<i>Arabidopsis</i> JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action

Welch, David; Hassan, Hala; Blilou, Ikram; Immink, Richard G. H.; Heidstra, Renze; Scheres, Ben

doi:10.1101/gad.440307

Cited by 259 publications

(330 citation statements)

References 29 publications

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“…In addition, our pair-wise analysis revealed that only two pairs showed protein-protein interactions. We confirmed the interaction between SHR and SCR, which plays an important role in the regulation of SHR movement as recently reported (Cui et al 2007, Welch et al 2007 (Fig. 7).…”

Section: Interaction Among Gras Proteins In Y2h Assaysupporting

confidence: 92%

“…Surprisingly, most GRAS proteins show no interaction among the members, except for SCR, SHR, and SCL23. Recent studies revealed that the protein-protein interaction between SCR and SHR is crucial to regulate the SHR movement (Cui et al 2007, Welch et al 2007. In this study, we not only confirmed the interaction between SCR and SHR, but also identified a novel SHR-interacting protein, SCL23, which is the most closely related to SCR among GRAS members.…”

Section: Discussionsupporting

confidence: 79%

“…Yeast two-hybrid assay was performed as described previously (Welch et al 2007) using the ProQuest Two Hybrid System (INVITROGEN, http://www.invitrogen. com).…”

Section: Yeast Two-hybrid (Y2h) Assaymentioning

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: Interaction Among Gras Proteins In Y2h Assaysupporting

confidence: 92%

Section: Discussionsupporting

confidence: 79%

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

et al. 2008

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“…For the C2H2 TF STZ, where mutants have enhanced tolerance to salt and abiotic stresses, we also saw enrichment in mitosis-related functions (Figure 4, box 4). As C2H2 family members from both plants and animals are known to regulate the cell cycle and DNA replication (Staudt et al, 2006;Welch et al, 2007), STZ enrichment for mitotic functions suggests that its stress response phenotype may involve direct regulation of cell division. Finally, bHLH122, known to be important for abiotic drought responses, targeted genes in immune processes (Figure 4, box 3), suggesting that it may also play a role in biotic defense.…”

Section: The Arabidopsis Cistromementioning

confidence: 99%

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

O’Malley¹,

Huang²,

Song³

et al. 2016

Cell

373

482

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SUMMARYThe cistrome is the complete set of transcription factor (TF) binding sites (cis-elements) in an organism, while an epicistrome incorporates tissue-specific DNA chemical modifications and TFspecific chemical sensitivities into these binding profiles. Robust methods to construct comprehensive cistrome and epicistrome maps are critical for elucidating complex transcriptional networks that underlie growth, behavior, and disease. Here, we describe DNA affinity purification sequencing (DAP-seq), a high-throughput TF binding site discovery method that interrogates genomic DNA with in-vitro-expressed TFs. Using DAP-seq, we defined the Arabidopsis cistrome by resolving motifs and peaks for 529 TFs. Because genomic DNA used in DAP-seq retains 5-methylcytosines, we determined that >75% (248/327) of Arabidopsis TFs surveyed were methylation sensitive, a property that strongly impacts the epicistrome landscape. DAP-seq datasets also yielded insight into the biology and binding site architecture of numerous TFs, demonstrating the value of DAP-seq for cost-effective cistromic and epicistromic annotation in any organism.

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“…Therefore, the SHR product seems to be the key signal in a short-range induction mechanism and in moving just one layer triggers endodermal differentiation from a cortical ground state adjacent to its vascular origin. The C2H2 zinc-fi nger protein JACKDAW (JKD) has been identifi ed as partner and target of SHR and SCR (Cui et al, 2007;Welch et al, 2007). JKD expression is initiated during the globular stage in a SHR/SCR independent way, but its continued expression depends on the presence of SHR and to a lesser extent SCR.…”

Section: Radial Patterning In the Ground Tissuementioning

confidence: 99%

Embryogenesis: Pattern Formation from a Single Cell

Capron

Chatfield

Provart

et al. 2009

The Arabidopsis Book

103

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During embryogenesis a single cell gives rise to a functional multicellular organism. In higher plants, as in many other multicellular systems, essential architectural features, such as body axes and major tissue layers are established early in embryogenesis and serve as a positional framework for subsequent pattern elaboration. In Arabidopsis, the apicalbasal axis and the radial pattern of tissues wrapped around it are already recognizable in young embryos of only about a hundred cells in size. This early axial pattern seems to provide a coordinate system for the embryonic initiation of shoot and root. Findings from genetic studies in Arabidopsis are revealing molecular mechanisms underlying the initial establishment of the axial core pattern and its subsequent elaboration into functional shoots and roots. The genetic programs operating in the early embryo organize functional cell patterns rapidly and reproducibly from minimal cell numbers. Understanding their molecular details could therefore greatly expand our ability to generate plant body patterns de novo, with important implications for plant breeding and biotechnology.

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Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action

Cited by 259 publications

References 29 publications

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

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

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape

Embryogenesis: Pattern Formation from a Single Cell

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