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Samalova M, Melnikava A, Elsayad K, Peaucelle A, Gahurova E, Gumulec J, Spyroglou I, Zemlyanskaya EV, Ubogoeva EV, Balkova D, Demko M, Blavet N, Alexiou P, Benes V, Mouille G, Hejatko J. Hormone-regulated expansins: Expression, localization, and cell wall biomechanics in Arabidopsis root growth. Plant Physiol 2023; 194:209-228. [PMID: 37073485 PMCID: PMC10762514 DOI: 10.1093/plphys/kiad228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Expansins facilitate cell expansion by mediating pH-dependent cell wall (CW) loosening. However, the role of expansins in controlling CW biomechanical properties in specific tissues and organs remains elusive. We monitored hormonal responsiveness and spatial specificity of expression and localization of expansins predicted to be the direct targets of cytokinin signaling in Arabidopsis (Arabidopsis thaliana). We found EXPANSIN1 (EXPA1) homogenously distributed throughout the CW of columella/lateral root cap, while EXPA10 and EXPA14 localized predominantly at 3-cell boundaries in the epidermis/cortex in various root zones. EXPA15 revealed cell-type-specific combination of homogenous vs. 3-cell boundaries localization. By comparing Brillouin frequency shift and AFM-measured Young's modulus, we demonstrated Brillouin light scattering (BLS) as a tool suitable for non-invasive in vivo quantitative assessment of CW viscoelasticity. Using both BLS and AFM, we showed that EXPA1 overexpression upregulated CW stiffness in the root transition zone (TZ). The dexamethasone-controlled EXPA1 overexpression induced fast changes in the transcription of numerous CW-associated genes, including several EXPAs and XYLOGLUCAN:XYLOGLUCOSYL TRANSFERASEs (XTHs), and associated with rapid pectin methylesterification determined by in situ Fourier-transform infrared spectroscopy in the root TZ. The EXPA1-induced CW remodeling is associated with the shortening of the root apical meristem, leading to root growth arrest. Based on our results, we propose that expansins control root growth by a delicate orchestration of CW biomechanical properties, possibly regulating both CW loosening and CW remodeling.
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Affiliation(s)
- Marketa Samalova
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Alesia Melnikava
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Kareem Elsayad
- Division of Anatomy, Centre for Anatomy & Cell Biology, Medical University of Vienna, Vienna 1090, Austria
| | | | - Evelina Gahurova
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Jaromir Gumulec
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
| | - Ioannis Spyroglou
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Elena V Zemlyanskaya
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630073, Russia
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Elena V Ubogoeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Darina Balkova
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Martin Demko
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Nicolas Blavet
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Panagiotis Alexiou
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | | | - Jan Hejatko
- CEITEC – Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
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Azarova DS, Omelyanchuk NA, Mironova VV, Zemlyanskaya EV, Lavrekha VV. DyCeModel: a tool for 1D simulation for distribution of plant hormones controlling tissue patterning. Vavilovskii Zhurnal Genet Selektsii 2023; 27:890-897. [PMID: 38213710 PMCID: PMC10777285 DOI: 10.18699/vjgb-23-103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 01/13/2024] Open
Abstract
To study the mechanisms of growth and development, it is necessary to analyze the dynamics of the tissue patterning regulators in time and space and to take into account their effect on the cellular dynamics within a tissue. Plant hormones are the main regulators of the cell dynamics in plant tissues; they form gradients and maxima and control molecular processes in a concentration-dependent manner. Here, we present DyCeModel, a software tool implemented in MATLAB for one-dimensional simulation of tissue with a dynamic cellular ensemble, where changes in hormone (or other active substance) concentration in the cells are described by ordinary differential equations (ODEs). We applied DyCeModel to simulate cell dynamics in plant meristems with different cellular structures and demonstrated that DyCeModel helps to identify the relationships between hormone concentration and cellular behaviors. The tool visualizes the simulation progress and presents a video obtained during the calculation. Importantly, the tool is capable of automatically adjusting the parameters by fitting the distribution of the substance concentrations predicted in the model to experimental data taken from the microscopic images. Noteworthy, DyCeModel makes it possible to build models for distinct types of plant meristems with the same ODEs, recruiting specific input characteristics for each meristem. We demonstrate the tool's efficiency by simulation of the effect of auxin and cytokinin distributions on tissue patterning in two types of Arabidopsis thaliana stem cell niches: the root and shoot apical meristems. The resulting models represent a promising framework for further study of the role of hormone-controlled gene regulatory networks in cell dynamics.
