entry of septum cells to their normal degradation program. Furthermore, we identified KAWAK, a direct target of NTT and STK, which is required for the correct formation of fruits in Arabidopsis These findings position NTT and STK as important factors in determining reproductive competence.
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Affiliation(s)
- Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Paulina Lozano-Sotomayor
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Maurizio Di Marzo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Ricardo Aarón Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Andrea Gómez-Felipe
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Jeanneth Pablo-Villa
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - David Diaz-Ramirez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Guanajuato, México
| | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, 46022, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, 46022, Spain
| | - Martin Sagasser
- Bielefeld University, Faculty of Biology, Chair of Genetics and Genomics of Plants, Bielefeld 33615, Germany
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Guanajuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
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Pan J, Chang P, Ye X, Zhu J, Li D, Cui C, Wen B, Ma Y, Zhu X, Fang W, Wang Y. Transcriptome-wide analysis of MADS-box family genes involved in aluminum and fluoride assimilation in Camellia sinensis. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:313-324. [PMID: 31892818 PMCID: PMC6905225 DOI: 10.5511/plantbiotechnology.18.0621a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/21/2018] [Indexed: 06/10/2023]
Abstract
MADS-box transcription factors (TFs) are involved in a variety of processes in flowering plants ranging from root growth to flower and fruit development. However, studies of the tolerance-related functions of MADS-box genes are very limited, and to date no such studies have been conducted on Camellia sinensis. To gain insight into the functions of genes of this family and to elucidate the role they may play in tissue development and Al and F response, we identified 45 MADS-box genes through transcriptomic analysis of C. sinensis. Phylogenetic analysis of these CsMADS-box genes, along with their homologues in Arabidopsis thaliana, enabled us to classify them into distinct groups, including: M-type (Mα), MIKC* and MIKCc (which contains the SOC1, AGL12, AGL32, SEP, ANR1, SVP, and FLC subgroups). Conserved motif analysis of the CsMADS-box proteins revealed diverse motif compositions indicating a complex evolutionary relationship. Finally, we examined the expression patterns of CsMADS-box genes in various tissues and under different Al and F concentration treatments. Our qPCR results showed that these CsMADS-box genes were involved in Al and F accumulation and root growth in C. sinensis. These findings lay the foundation for future research on the function of CsMADS-box genes and their role in response to Al and F accumulation in root tissues.
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Affiliation(s)
- Junting Pan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Pinpin Chang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoli Ye
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiaojiao Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dongqin Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chuanlei Cui
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bo Wen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuhua Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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van Dam S, Võsa U, van der Graaf A, Franke L, de Magalhães JP. Gene co-expression analysis for functional classification and gene-disease predictions. Brief Bioinform 2018; 19:575-592. [PMID: 28077403 PMCID: PMC6054162 DOI: 10.1093/bib/bbw139] [Citation(s) in RCA: 422] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/01/2016] [Indexed: 01/06/2023] Open
Abstract
Gene co-expression networks can be used to associate genes of unknown function with biological processes, to prioritize candidate disease genes or to discern transcriptional regulatory programmes. With recent advances in transcriptomics and next-generation sequencing, co-expression networks constructed from RNA sequencing data also enable the inference of functions and disease associations for non-coding genes and splice variants. Although gene co-expression networks typically do not provide information about causality, emerging methods for differential co-expression analysis are enabling the identification of regulatory genes underlying various phenotypes. Here, we introduce and guide researchers through a (differential) co-expression analysis. We provide an overview of methods and tools used to create and analyse co-expression networks constructed from gene expression data, and we explain how these can be used to identify genes with a regulatory role in disease. Furthermore, we discuss the integration of other data types with co-expression networks and offer future perspectives of co-expression analysis.
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Affiliation(s)
- Sipko van Dam
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
| | - Urmo Võsa
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
| | | | - Lude Franke
- Department of Genetics, UMCG HPC CB50, RB Groningen, Netherlands
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Aguilar-Rangel MR, Chávez Montes RA, González-Segovia E, Ross-Ibarra J, Simpson JK, Sawers RJ. Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño. PeerJ 2017; 5:e3737. [PMID: 28852597 PMCID: PMC5572453 DOI: 10.7717/peerj.3737] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/04/2017] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Gene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions. METHODS Allele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments. RESULTS A total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates. DISCUSSION Prior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation.
