DATF: a database of Arabidopsis transcription factors

Guo, An‐Yuan; He, Kongwang; Liu, Di; Bai, Shu-Nong; Gu, Xiaocheng; Wei, Liping; Luo, Jianxun

doi:10.1093/bioinformatics/bti334

Cited by 294 publications

(227 citation statements)

References 12 publications

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“…After the completion of sequencing of the Arabidopsis genome, there have been several large-scale analyses of the Arabidopsis TFs (Czechowski et al 2004;Gong et al 2004;Tian et al 2004;Guo et al 2005;Iida et al 2005;Okushima et al 2005;Overvoorde et al 2005). Previously, functional genomic analyses on two well-known transcription regulator gene families, AUXIN RESPONSE FACTOR (ARF) and AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA), provided insights into the unique and overlapping functions of the members of these two families Overvoorde et al 2005).…”

Section: Discussionmentioning

confidence: 99%

“…However, our knowledge of the biological roles and the biochemical properties of the majority of Arabidopsis TFs are fragmented. In recent years, there have been various attempts to analyzing the Arabidopsis TFs at a large scale (Czechowski et al 2004;Gong et al 2004;Tian et al 2004;Guo et al 2005;Iida et al 2005;Okushima et al 2005;Overvoorde et al 2005).…”

Section: Introductionmentioning

confidence: 99%

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Large-scale analysis of the GRAS gene family in Arabidopsis thaliana

et al. 2008

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GRAS proteins belong to a plant-specific transcription factor family. Currently, 33 GRAS members including a putative expressed pseudogene have been identified in the Arabidopsis genome. With a reverse genetic approach, we have constructed a ''phenome-ready unimutant collection'' of the GRAS genes in Arabidopsis thaliana. Of this collection, we focused on loss-of-function mutations in 23 novel GRAS members. Under standard conditions, homozygous mutants have no obvious morphological phenotypes compared with those of wild-type plants. Expression analysis of GRAS genes using quantitative realtime RT-PCR (qRT-PCR), microarray data mining, and promoter::GUS reporter fusions revealed their tissuespecific expression patterns. Our analysis of protein-protein interaction and subcellular localization of individual GRAS members indicated their roles as transcription regulators. In our yeast two-hybrid (Y2H) assay, we confirmed the protein-protein interaction between SHORT-ROOT (SHR) and SCARECROW (SCR). Furthermore, we identified a new SHR-interacting protein, SCARECROW-LIKE23 (SCL23), which is the most closely related to SCR. Our large-scale analysis provides a comprehensive evaluation on the Arabidopsis GRAS members, and also our phenome-ready unimutant collection will be a useful resource to better understand individual GRAS proteins that play diverse roles in plant growth and development.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Large-scale analysis of the GRAS gene family in Arabidopsis thaliana

et al. 2008

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“…The Arabidopsis genome contains some 2000 TFs (1922 loci, 2290 gene models) that have been classified into 64 families based on DNA binding domain homologies (Guo et al, 2005). Given the extent and diversity of these Arabidopsis TFs, the question arises as to whether individual families of TFs evolved the capacity to function non-cell-autonomously, or whether specific members within each family gained (or lost) this ability.…”

Section: Introductionmentioning

confidence: 99%

Analysis of Arabidopsis Transcription Factor Families Revealed Extensive Capacity for Cell-to-Cell Movement as Well as Discrete Trafficking Patterns

Rim

Huang

Chu

et al. 2011

Molecules and Cells

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In plants, cell-to-cell communication is pivotal for the orchestration of cell fate determination, organ development, and the integration of whole plant physiology. One of the strategies for intercellular communication uses symplasmic communication channels, called plasmodesmata (PD). These PD establish unique cytoplasmic channels for the intercellular exchange not only of metabolites and small signaling molecules, but also of regulatory proteins and RNAs to allow for local orchestration of development and physiology. A number of non-cell-autonomous transcription factors (NCATFs) have been shown to function in the coordination of specific regulatory networks. To further explore the potential of such NCATFs, a genome-wide screen was performed on the transcription factor (TF) families in Arabidopsis. We here report that, among the 76 TFs examined, 22 were shown to move beyond their sites of transcription in the root apex; these NCATFs belonged to 17 TF families, including homeobox, GRAS, and MYB. Expression studies performed on variously-sized mCherry constructs identified a range of PD size exclusion limits within tissues of the root. In addition, our studies showed that actual protein level was an important factor controlling the range of TF intercellular movement. Interestingly, our studies on CAPRICE movement revealed tissue-specificity with respect to the mode of intercellular trafficking. These findings are discussed with respect to the regulation between cell-autonomous or non-cell-autonomous action.

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“…Gene sequences and their flanking regions were excised from the genome sequence using an original Perl script (http://www.perl.org/). We redefined 1,906 genes and classified them into 48 different TF families based on our analysis of how they were represented in four different TF databases (RARTF, Iida et al 2005;AtTFDB, Davuluri et al 2003;PlnTFDB, Riano-Pachon et al 2007; DATF, Guo et al 2005) (Table S1). The conserved domain of each family was identified by HMMER3 (http://hmmer.org/) and manual curation.…”

Section: The Data and Software Implemented In Fioredbmentioning

confidence: 99%

“…In addition, information from the Arabidopsis Small RNA Project (ASRP) (Backman et al 2008) for miRNAs/tasiRNAs is provided if the gene is targeted by them. An example of the gene view is shown in Figure 1I Guo et al 2005) is displayed. From this page, FioreDB provides a number of useful direct link to external databases such as TAIR, ASRP, T-DNA express (Alonso et al 2003), ATTED-II (Obayashi et al 2009) and the SALAD database (Mihara et al 2010).…”

Section: Browsing Gene Informationmentioning

confidence: 99%