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Affiliation(s)
- D S Azarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Omelyanchuk
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V V Mironova
- Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud University, Nijmegen, the Netherlands
| | - E V Zemlyanskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - V V Lavrekha
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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Petrov SI, Zemlyanskaya EV, Novitskaya ON. [The effect of surgical treatment of tuberculous abscesses and tuberculoma of the brain on the dynamics of neurological symptoms]. Zh Nevrol Psikhiatr Im S S Korsakova 2023; 123:130-135. [PMID: 37084378 DOI: 10.17116/jnevro2023123041130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
OBJECTIVE To evaluate the efficacy of surgery in reducing neurological symptoms in patients with focal brain tuberculosis. MATERIAL AND METHODS Seventy-four patients with tuberculosis meningoencephalitis were studied. Among them, 20 people with a life expectancy of at least 6 months were identified, in whom foci with a ring-shaped accumulation of contrast along the periphery were determined during MSCT of the brain. Formed tuberculomas and abscesses were removed from 7 patients (group 1) under neuronavigation control. Indications for the operation were: the absence of a reduction in size for 3-4 months, the limitation of the lesion to 1-2 foci with reduction of perifocal edema according to MSCT and normalization of cerebrospinal fluid. Six patients had contraindications or refusals from operations (group 2). In 7 patients, there was a decrease in formations by the control period (group 3). Neurological symptoms in the groups at the beginning of the observation were similar. The duration of observation was 6-8 months. RESULTS In group 1, patients were discharged with improvement, postoperative cysts were determined in all of them at discharge. In group 2, 67% died. In group 3, 43% of patients had a complete reduction of foci during conservative treatment, in 57% cysts formed in place of foci. Neurological symptoms decreased in all groups, with the most decrease in group 1. However, statistical analysis did not show significant differences between the groups regarding the reduction of neurological symptoms. A significant difference in the mortality criterion between groups 1 and 2 was obtained. CONCLUSION Despite the absence of a significant effect on the reduction of neurological symptoms, the high survival rate of operated patients shows the need to remove tuberculosis formations in all the cases.
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Affiliation(s)
- S I Petrov
- Irkutsk, Medical Academy of Postgraduate Education - Branch of Russian Medical Academy of Continuing Professional Education, Irkutsk, Russia
- Irkutsk Regional Clinical Hospital, Irkutsk, Russia
- Irkutsk Regional Clinical Tuberculosis Hospital, Irkutsk, Russia
| | - E V Zemlyanskaya
- Irkutsk Regional Clinical Tuberculosis Hospital, Irkutsk, Russia
| | - O N Novitskaya
- Irkutsk Regional Clinical Tuberculosis Hospital, Irkutsk, Russia
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Lavrekha VV, Levitsky VG, Tsukanov AV, Bogomolov AG, Grigorovich DA, Omelyanchuk N, Ubogoeva EV, Zemlyanskaya EV, Mironova V. CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana. Front Plant Sci 2022; 13:942710. [PMID: 36061801 PMCID: PMC9434332 DOI: 10.3389/fpls.2022.942710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (https://plamorph.sysbio.ru/ciscross/) that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana genes.
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Affiliation(s)
- Viktoriya V. Lavrekha
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Victor G. Levitsky
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Anton V. Tsukanov
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Anton G. Bogomolov
- Department of Cell Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Dmitry A. Grigorovich
- Service of Information Technologies, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Nadya Omelyanchuk
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Elena V. Ubogoeva
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Victoria Mironova
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Department of Plant Systems Physiology, RIBES, Radboud University, Nijmegen, Netherlands
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Bagautdinova ZZ, Omelyanchuk N, Tyapkin AV, Kovrizhnykh VV, Lavrekha VV, Zemlyanskaya EV. Salicylic Acid in Root Growth and Development. Int J Mol Sci 2022; 23:ijms23042228. [PMID: 35216343 PMCID: PMC8875895 DOI: 10.3390/ijms23042228] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
In plants, salicylic acid (SA) is a hormone that mediates a plant’s defense against pathogens. SA also takes an active role in a plant’s response to various abiotic stresses, including chilling, drought, salinity, and heavy metals. In addition, in recent years, numerous studies have confirmed the important role of SA in plant morphogenesis. In this review, we summarize data on changes in root morphology following SA treatments under both normal and stress conditions. Finally, we provide evidence for the role of SA in maintaining the balance between stress responses and morphogenesis in plant development, and also for the presence of SA crosstalk with other plant hormones during this process.