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Affiliation(s)
- M. Rocío Aguilar-Rangel
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Ricardo A. Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
- ABACUS: Laboratorio de Matemáticas Aplicadas y Cómputo de Alto Rendimiento del Departamento de Matemáticas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ocoyoacac, Estado de México, Mexico
| | - Eric González-Segovia
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, Center for Population Biology and Genome Center, University of California, Davis, CA, United States of America
| | - June K. Simpson
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Ruairidh J.H. Sawers
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
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PIñeyro-Nelson A, Almeida AMRD, Sass C, Iles WJD, Specht CD. Change of Fate and Staminodial Laminarity as Potential Agents of Floral Diversification in the Zingiberales. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2017; 328:41-54. [PMID: 28120453 DOI: 10.1002/jez.b.22724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 11/30/2016] [Accepted: 12/02/2016] [Indexed: 12/30/2022]
Abstract
The evolution of floral morphology in the monocot order Zingiberales shows a trend in which androecial whorl organs are progressively modified into variously conspicuous "petaloid" structures with differing degrees of fertility. Petaloidy of androecial members results from extensive laminarization of an otherwise radially symmetric structure. The genetic basis of the laminarization of androecial members has been addressed through recent candidate gene studies focused on understanding the spatiotemporal expression patterns of genes known to be necessary to floral organ formation. Here, we explore the correlation between gene duplication events and floral and inflorescence morphological diversification across the Zingiberales by inferring ancestral character states and gene copy number using the most widely accepted phylogenetic hypotheses. Our results suggest that the duplication and differential loss of GLOBOSA (GLO) copies is correlated with a change in the degree of the laminarization of androecial members. We also find an association with increased diversification in most families. We hypothesize that retention of paralogs in flower development genes could have led to a developmental shift affecting androecial organs with potential adaptive consequences, thus favoring diversification in some lineages but not others.
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Affiliation(s)
- Alma PIñeyro-Nelson
- Department of Food and Animal Production, Autonomous Metropolitan University, Xochimilco, Mexico City, Mexico
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
| | - Ana Maria Rocha De Almeida
- Programa de Pós-Graduação em Genética e Biodiversidade, Universidade Federal da Bahia, Rua Barão de Geremoabo, Salvador/BA, Brazil
- Department of Biological Sciences, California State University East Bay (CSUEB), Hayward, California
| | - Chodon Sass
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
| | - William James Donaldson Iles
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
| | - Chelsea Dvorak Specht
- Department of Plant and Microbial Biology, Department of Integrative Biology, and the University and Jepson Herbaria, University of California-Berkeley, Berkeley, California
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22
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García-Cruz KV, García-Ponce B, Garay-Arroyo A, Sanchez MDLP, Ugartechea-Chirino Y, Desvoyes B, Pacheco-Escobedo MA, Tapia-López R, Ransom-Rodríguez I, Gutierrez C, Alvarez-Buylla ER. The MADS-box XAANTAL1 increases proliferation at the Arabidopsis root stem-cell niche and participates in transition to differentiation by regulating cell-cycle components. ANNALS OF BOTANY 2016; 118:787-796. [PMID: 27474508 PMCID: PMC5055633 DOI: 10.1093/aob/mcw126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 05/16/2016] [Indexed: 05/08/2023]
Abstract
Background Morphogenesis depends on the concerted modulation of cell proliferation and differentiation. Such modulation is dynamically adjusted in response to various external and internal signals via complex transcriptional regulatory networks that mediate between such signals and regulation of cell-cycle and cellular responses (proliferation, growth, differentiation). In plants, which are sessile, the proliferation/differentiation balance is plastically adjusted during their life cycle and transcriptional networks are important in this process. MADS-box genes are key developmental regulators in eukaryotes, but their role in cell proliferation and differentiation modulation in plants remains poorly studied. Methods We characterize the XAL1 loss-of-function xal1-2 allele and overexpression lines using quantitative cellular and cytometry analyses to explore its role in cell cycle, proliferation, stem-cell patterning and transition to differentiation. We used quantitative PCR and cellular markers to explore if XAL1 regulates cell-cycle components and PLETHORA1 (PLT1) gene expression, as well as confocal microscopy to analyse stem-cell niche organization. Key Results We previously showed that XAANTAL1 (XAL1/AGL12) is necessary for Arabidopsis root development as a promoter of cell proliferation in the root apical meristem. Here, we demonstrate that XAL1 positively regulates the expression of PLT1 and important components of the cell cycle: CYCD3;1, CYCA2;3, CYCB1;1, CDKB1;1 and CDT1a. In addition, we show that xal1-2 mutant plants have a premature transition to differentiation with root hairs appearing closer to the root tip, while endoreplication in these plants is partially compromised. Coincidently, the final size of cortex cells in the mutant is shorter than wild-type cells. Finally, XAL1 overexpression-lines corroborate that this transcription factor is able to promote cell proliferation at the stem-cell niche. Conclusion XAL1 seems to be an important component of the networks that modulate cell proliferation/differentiation transition and stem-cell proliferation during Arabidopsis root development; it also regulates several cell-cycle components.
