scholarly journals Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor

2014 ◽  
Vol 14 (1) ◽  
pp. 29 ◽  
Author(s):  
Martiniano M Ricardi ◽  
Rodrigo M González ◽  
Silin Zhong ◽  
Pía G Domínguez ◽  
Tomas Duffy ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factor ◽  
Drought Stress ◽  
Genome Wide ◽  
Genome Wide Data

Foxtail millet WRKY genes and drought stress

2016 ◽  
Vol 155 (5) ◽  
pp. 777-790 ◽  
Author(s):  
L. ZHANG ◽  
H. SHU ◽  
A. Y. ZHANG ◽  
B. L. LIU ◽  
G. F. XING ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Drought Stress ◽  
Quantitative Polymerase Chain Reaction ◽  
Foxtail Millet ◽  
Wrky Transcription Factor ◽  
Sequencing Data ◽  
Genome Wide ◽  
Functional Analyses ◽  
Encoding Genes

SUMMARYFoxtail millet (Setaria italica (L.) P. Beauv.) is a naturally stress-tolerant plant, a major reserve crop and a model for panicoid grasses. The recent completion of the S. italica genome facilitates identification and characterization of WRKY transcription factor family proteins that are important regulators of major plant processes, including growth, development and stress response. The present study identified 103 WRKY transcription factor-encoding genes in the S. italica genome. The genes were named SiWRKY1–SiWRKY103 according to their order on the chromosomes. A comprehensive expression analysis of SiWRKY genes among four different tissues was performed using publicly available RNA sequencing data. Eighty-four SiWRKY genes were more highly expressed in root tissue than in other tissues and nine genes were only expressed in roots. Additionally, real-time quantitative polymerase chain reaction was performed to comprehensively analyse the expression of all SiWRKY genes in response to dehydration. Results indicated that most SiWRKY genes (over 0.8) were up-regulated by drought stress. In conclusion, genome-wide identification and expression profiling of SiWRKY genes provided a set of candidates for cloning and functional analyses in plants’ response to drought stress.

DESIGN OF A NEW ETHYLENE PLANT HORMONE SENSOR BASED ON GENOME-WIDE DATA ANALYSIS OF EIN3 TRANSCRIPTION FACTOR BINDING

2021 ◽  
Vol 1 (19) ◽  
pp. 199-200
Author(s):  
V.G. Levitsky ◽  
D.Y. Oshchepkov ◽  
E. Zemlyanskaya
Keyword(s):  
Transcription Factor ◽  
Data Analysis ◽  
Binding Site ◽  
Plant Hormone ◽  
Transcriptional Response ◽  
Factor Binding ◽  
Structural Variant ◽  
Ethylene Plant ◽  
Genome Wide ◽  
Genome Wide Data

A new structural variant of the transcription factor EIN3 binding site has been obtained. This structural variant is strongly associated with the transcriptional response to ethylene and is preferred for EIN3 binding. Based on this structural variant, a new genetic ethylene sensor was developed.

scholarly journals Necrotic upper tips1mimics heat and drought stress and encodes a protoxylem-specific transcription factor in maize

2020 ◽  
Vol 117 (34) ◽  
pp. 20908-20919 ◽  
Author(s):  
Zhaobin Dong ◽  
Zhennan Xu ◽  
Ling Xu ◽  
Mary Galli ◽  
Andrea Gallavotti ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factor ◽  
Drought Stress ◽  
Target Genes ◽  
Water Movement ◽  
High Water ◽  
Leaf Sheath ◽  
Coding Region ◽  
Downstream Target ◽  
Vessel Integrity

Maintaining sufficient water transport during flowering is essential for proper organ growth, fertilization, and yield. Water deficits that coincide with flowering result in leaf wilting, necrosis, tassel browning, and sterility, a stress condition known as “tassel blasting.” We identified a mutant,necrotic upper tips1(nut1), that mimics tassel blasting and drought stress and reveals the genetic mechanisms underlying these processes. Thenut1phenotype is evident only after the floral transition, and the mutants have difficulty moving water as shown by dye uptake and movement assays. These defects are correlated with reduced protoxylem vessel thickness that indirectly affects metaxylem cell wall integrity and function in the mutant.nut1is caused by anActransposon insertion into the coding region of a uniqueNACtranscription factor within theVNDclade ofArabidopsis. NUT1 localizes to the developing protoxylem of root, stem, and leaf sheath, but not metaxylem, and its expression is induced by flowering. NUT1 downstream target genes function in cell wall biosynthesis, apoptosis, and maintenance of xylem cell wall thickness and strength. These results show that maintaining protoxylem vessel integrity during periods of high water movement requires the expression of specialized, dynamically regulated transcription factors within the vasculature.

scholarly journals Genome-wide analysis of NAC transcription factor family in maize under drought stress and rewatering