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Affiliation(s)
- Zulfira Z. Bagautdinova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
| | - Nadya Omelyanchuk
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
| | - Aleksandr V. Tyapkin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Vasilina V. Kovrizhnykh
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
| | - Viktoriya V. Lavrekha
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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Ubogoeva EV, Zemlyanskaya EV, Xu J, Mironova V. Mechanisms of stress response in the root stem cell niche. J Exp Bot 2021; 72:6746-6754. [PMID: 34111279 PMCID: PMC8513250 DOI: 10.1093/jxb/erab274] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/09/2021] [Indexed: 05/25/2023]
Abstract
As plants are sessile organisms unable to escape from environmental hazards, they need to adapt for survival. The stem cell niche in the root apical meristem is particularly sensitive to DNA damage induced by environmental stresses such as chilling, flooding, wounding, UV, and irradiation. DNA damage has been proven to cause stem cell death, with stele stem cells being the most vulnerable. Stress also induces the division of quiescent center cells. Both reactions disturb the structure and activity of the root stem cell niche temporarily; however, this preserves root meristem integrity and function in the long term. Plants have evolved many mechanisms that ensure stem cell niche maintenance, recovery, and acclimation, allowing them to survive in a changing environment. Here, we provide an overview of the cellular and molecular aspects of stress responses in the root stem cell niche.
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Affiliation(s)
| | - Elena V Zemlyanskaya
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Jian Xu
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Victoria Mironova
- Institute of Cytology and Genetics, Novosibirsk, Russia
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Zemlyanskaya EV, Dolgikh VA, Levitsky VG, Mironova V. Transcriptional regulation in plants: Using omics data to crack the cis-regulatory code. Curr Opin Plant Biol 2021; 63:102058. [PMID: 34098218 DOI: 10.1016/j.pbi.2021.102058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Innovative omics technologies, advanced bioinformatics, and machine learning methods are rapidly becoming integral tools for plant functional genomics, with tremendous recent advances made in this field. In transcriptional regulation, an initial lag in the accumulation of plant omics data relative to that of animals stimulated the development of computational methods capable of extracting maximum information from the available data sets. Recent comprehensive studies of transcription factor-binding profiles in Arabidopsis and maize and the accumulation of uniformly processed omics data in public databases have brought plant biologists into the big leagues, with many cutting-edge methods available. Here, we summarize the state-of-the-art bioinformatics approaches used to predict or infer the cis-regulatory code behind transcriptional gene regulation, focusing on their plant research applications.
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Affiliation(s)
- Elena V Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Vladislav A Dolgikh
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Victor G Levitsky
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Victoria Mironova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia; Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands.
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Xu SY, Zemlyanskaya EV, Gonchar DA, Sun Z, Weigele P, Fomenkov A, Degtyarev SK, Roberts RJ. Characterization of BisI Homologs. Front Microbiol 2021; 12:689929. [PMID: 34276622 PMCID: PMC8281217 DOI: 10.3389/fmicb.2021.689929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/10/2021] [Indexed: 11/26/2022] Open
Abstract
BisI is a sequence-specific and 5-methylcytosine (m5C)-dependent restriction endonuclease (REase), that cleaves the modified DNA sequence Gm5CNGC (G indicates that the cytosine opposite to G is modified). We expressed and purified a number of BisI homologs from sequenced bacterial genomes and used Illumina sequencing to determine the Pam7902I (Esp638I-like) cleavage sites in phage Xp12 DNA. One BisI homolog KpnW2I is EcoBLMcrX-like, cleaving GCNGC/RCNGY/RCNRC sites with m5C. We also cloned and expressed three BisI homologs from metagenome sequences derived from thermophilic sources. One enzyme EsaTMI is active at 37 to 65°C. EsaHLI cleaves GCNGC sites with three to four m5C and is active up to 50°C. In addition, we determined the number and position of m5C in BisI sites for efficient cleavage. BisI cleavage efficiency of GCNGC site is as following: Gm5CNGC (two internal m5C) > Gm5CNGC (one internal m5C) > GCNGm5C (one external m5C) > > GCNGC (unmodified). Three or four m5C in GCNGC site also supports BisI cleavage although partial inhibition was observed on duplex oligos with four m5C. BisI can be used to partially cleave a desired GCNGC site targeted with a complementary oligonucleotide (hemi-methylated). The m5C-dependent BisI variants will be useful for epigenetic research.