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Affiliation(s)
- Karla V. García-Cruz
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Coyoacán, México D.F. 04510, México
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Coyoacán, México D.F. 04510, México
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Coyoacán, México D.F. 04510, México
| | - María De La Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Coyoacán, México D.F. 04510, México
| | - Yamel Ugartechea-Chirino
- Centro de Investigación en Dinámica Celular, Facultad de Ciencias, Universidad Autónoma de Morelos, Av. Universidad 1001, Col Chamilpa, Cuernavaca, Morelos, 62209, México
| | - Bénédicte Desvoyes
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Mario A. Pacheco-Escobedo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Coyoacán, México D.F. 04510, México
| | - Rosalinda Tapia-López
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Coyoacán, México D.F. 04510, México
| | - Ivan Ransom-Rodríguez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Coyoacán, México D.F. 04510, México
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Elena R. Alvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Coyoacán, México D.F. 04510, México
- *For correspondence. E-mail
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23
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Banf M, Rhee SY. Computational inference of gene regulatory networks: Approaches, limitations and opportunities. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:41-52. [PMID: 27641093 DOI: 10.1016/j.bbagrm.2016.09.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 09/08/2016] [Accepted: 09/08/2016] [Indexed: 10/21/2022]
Abstract
Gene regulatory networks lie at the core of cell function control. In E. coli and S. cerevisiae, the study of gene regulatory networks has led to the discovery of regulatory mechanisms responsible for the control of cell growth, differentiation and responses to environmental stimuli. In plants, computational rendering of gene regulatory networks is gaining momentum, thanks to the recent availability of high-quality genomes and transcriptomes and development of computational network inference approaches. Here, we review current techniques, challenges and trends in gene regulatory network inference and highlight challenges and opportunities for plant science. We provide plant-specific application examples to guide researchers in selecting methodologies that suit their particular research questions. Given the interdisciplinary nature of gene regulatory network inference, we tried to cater to both biologists and computer scientists to help them engage in a dialogue about concepts and caveats in network inference. Specifically, we discuss problems and opportunities in heterogeneous data integration for eukaryotic organisms and common caveats to be considered during network model evaluation. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Michael Banf
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford 93405, United States.
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford 93405, United States.
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24
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González-Morales SI, Chávez-Montes RA, Hayano-Kanashiro C, Alejo-Jacuinde G, Rico-Cambron TY, de Folter S, Herrera-Estrella L. Regulatory network analysis reveals novel regulators of seed desiccation tolerance in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2016; 113:E5232-41. [PMID: 27551092 PMCID: PMC5024642 DOI: 10.1073/pnas.1610985113] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Desiccation tolerance (DT) is a remarkable process that allows seeds in the dry state to remain viable for long periods of time that in some instances exceed 1,000 y. It has been postulated that seed DT evolved by rewiring the regulatory and signaling networks that controlled vegetative DT, which itself emerged as a crucial adaptive trait of early land plants. Understanding the networks that regulate seed desiccation tolerance in model plant systems would provide the tools to understand an evolutionary process that played a crucial role in the diversification of flowering plants. In this work, we used an integrated approach that included genomics, bioinformatics, metabolomics, and molecular genetics to identify and validate molecular networks that control the acquisition of DT in Arabidopsis seeds. Two DT-specific transcriptional subnetworks were identified related to storage of reserve compounds and cellular protection mechanisms that act downstream of the embryo development master regulators LEAFY COTYLEDON 1 and 2, FUSCA 3, and ABSCICIC ACID INSENSITIVE 3. Among the transcription factors identified as major nodes in the DT regulatory subnetworks, PLATZ1, PLATZ2, and AGL67 were confirmed by knockout mutants and overexpression in a desiccation-intolerant mutant background to play an important role in seed DT. Additionally, we found that constitutive expression of PLATZ1 in WT plants confers partial DT in vegetative tissues.