2020 ◽  
Vol 26 (4) ◽  
pp. 705-717 ◽  
Author(s):  
Guorui Wang ◽  
Zhen Yuan ◽  
Pengyu Zhang ◽  
Zhixue Liu ◽  
Tongchao Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Drought Stress ◽  
Nac Transcription Factor ◽  
Transcription Factor Family ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Rice (Oryza Sativa L.) Whole Grain Genome-Wide Association Study for Neutral Sugar Content

2021 ◽  
Author(s):  
Rahele Panahabadi ◽  
Lauren S. McKee ◽  
Asadollah Ahmadikhah ◽  
Pär K. Ingvarsson ◽  
Naser Farrokhi
Keyword(s):  
Cell Wall ◽  
Transcription Factor ◽  
Protein Kinase ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Arabinogalactan Protein ◽  
Whole Grain ◽  
Genome Wide ◽  
Cell Wall Matrix

Abstract Background Cell wall matrix polysaccharides are structurally complex and diverse, but our knowledge about their synthesis is limited. The building blocks (monosaccharides) of these polysaccharides have critical role in defining the number and the ultrastructure (size) of rice grains, and therefore would have great influence on seed vigor, yield and quality. Genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in defining plant cell wall structure and modifications. The monosaccharides that contribute to major cell wall matrix polysaccharides in whole grains of 197 rice accessions were quantified using acid hydrolysis and high-performance anion-exchange chromatography with pulsed amperometric detection. A GWAS of calculated monosaccharide content in rice whole grain (RWG) was carried out using 33,812 single-nucleotide polymorphisms (SNPs) to identify corresponding markers in 200 kbp flanking regions.Results In total, 49 significant SNPs contained in 19 genomic regions (QTLs) on eight chromosomes of rice were determined to be associated with monosaccharides content. The candidate genes in QTL regions included the following: arabinose content was associated with α-N-arabinofuranosidase, pectinesterase inhibitor, a glycoside hydrolase (GH) from family 16 (GH16 enzyme); xylose content was associated with ethylene-responsive element-binding protein and a pyruvate kinase; mannose content was associated with a MYB family transcription factor and S-domain receptor-like protein kinase; galactose content was associated with a glycocyltransferase (GT) from family 8 (GT8 enzyme), GRAS family transcription factor, glutathione S-transferase, GH16 and GH17 enzymes; fucose content was associated with a GH16 enzyme, lysine-rich arabinogalactan protein 19 and a receptor protein kinase; and finally rhamnose content was associated with OsFBX41, pectinesterase, COBRA-like protein, and OsSAUR13 (Auxin-responsive SAUR).Conclusion The results of this study should improve our understanding of the genetic basis of the factors that might be involved in the biosynthesis and turnover of major matrix polysaccharides present in RWG. Several QTLs were identified on different chromosomes, all are reported for first. Further, our data provide insight that will be useful in the design of future breeding programs, allowing breeders to use available genetic resources more effectively in meeting global food demand and supply.

scholarly journals NAC transcription factor RD26 is a regulator of root hair morphogenic plasticity

2021 ◽  
Author(s):  
Iman Kamranfar ◽  
Salma Balazadeh ◽  
Bernd Mueller-Roeber
Keyword(s):  
Cell Wall ◽  
Transcription Factor ◽  
Drought Stress ◽  
Root Hair ◽  
Regulatory Network ◽  
Hair Growth ◽  
Root Hairs ◽  
Nac Transcription Factor ◽  
Numerous Cell ◽  
Root Hair Growth

AbstractRoot hairs are outgrowths of epidermal cells central for water and nutrient acquisition. Root hair growth is plastically modified by environmental cues. A frequent response to water limitation is active shortening of root hairs, involving largely unknown molecular mechanisms. A root hair-specific cis-regulatory element (RHE) integrates developmental cues with downstream signalling of root hair morphogenesis. Here, we demonstrate NAC transcription factor RD26 to be a key expressional regulator of this drought stress-triggered developmental response in Arabidopsis thaliana. RD26 directly represses RSL4 and RSL1, two master transcription regulators of root hair morphogenesis, by binding RHE. RD26 further represses core cell wall modification genes including expansins (EXPA7, EXPA18), hydroxyproline-rich glycoproteins (LRX1), xyloglucan endotransglucosylases/hydrolases (XTH12, 13, 14, 26), class III peroxidases (PRX44) and plasma membrane H+-ATPase (AHA7) through RHE. Of note, several RD26-repressed genes are activated by RSL4. Thus, by repressing RSL4 and numerous cell wall-related genes, RD26 governs a robust gene regulatory network for restricting root hair growth under drought. A similar regulatory network exists in tomato, indicating evolutionary conservation across species.Significance statementIn plants, root hairs play a vital role for water and nutrient acquisition, soil anchorage, and microbial interactions. During drought stress, root hair growth is suppressed as an adaptive strategy to save cellular energy. We identified NAC transcription factor RD26 as a key regulator of this developmental plasticity in the model plant Arabidopsis thaliana. RD26 directly and negatively controls the transcriptional activity of key root hair developmental genes, RSL1 and RSL4. Furthermore, RD26 suppresses the expression of several functional genes underlying root hair development including numerous cell wall-related genes. RD26 thus governs a robust gene regulatory network underlying the developmental response to drought stress. A similar regulatory network exists in tomato indicating evolutionary conservation of this mechanism across species.