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Affiliation(s)
| | | | | | - Zhiyi Sun
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Peter Weigele
- New England Biolabs, Inc., Ipswich, MA, United States
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Wiebe DS, Omelyanchuk NA, Mukhin AM, Grosse I, Lashin SA, Zemlyanskaya EV, Mironova VV. Fold-Change-Specific Enrichment Analysis (FSEA): Quantification of Transcriptional Response Magnitude for Functional Gene Groups. Genes (Basel) 2020; 11:genes11040434. [PMID: 32316383 PMCID: PMC7230499 DOI: 10.3390/genes11040434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 11/24/2022] Open
Abstract
Gene expression profiling data contains more information than is routinely extracted with standard approaches. Here we present Fold-Change-Specific Enrichment Analysis (FSEA), a new method for functional annotation of differentially expressed genes from transcriptome data with respect to their fold changes. FSEA identifies Gene Ontology (GO) terms, which are shared by the group of genes with a similar magnitude of response, and assesses these changes. GO terms found by FSEA are fold-change-specifically (e.g., weakly, moderately, or strongly) affected by a stimulus under investigation. We demonstrate that many responses to abiotic factors, mutations, treatments, and diseases occur in a fold-change-specific manner. FSEA analyses suggest that there are two prevailing responses of functionally-related gene groups, either weak or strong. Notably, some of the fold-change-specific GO terms are invisible by classical algorithms for functional gene enrichment, Singular Enrichment Analysis (SEA), and Gene Set Enrichment Analysis (GSEA). These are GO terms not enriched compared to the genome background but strictly regulated by a factor within specific fold-change intervals. FSEA analysis of a cancer-related transcriptome suggested that the gene groups with a tightly coordinated response can be the valuable source to search for possible regulators, markers, and therapeutic targets in oncogenic processes. Availability and Implementation: FSEA is implemented as the FoldGO Bioconductor R package and a web-server.
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Affiliation(s)
- Daniil S. Wiebe
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Nadezhda A. Omelyanchuk
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Aleksei M. Mukhin
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Sergey A. Lashin
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Victoria V. Mironova
- Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences (SB RAS), 630090 Novosibirsk, Russia; (D.S.W.)
- LCT & EB, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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Dolgikh VA, Pukhovaya EM, Zemlyanskaya EV. Shaping Ethylene Response: The Role of EIN3/EIL1 Transcription Factors. Front Plant Sci 2019; 10:1030. [PMID: 31507622 PMCID: PMC6718143 DOI: 10.3389/fpls.2019.01030] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/23/2019] [Indexed: 05/05/2023]
Abstract
EIN3/EIL1 transcription factors are the key regulators of ethylene signaling that sustain a variety of plant responses to ethylene. Since ethylene regulates multiple aspects of plant development and stress responses, its signaling outcome needs proper modulation depending on the spatiotemporal and environmental conditions. In this review, we summarize recent advances on the molecular mechanisms that underlie EIN3/EIL1-directed ethylene signaling in Arabidopsis. We focus on the role of EIN3/EIL1 in tuning transcriptional regulation of ethylene response in time and space. Besides, we consider the role of EIN3/EIL1-independent regulation of ethylene signaling.
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Affiliation(s)
- Vladislav A. Dolgikh
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgeniya M. Pukhovaya
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- *Correspondence: Elena V. Zemlyanskaya,
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Zemlyanskaya EV, Omelyanchuk NA, Ubogoeva EV, Mironova VV. Deciphering Auxin-Ethylene Crosstalk at a Systems Level. Int J Mol Sci 2018; 19:ijms19124060. [PMID: 30558241 PMCID: PMC6321013 DOI: 10.3390/ijms19124060] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 01/17/2023] Open
Abstract
The auxin and ethylene pathways cooperatively regulate a variety of developmental processes in plants. Growth responses to ethylene are largely dependent on auxin, the key regulator of plant morphogenesis. Auxin, in turn, is capable of inducing ethylene biosynthesis and signaling, making the interaction of these hormones reciprocal. Recent studies discovered a number of molecular events underlying auxin-ethylene crosstalk. In this review, we summarize the results of fine-scale and large-scale experiments on the interactions between the auxin and ethylene pathways in Arabidopsis. We integrate knowledge on molecular crosstalk events, their tissue specificity, and associated phenotypic responses to decipher the crosstalk mechanisms at a systems level. We also discuss the prospects of applying systems biology approaches to study the mechanisms of crosstalk between plant hormones.
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Affiliation(s)
- Elena V Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Nadya A Omelyanchuk
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Elena V Ubogoeva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Victoria V Mironova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia.