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Affiliation(s)
- Sandra Isabel González-Morales
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Guanajuato, Mexico
| | - Ricardo A Chávez-Montes
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Guanajuato, Mexico
| | - Corina Hayano-Kanashiro
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Guanajuato, Mexico
| | - Gerardo Alejo-Jacuinde
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Guanajuato, Mexico
| | - Thelma Y Rico-Cambron
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Guanajuato, Mexico
| | - Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Guanajuato, Mexico
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)/Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, 36500 Irapuato, Guanajuato, Mexico
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25
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Differential Regulatory Analysis Based on Coexpression Network in Cancer Research. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4241293. [PMID: 27597964 PMCID: PMC4997028 DOI: 10.1155/2016/4241293] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/09/2016] [Accepted: 06/12/2016] [Indexed: 12/15/2022]
Abstract
With rapid development of high-throughput techniques and accumulation of big transcriptomic data, plenty of computational methods and algorithms such as differential analysis and network analysis have been proposed to explore genome-wide gene expression characteristics. These efforts are aiming to transform underlying genomic information into valuable knowledges in biological and medical research fields. Recently, tremendous integrative research methods are dedicated to interpret the development and progress of neoplastic diseases, whereas differential regulatory analysis (DRA) based on gene coexpression network (GCN) increasingly plays a robust complement to regular differential expression analysis in revealing regulatory functions of cancer related genes such as evading growth suppressors and resisting cell death. Differential regulatory analysis based on GCN is prospective and shows its essential role in discovering the system properties of carcinogenesis features. Here we briefly review the paradigm of differential regulatory analysis based on GCN. We also focus on the applications of differential regulatory analysis based on GCN in cancer research and point out that DRA is necessary and extraordinary to reveal underlying molecular mechanism in large-scale carcinogenesis studies.
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26
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Khong GN, Pati PK, Richaud F, Parizot B, Bidzinski P, Mai CD, Bès M, Bourrié I, Meynard D, Beeckman T, Selvaraj MG, Manabu I, Genga AM, Brugidou C, Nang Do V, Guiderdoni E, Morel JB, Gantet P. OsMADS26 Negatively Regulates Resistance to Pathogens and Drought Tolerance in Rice. PLANT PHYSIOLOGY 2015; 169:2935-49. [PMID: 26424158 PMCID: PMC4677910 DOI: 10.1104/pp.15.01192] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/28/2015] [Indexed: 05/19/2023]
Abstract
Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g. flowering and floral organ identity) as well as stress-related developmental processes, such as abscission, fruit ripening, and senescence. Overexpression of the rice (Oryza sativa) MADS26 gene in rice has revealed a possible function related to stress response. Here, we show that OsMADS26-down-regulated plants exhibit enhanced resistance against two major rice pathogens: Magnaporthe oryzae and Xanthomonas oryzae. Despite this enhanced resistance to biotic stresses, OsMADS26-down-regulated plants also displayed enhanced tolerance to water deficit. These phenotypes were observed in both controlled and field conditions. Interestingly, alteration of OsMADS26 expression does not have a strong impact on plant development. Gene expression profiling revealed that a majority of genes misregulated in overexpresser and down-regulated OsMADS26 lines compared with control plants are associated to biotic or abiotic stress response. Altogether, our data indicate that OsMADS26 acts as an upstream regulator of stress-associated genes and thereby, a hub to modulate the response to various stresses in the rice plant.
