A5023123648- Plant Molecular Biology Research
- Plant Reproductive Biology
- Genomics and Chromatin Dynamics
- Gene expression and cancer classification
- Plant Gene Expression Analysis
- RNA Research and Splicing
- Plant nutrient uptake and metabolism
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Plant tissue culture and regeneration
- Plant Physiology and Cultivation Studies
- Photosynthetic Processes and Mechanisms
- Postharvest Quality and Shelf Life Management
- Light effects on plants
- Plant Stress Responses and Tolerance
- Plant responses to water stress
- Polysaccharides and Plant Cell Walls
- Epigenetics and DNA Methylation
- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Bacteriophages and microbial interactions
- Single-cell and spatial transcriptomics
- GABA and Rice Research
Institute of Cytology and Genetics
2016-2025
Novosibirsk State University
2016-2025
Siberian Branch of the Russian Academy of Sciences
2016-2025
Central European Institute of Technology – Masaryk University
2017
SynZyme Technologies (United States)
2013
Abstract Expansins facilitate cell expansion by mediating pH-dependent wall (CW) loosening. However, the role of expansins in controlling CW biomechanical properties specific tissues and organs remains elusive. We monitored hormonal responsiveness spatial specificity expression localization predicted to be direct targets cytokinin signaling Arabidopsis (Arabidopsis thaliana). found EXPANSIN1 (EXPA1) homogenously distributed throughout columella/lateral root cap, while EXPA10 EXPA14 localized...
A rhizosphere (a narrow area of soil around plant roots) is an ecological niche, within which beneficial microorganisms and pathogens compete with each other for organic carbon compounds the opportunity to colonize roots. The roots secrete rhizodeposits into rhizosphere, include border cells, products root cell death liquids secreted by living cells (root exudates). Border have their name due location in next (at soil), represent terminal differentiation columella adjacent lateral cap cells....
Recognition of composite elements consisting two transcription factor binding sites gets behind the studies tissue-, stage- and condition-specific transcription. Genome-wide data on generated with ChIP-seq method facilitate an identification elements, but existing bioinformatics tools either require datasets for both partner factors, or omit motifs overlapping. Here we present universal Motifs Co-Occurrence Tool (MCOT) that retrieves maximum information about overrepresented from a single...
Abstract Auxin plays a pivotal role in virtually every aspect of plant morphogenesis. It simultaneously orchestrates diverse variety processes such as cell wall biogenesis, transition through the cycle, or metabolism wide range chemical substances. The coordination principles for complex orchestration are poorly understood at systems level. Here, we perform an RNA-seq experiment to study transcriptional response auxin treatment within gene groups different biological processes, molecular...
Gene regulatory networks (GRNs) – interpretable graph models of gene expression regulation are a pivotal tool for understanding and investigating the mechanisms utilized by cells during development in response to various internal external stimuli. Historically, first approach GRN reconstruction was based on analysis published data (including those summarized databases). Currently, primary inference is omics (mainly transcriptomic) data; number mathematical methods have been adapted that....
The description of the path from a gene to trait, as main task many areas in biology, is currently being equipped with new methods affecting not only experimental techniques, but also analysis results. pleiotropic effect due its participation numerous biological processes involved different traits. A widespread use genome-wide sequencing transcripts and transcription factor (TF) binding regions has made following tasks relevant: unveiling effects TFs based on functions their target genes;...
Abstract Multistep phosphorelay (MSP) signaling integrates hormonal and environmental signals to control both plant development adaptive responses. Type-A RESPONSE REGULATOR (RRA) genes, the downstream members of MSP cascade cytokinin primary response are thought mediate primarily negative feedback regulation (cytokinin-induced) signaling. However, transcriptional data also suggest involvement RRA genes in stress-related By employing evolutionary conservation with well-characterized...
ABSTRACT Expansins facilitate cell expansion via mediating pH-dependent wall (CW) loosening. However, the role of expansins in control biomechanical CW properties tissue and organ context remains elusive. We determined hormonal responsiveness specificity expression localization predicted to be direct targets cytokinin signalling. found EXPA1 homogenously distributed throughout columella/ lateral root cap, while EXPA10 EXPA14 localized predominantly at three-cell boundaries epidermis/cortex...
Abstract Auxin is a key plant regulatory molecule, which acts upon plethora of cellular processes, including those related to cell differentiation and elongation. Despite the stunning progress in all disciplines auxin research, mechanisms auxin-mediated rapid promotion expansion underlying rearrangement wall components are poorly understood. This partly due limitations current methodologies for probing auxin. Here we describe click chemistry-based approach, using an azido derivative...
Auxin and ethylene pathways cooperatively regulate a variety of developmental processes in plants. Growth responses to are largely dependent on auxin, the key regulator plant morphogenesis. Auxin, turn, is capable inducing biosynthesis signaling making interaction these hormones reciprocal. Recent studies discovered bunch molecular events underlying auxin-ethylene crosstalk. In this review, we summarize results fine-scale large-scale experiments auxin Arabidopsis. We integrate knowledge...
In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master factors to biological processes under their control, remain insufficiently characterized despite crucial function. Here, we identify a TFRN involved in response key auxin and define its impact on auxin-driven processes. To reconstruct TFRN, developed three-step procedure, is based integrated analysis of differentially expressed gene lists representative collection binding profiles. Its...
The plant hormone ethylene regulates numerous developmental processes and stress responses. Ethylene signaling proceeds via a linear pathway, which activates transcription factor (TF) EIN3, primary transcriptional regulator of response. EIN3 influences gene expression upon binding to specific sequence in promoters. This interaction, however, might be considerably affected by additional co-factors. In this work, we perform whole genome bioinformatics study identify the impact epigenetic...
Plant hormone ethylene regulates a wide range of physiological processes during plant development and coordinates different stress responses. Among others controls such practically significant characteristics agricultural crops as fruit ripening rates tolerance to conditions. That is why understanding molecular mechanisms underlying action one the basic questions in biology that addressed context both fundamental research application agriculture. Ethylene biosynthesis from methionine amino...
(1) Background: The widespread application of ChIP-seq technology requires annotation cis-regulatory modules through the search co-occurred motifs. (2) Methods: We present web server Motifs Co-Occurrence Tool (Web-MCOT) that for a single dataset detects composite elements (CEs) or overrepresented homo- and heterotypic pairs motifs with spacers overlaps, any mutual orientations, uncovering various similarities to recognition models within first (Anchor) motif in CEs respects target...
Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives systematic evaluation upstream regulators gene lists. Plant Cistrome database, large collection TF binding detected using DAP-seq method, made it possible Arabidopsis. Here we re-processed raw data with MACS2, most popular peak caller that leads among other ones according to quality metrics. In benchmarking study, confirmed improved supported more precise list...
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 respect to their fold changes. FSEA identifies Ontology (GO) terms, which are shared by the group similar magnitude response, and assesses these GO terms found fold-change-specifically (e.g., weakly, moderately, or strongly)...
(1) Background: Transcription factors (TFs) are main regulators of eukaryotic gene expression. The cooperative binding to genomic DNA at least two TFs is the widespread mechanism transcription regulation. Cooperating can be revealed through analysis co-occurrence their motifs. (2) Methods: We applied motifs tool (MCOT) that predicted pairs spaced or overlapped (composite elements, CEs) for a single ChIP-seq dataset. improved MCOT capability prediction asymmetric CEs with one participating...