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
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Zemlyanskaya EV, Wiebe DS, Omelyanchuk NA, Levitsky VG, Mironova VV. Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L. J Bioinform Comput Biol 2017; 14:1641009. [PMID: 27122321 DOI: 10.1142/s0219720016410092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Auxin is the major regulator of plant growth and development. It regulates gene expression via a family of transcription factors (ARFs) that bind to auxin responsive elements (AuxREs) in the gene promoters. The canonical AuxREs found in regulatory regions of many auxin responsive genes contain the TGTCTC core motif, whereas ARF binding site is a degenerate TGTCNN with TGTCGG strongly preferred. Thereby two questions arise: which TGTCNN variants are functional AuxRE cores and whether different TGTCNN variants have distinct functional roles? In this study, we performed meta-analysis of microarray data to reveal TGTCNN variants essential for auxin response and to characterize their functional features. Our results indicate that four TGTCNN motifs (TGTCTC, TGTCCC, TGTCGG, and TGTCTG) are associated with auxin up-regulation and two (TGTCGG, TGTCAT) with auxin down-regulation, but to a lesser extent. The genes having some of these motifs in their regulatory regions showed time-specific auxin response. Functional annotation of auxin up- and down-regulated genes also revealed GO terms specific for the auxin-regulated genes with certain TGTCNN variants in their promoters. Our results provide an idea that various TGTCNN motifs may play distinct roles in the auxin regulation of gene expression.
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Affiliation(s)
- Elena V Zemlyanskaya
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
| | - Daniil S Wiebe
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
| | - Nadezhda A Omelyanchuk
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
| | - Victor G Levitsky
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
| | - Victoria V Mironova
- * Department for Systems Biology, Institute of Cytology and Genetics SB RAS, 10 Lavrentyev Ave., Novosibirsk 630090, Russia.,† Laboratory of Computational Transcriptomics and Evolutionary Bioinformatics, Novosibirsk State University, 2 Pirogov Str., Novosibirsk 630090, Russia
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Zemlyanskaya EV, Levitsky VG, Oshchepkov DY, Grosse I, Mironova VV. The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana. Front Plant Sci 2016; 7:2044. [PMID: 28119721 PMCID: PMC5220190 DOI: 10.3389/fpls.2016.02044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/21/2016] [Indexed: 05/08/2023]
Abstract
The plant hormone ethylene regulates numerous developmental processes and stress responses. Ethylene signaling proceeds via a linear pathway, which activates transcription factor (TF) EIN3, a primary transcriptional regulator of ethylene response. EIN3 influences gene expression upon binding to a specific sequence in gene promoters. This interaction, however, might be considerably affected by additional co-factors. In this work, we perform whole genome bioinformatics study to identify the impact of epigenetic factors in EIN3 functioning. The analysis of publicly available ChIP-Seq data on EIN3 binding in Arabidopsis thaliana showed bimodality of distribution of EIN3 binding regions (EBRs) in gene promoters. Besides a sharp peak in close proximity to transcription start site, which is a common binding region for a wide variety of TFs, we found an additional extended peak in the distal promoter region. We characterized all EBRs with respect to the epigenetic status appealing to previously published genome-wide map of nine chromatin states in A. thaliana. We found that the implicit distal peak was associated with a specific chromatin state (referred to as chromatin state 4 in the primary source), which was just poorly represented in the pronounced proximal peak. Intriguingly, EBRs corresponding to this chromatin state 4 were significantly associated with ethylene response, unlike the others representing the overwhelming majority of EBRs related to the explicit proximal peak. Moreover, we found that specific EIN3 binding sequences predicted with previously described model were enriched in the EBRs mapped to the chromatin state 4, but not to the rest ones. These results allow us to conclude that the interplay of genetic and epigenetic factors might cause the distinct modes of EIN3 regulation.
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Affiliation(s)
- Elena V. Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), NovosibirskRussia
- Department of Natural Sciences, Novosibirsk State UniversityNovosibirsk, Russia
- *Correspondence: Elena V. Zemlyanskaya,
| | - Victor G. Levitsky
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), NovosibirskRussia
- Department of Natural Sciences, Novosibirsk State UniversityNovosibirsk, Russia
| | - Dmitry Y. Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), NovosibirskRussia
| | - Ivo Grosse
- Department of Natural Sciences, Novosibirsk State UniversityNovosibirsk, Russia
- Institute of Computer Science, Martin Luther University Halle-WittenbergHalle(Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-LeipzigLeipzig, Germany
| | - Victoria V. Mironova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), NovosibirskRussia
- Department of Natural Sciences, Novosibirsk State UniversityNovosibirsk, Russia
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