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Affiliation(s)
- Giang Ngan Khong
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Pratap Kumar Pati
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Frédérique Richaud
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Boris Parizot
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Przemyslaw Bidzinski
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Chung Duc Mai
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Martine Bès
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Isabelle Bourrié
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Donaldo Meynard
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Tom Beeckman
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Michael Gomez Selvaraj
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Ishitani Manabu
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Anna-Maria Genga
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Christophe Brugidou
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Vinh Nang Do
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Emmanuel Guiderdoni
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Jean-Benoit Morel
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
| | - Pascal Gantet
- Université de Montpellier, Unité Mixte de Recherche Diversité, Adaptation, et Développement des Plantes, 34095 Montpellier cedex 5, France (G.N.K., I.B., P.G.);Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, 34398 Montpellier cedex 5, France (G.N.K., P.K.P., F.R., M.B., D.M., E.G.);Department of Biotechnology, Guru Nanak Dev University, Amritsar 143 005, India (P.K.P.);Department of Plant Systems Biology, Flanders Institute for Biotechnology, 9052 Ghent, Belgium (B.P., T.B.);Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (B.P., T.B.);Institut National de la Recherche Agronomique, Unité Mixte de Recherche Biologie et Génétique des Interactions Plante-Parasite, 34398 Montpellier, France (P.B., J.-B.M.);Laboratoire Mixte International Rice Functional Genomics and Plant Biotechnology, Institut de Recherche pour le Développement, University of Science and Technology of Hanoi, Agricultural Genetics Institute, 00 000 Hanoi, Vietnam (C.D.M., V.N.D., P.G.);International Center for Tropical Agriculture, 6713 Cali, Colombia (M.G.S., I.M.);Consiglio Nazionale delle Ricerche, Institute of Agricultural Biology and Biotechnology, 20133 Milan, Italy (A.-M.G.); andInstitut de Recherche pour le Développement, Unité Mixte de Recherche Interactions Plantes Microorganismes et Environnement, 34398 Montpellier cedex, France (C.B.)
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Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER. Descriptive vs. mechanistic network models in plant development in the post-genomic era. Methods Mol Biol 2015; 1284:455-79. [PMID: 25757787 DOI: 10.1007/978-1-4939-2444-8_23] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Network modeling is now a widespread practice in systems biology, as well as in integrative genomics, and it constitutes a rich and diverse scientific research field. A conceptually clear understanding of the reasoning behind the main existing modeling approaches, and their associated technical terminologies, is required to avoid confusions and accelerate the transition towards an undeniable necessary more quantitative, multidisciplinary approach to biology. Herein, we focus on two main network-based modeling approaches that are commonly used depending on the information available and the intended goals: inference-based methods and system dynamics approaches. As far as data-based network inference methods are concerned, they enable the discovery of potential functional influences among molecular components. On the other hand, experimentally grounded network dynamical models have been shown to be perfectly suited for the mechanistic study of developmental processes. How do these two perspectives relate to each other? In this chapter, we describe and compare both approaches and then apply them to a given specific developmental module. Along with the step-by-step practical implementation of each approach, we also focus on discussing their respective goals, utility, assumptions, and associated limitations. We use the gene regulatory network (GRN) involved in Arabidopsis thaliana Root Stem Cell Niche patterning as our illustrative example. We show that descriptive models based on functional genomics data can provide important background information consistent with experimentally supported functional relationships integrated in mechanistic GRN models. The rationale of analysis and modeling can be applied to any other well-characterized functional developmental module in multicellular organisms, like plants and animals.
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Affiliation(s)
- J Davila-Velderrain
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, México D.F., 04510, Mexico
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28
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Vermeirssen V, De Clercq I, Van Parys T, Van Breusegem F, Van de Peer Y. Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress. THE PLANT CELL 2014; 26:4656-79. [PMID: 25549671 PMCID: PMC4311199 DOI: 10.1105/tpc.114.131417] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 11/27/2014] [Accepted: 12/10/2014] [Indexed: 05/19/2023]
Abstract
The abiotic stress response in plants is complex and tightly controlled by gene regulation. We present an abiotic stress gene regulatory network of 200,014 interactions for 11,938 target genes by integrating four complementary reverse-engineering solutions through average rank aggregation on an Arabidopsis thaliana microarray expression compendium. This ensemble performed the most robustly in benchmarking and greatly expands upon the availability of interactions currently reported. Besides recovering 1182 known regulatory interactions, cis-regulatory motifs and coherent functionalities of target genes corresponded with the predicted transcription factors. We provide a valuable resource of 572 abiotic stress modules of coregulated genes with functional and regulatory information, from which we deduced functional relationships for 1966 uncharacterized genes and many regulators. Using gain- and loss-of-function mutants of seven transcription factors grown under control and salt stress conditions, we experimentally validated 141 out of 271 predictions (52% precision) for 102 selected genes and mapped 148 additional transcription factor-gene regulatory interactions (49% recall). We identified an intricate core oxidative stress regulatory network where NAC13, NAC053, ERF6, WRKY6, and NAC032 transcription factors interconnect and function in detoxification. Our work shows that ensemble reverse-engineering can generate robust biological hypotheses of gene regulation in a multicellular eukaryote that can be tested by medium-throughput experimental validation.
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Affiliation(s)
- Vanessa Vermeirssen
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Inge De Clercq
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Thomas Van Parys
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
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