scholarly journals aiMeRA: A generic modular response analysis R package and its application to estrogen and retinoic acid receptors crosstalk

2020 ◽  
Author(s):  
Gabriel Jimenez-Dominguez ◽  
Patrice Ravel ◽  
Stéphan Jalaguier ◽  
Vincent Cavaillès ◽  
Jacques Colinge
Keyword(s):  
Transcription Factor ◽  
Retinoic Acid ◽  
R Package ◽  
Retinoic Acid Receptors ◽  
Response Analysis ◽  
Sequencing Data ◽  
Genome Wide ◽  
Genome Wide Data ◽  
Modular Response Analysis ◽  
Mathematical Derivation

AbstractModular response analysis (MRA) is a widely used modeling technique to uncover coupling strengths in molecular networks under a steady-state condition by means of perturbation experiments. We propose an extension of this methodology to search genomic data for new associations with a network modeled by MRA and to improve the predictive accuracy of MRA models. These extensions are illustrated by exploring the cross talk between estrogen and retinoic acid receptors, two nuclear receptors implicated in several hormone-driven cancers such as breast. We also present a novel, rigorous and elegant mathematical derivation of MRA equations, which is the foundation of this work and of an R package that is freely available at https://github.com/bioinfo-ircm/aiMeRA/. This mathematical analysis should facilitate MRA understanding by newcomers.Author summaryEstrogen and retinoic acid receptors play an important role in several hormone-driven cancers and share co-regulators and co-repressors that modulate their transcription factor activity. The literature shows evidence for crosstalk between these two receptors and suggests that spatial competition on the promoters could be a mechanism. We used MRA to explore the possibility that key co-repressors, i.e., NRIP1 (RIP140) and LCoR could also mediate crosstalk by exploiting new quantitative (qPCR) and RNA sequencing data. The transcription factor role of the receptors and the availability of genome-wide data enabled us to explore extensions of the MRA methodology to explore genome-wide data sets a posteriori, searching for genes associated with a molecular network that was sampled by perturbation experiments. Despite nearly two decades of use, we felt that MRA lacked a systematic mathematical derivation. We present here an elegant and rather simple analysis that should greatly facilitate newcomers’ understanding of MRA details. Moreover, an easy-to-use R package is released that should make MRA accessible to biology labs without mathematical expertise. Quantitative data are embedded in the R package and RNA sequencing data are available from GEO.

scholarly journals A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package

2019 ◽  
Vol 47 (21) ◽  
pp. e139-e139 ◽  
Author(s):  
Victor Levitsky ◽  
Elena Zemlyanskaya ◽  
Dmitry Oshchepkov ◽  
Olga Podkolodnaya ◽  
Elena Ignatieva ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Fold Increase ◽  
Transcription Factor Binding ◽  
Single Chip ◽  
Maximum Information ◽  
Factor Binding ◽  
Protein Protein Interaction ◽  
Genome Wide ◽  
Genome Wide Data

Abstract Recognition of composite elements consisting of two transcription factor binding sites gets behind the studies of tissue-, stage- and condition-specific transcription. Genome-wide data on transcription factor binding generated with ChIP-seq method facilitate an identification of composite elements, but the existing bioinformatics tools either require ChIP-seq datasets for both partner transcription factors, or omit composite elements with motifs overlapping. Here we present an universal Motifs Co-Occurrence Tool (MCOT) that retrieves maximum information about overrepresented composite elements from a single ChIP-seq dataset. This includes homo- and heterotypic composite elements of four mutual orientations of motifs, separated with a spacer or overlapping, even if recognition of motifs within composite element requires various stringencies. Analysis of 52 ChIP-seq datasets for 18 human transcription factors confirmed that for over 60% of analyzed datasets and transcription factors predicted co-occurrence of motifs implied experimentally proven protein-protein interaction of respecting transcription factors. Analysis of 164 ChIP-seq datasets for 57 mammalian transcription factors showed that abundance of predicted composite elements with an overlap of motifs compared to those with a spacer more than doubled; and they had 1.5-fold increase of asymmetrical pairs of motifs with one more conservative ‘leading’ motif and another one ‘guided’.

Sign in / Sign up

Export Citation Format

Share Document