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FootprintDB: Analysis of Plant Cis-Regulatory Elements, Transcription Factors, and Binding Interfaces [chapter]

Bruno Contreras-Moreira, Alvaro Sebastian
2016 Msphere  
Two real-world examples are shown where this software was used to analyze transcriptional regulation in plants.  ...  It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank.  ...  Acknowledgments We would like to thank our colleagues C. Dubos, L Bülow, N. Saibo, T. Serra and J. van Helden for past and current collaborations.  ... 
doi:10.1007/978-1-4939-6396-6_17 pmid:27557773 fatcat:wnjluag6mfazflewblzgmvosqi

The Diverse Salt-Stress Response of Arabidopsis ctr1-1 and ein2-1Ethylene Signaling Mutants Is Linked to Altered Root Auxin Homeostasis

Irina I. Vaseva, Kiril Mishev, Thomas Depaepe, Valya Vassileva, Dominique Van Der Van Der Straeten
2021 Plants  
The constantly operating ethylene-signaling pathway in ctr1-1 was linked to increased auxin biosynthesis.  ...  The R2D2 auxin sensorallowed mapping this active auxin increase to the root epidermal cells in the late Cell Division (CDZ) and Transition Zone (TZ).  ...  Acknowledgments: The support by the Euro-BioImaging Node in Sofia, Bulgaria (https://www., PID: 336) which provided the confocal microscope facility is highly appreciated.  ... 
doi:10.3390/plants10030452 pmid:33673672 pmcid:PMC7997360 fatcat:vxst2aszorgp7c5hess665lfey

Evolution and applications of plant pathway resources and databases

Y. Sucaet, T. Deva
2011 Briefings in Bioinformatics  
We lay out trends and challenges in the ongoing efforts to integrate plant pathway databases and the applications of database integration.  ...  We propose Good Database Practice as a possible model for collaboration and to ease future integration efforts.  ...  Acknowledgements The authors are thankful to Prof.  ... 
doi:10.1093/bib/bbq083 pmid:21949268 fatcat:v4w7i5b47zhj7idwb7k5wrpdgi

Design and Analysis of Native Photorespiration Gene Motifs of Promoter Untranslated Region Combinations Under Short Term Abiotic Stress Conditions

Debarati Basu, Paul F. South
2022 Frontiers in Plant Science  
and AthaMap.  ...  In addition, we created suites of new GREs with higher transcriptional efficacies by combining the best performing promoter-UTR sequences.  ...  Both authors contributed to the article and approved the submitted version.  ... 
doi:10.3389/fpls.2022.828729 pmid:35251099 pmcid:PMC8888687 fatcat:7znx5eblg5bendfjdjt5axwdta

Functional Antagonism of WRI1 and TCP20 Modulates GH3.3 Expression to Maintain Auxin Homeostasis in Roots

Que Kong, Pui Man Low, Audrey R. Q. Lim, Yuzhou Yang, Ling Yuan, Wei Ma
2022 Plants  
EMSAs demonstrated that AtWRI1 antagonized TCP20 from binding to proGH3.3.  ...  Cross-family transcription factor interactions play pivotal roles in plant gene regulatory networks.  ...  Acknowledgments: We thank Michael Thomashow (Michigan State University) for the Arabidopsis transcription factor library, Hao Yu and Chengxiang Li (National University of Singapore) for the vector of dual-luciferase  ... 
doi:10.3390/plants11030454 pmid:35161435 pmcid:PMC8840716 fatcat:csy7jde4mrbtrltpgx2piiszr4

MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations

Jens Keilwagen, Jan Baumbach, Thomas A Kohl, Ivo Grosse
2009 Genome Biology  
Valuable binding-site annotation data are stored in databases.  ...  However, several types of errors can, and do, occur in the process of manually incorporating annotation data from the scientific literature into these databases.  ...  helpful discussions, two anonymous reviewers for their valuable comments, Alexander Goesmann, Achim Neumann, and Ralf Nolte for expert technical support, and Richard Münch for his help with the RegulonDB data  ... 
doi:10.1186/gb-2009-10-5-r46 pmid:19409082 pmcid:PMC2718512 fatcat:bvhiiqxs3ndn5lbh35u3lcwnje

Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model

Papapit Ingkasuwan, Supatcharee Netrphan, Sukon Prasitwattanaseree, Morakot Tanticharoen, Sakarindr Bhumiratana, Asawin Meechai, Jeerayut Chaijaruwanich, Hideki Takahashi, Supapon Cheevadhanarak
2012 BMC Systems Biology  
The robustness of gene-to-gene regulatory network was further analyzed by TF binding site prediction and by evaluating global co-expression of TFs and target starch metabolic enzymes.  ...  A total of 1,480 diurnally regulated genes included 21 starch metabolic enzymes, 6 clock-associated genes, and 106 transcription factors (TF).  ...  Acknowledgements We are grateful to Dr. Akinori Suzuki and Ms. Yumiko Tsuchiya, RIKEN Plant Science Center, for technical support in growing Arabidopsis and qRT-PCR experiment.  ... 
doi:10.1186/1752-0509-6-100 pmid:22898356 pmcid:PMC3490714 fatcat:mls3xsihpbajxj6w3hlhujrglm

Cytokinin-Regulated Expression of Arabidopsis thaliana PAP Genes and Its Implication for the Expression of Chloroplast-Encoded Genes

Aleksandra A. Andreeva, Radomira Vankova, Ivan A. Bychkov, Natalia V. Kudryakova, Maria N. Danilova, Jozef Lacek, Elena S. Pojidaeva, Victor V. Kusnetsov
2020 Biomolecules  
The disruption of PAP genes contributed to the abolishment of positive CK effect on the accumulation of the chloroplast gene transcripts and transcripts of the nuclear genes for plastid transcription machinery  ...  as can be judged from the analysis of pap1 and pap6 mutants.  ...  In silico examination of 5 region of PAP1 revealed the presence of type-B ARR consensus binding sites (A/G)GAT) suggesting the possibility that PAP1 may be a CK-dependent target gene.  ... 
doi:10.3390/biom10121658 pmid:33322466 fatcat:dy6225l4fjgifoyyeuzj2uorbm

Associative pattern recognition for biological regulation data

Yiou Xiao
2017 ACM SIGBioinformatics Record  
In gene regulatory network inference, we propose a framework for refining weak networks based on transcription factor binding sites, thus improved the precision of predicted edges by up to 52%.  ...  In particular, we emphasize efficiently recognizing associative patterns between genes, transcription factors, histone modifications and functional labels using heterogeneous data sources (numeric, sequences  ...  each transcription factor has its own binding site; (c) one single regulator can bind to any of the three binding sites.  ... 
doi:10.1145/3148241.3148242 fatcat:nticslp3bra55iksan3hwzvq2i

Redundant ERF-VII transcription factors bind an evolutionarily-conserved cis-motif to regulate hypoxia-responsive gene expression in Arabidopsis

Philipp Gasch, Moritz Fundinger, Jana T. Müller, Travis Lee, Julia Bailey-Serres, Angelika Mustroph
2015 The Plant Cell  
Upregulation of over half of these mRNAs involves stabilization of five group VII ethylene response factor (ERF-VII) transcription factors, which are routinely degraded via the N-end rule pathway of proteolysis  ...  An evolutionarily conserved 12-bp cis-regulatory motif that binds to and is sufficient for activation by RAP2.2 and RAP2.12 is identified through a comparative phylogenetic motif search, promoter dissection  ...  In fact, an ERF from group IXc was shown to alter its binding site affinity in a stressspecific manner (Cheng et al., 2013) , and there is evidence from ChIP analyses that RAP2.3 binds genomic regions  ... 
doi:10.1105/tpc.15.00866 pmid:26668304 pmcid:PMC4746684 fatcat:h7kpkqswebgmhgtuefm5yqfspq

Nitrate sensing by the maize root apex transition zone: a merged transcriptomic and proteomic survey

Sara Trevisan, Alessandro Manoli, Laura Ravazzolo, Alessandro Botton, Micaela Pivato, Antonio Masi, Silvia Quaggiotti
2015 Journal of Experimental Botany  
Nitrate is an essential nutrient for plants, and crops depend on its availability for growth and development, but its presence in agricultural soils is far from stable.  ...  In order to overcome nitrate fluctuations in soil, plants have developed adaptive mechanisms allowing them to grow despite changes in external nitrate availability.  ...  In silico analysis of 1000 bp upstream of the start codons of the co-regulated genes revealed that group-specific binding sites may be attributed to each group (Table 2) .  ... 
doi:10.1093/jxb/erv165 pmid:25911739 pmcid:PMC4473975 fatcat:djkappp4qzcvbohpwjlm6dnbl4

The native cistrome and sequence motif families of the maize ear

Savannah D. Savadel, Thomas Hartwig, Zachary M. Turpin, Daniel L. Vera, Pei-Yau Lung, Xin Sui, Max Blank, Wolf B. Frommer, Jonathan H. Dennis, Jinfeng Zhang, Hank W. Bass, Nathan M. Springer
2021 PLoS Genetics  
Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites.  ...  Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g.  ...  Transcriptional gene regulation generally depends on transcription factors (TFs), which bind either directly, or indirectly as parts of complexes, to specific DNA binding sites in gene promoters or distal  ... 
doi:10.1371/journal.pgen.1009689 pmid:34383745 pmcid:PMC8360572 fatcat:x6qklyzc7bcylkifhgbeemyzia

Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network

Simon Scofield, Alexander Murison, Angharad Jones, John Fozard, Mitsuhiro Aida, Leah R. Band, Malcolm Bennett, James A. H. Murray
2018 Development  
relationships between STM and factors involved in multiple aspects of SAM function.  ...  The Arabidopsis homeodomain transcription factor SHOOT MERISTEMLESS (STM) is crucial for shoot apical meristem (SAM) function, yet the components and structure of the STM gene regulatory network (GRN)  ...  Acknowledgements We are most grateful to David Jackson for pSTM::STM-YFP, to Wolfgang Werr for pSTM::GUS and to Rüdiger Simon for p35S::STM-GR.  ... 
doi:10.1242/dev.157081 pmid:29650590 pmcid:PMC5992597 fatcat:siqfqvsnabhsnhs2en7kp3l56q

Coordinate Regulation of Metabolites Glycosylation and Stress Hormones Biosynthesis by TT8 in Arabidopsis

Amit Rai, Shivshankar Umashankar, Megha Rai, Boon Kiat Lim, Johanan Aow Shao Bing, Sanjay Swarup
2016 Plant Physiology  
We thank Agilent Technologies (Singapore) for their support in providing metabolomics and genomics instrumentation, software, and advice.  ...  The predicted bHLH binding sites in the promoter region of these genes were determined using AtcisDB (TAIR9) from the AGRIS server (Yilmaz et al., 2011 ), AthaMap (June 2014 version; Hehl and Bülow, 2014  ...  The model involves TT8 as a key transcription factor that directly binds to the promoters of genes involved in these two processes.  ... 
doi:10.1104/pp.16.00421 pmid:27432888 pmcid:PMC4972274 fatcat:iwwewfn5cra57jhpmxqvqxtmye

NIN-like Protein7 and PROTELYSIS6 Functional Interaction Enhances Tolerance to Sucrose, ABA, and Submergence

Mari-Cruz Castillo, Álvaro Costa-Broseta, Beatriz Gayubas, José León
2021 Plant Physiology  
Nitrate assimilation and signaling regulate plant growth through the relevant function of the transcription factor NIN-like Protein7 (NLP7).  ...  NO-mediated regulation requires efficient sensing via the PROTEOLYSIS6 (PRT6)-mediated proteasome-triggered degradation of group VII of ethylene response transcription factors (ERFVIIs) through the Cys  ...  We have analyzed the -1000 bp promoter 426 region of NLP7 locus with AthaMap (; Hehl et al., 2016) 427 searching for potential binding sites of transcription factors already 428 characterized  ... 
doi:10.1093/plphys/kiab382 pmid:34618055 pmcid:PMC8644111 fatcat:y5wk47rak5halascdsllmwbvuu
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