Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by ARBA machine learning models
Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
Arabidopsis JACKDAW and MAGPIE zinc finger proteins delimit asymmetric cell division and stabilize tissue boundaries by restricting SHORT-ROOT action.
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JKD and MGP act in a SHR-dependent feed-forward loop restricting SHR/SCR range of action.
"JACKDAW and MAGPIE genes, which encode members of a plant-specific family of zinc finger proteins, act in a SHR-dependent feed-forward loop to regulate the range of action of SHORT-ROOT and SCARECROW"
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JKD expression is SHR-independent and it regulates the SCR domain; MGP expression is SHR/SCR-dependent.
"JACKDAW expression is initiated independent of SHORT-ROOT and regulates the SCARECROW expression domain outside the stele, while MAGPIE expression depends on SHORT-ROOT and SCARECROW"
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JKD and MGP regulate tissue boundaries and asymmetric cell division.
"JACKDAW and MAGPIE regulate tissue boundaries and asymmetric cell division and can control SHORT-ROOT and SCARECROW activity in a transcriptional and protein interaction network"
JACKDAW controls epidermal patterning in the Arabidopsis root meristem through a non-cell-autonomous mechanism.
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JKD acts non-cell-autonomously from the cortex in epidermal patterning.
"Tissue-specific induction experiments indicate non-cell-autonomous action of JKD from the underlying cortex cell layer to specify epidermal cell fate"
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JKD localizes to QC and ground tissue and delimits SHR movement.
"JACKDAW (JKD), a zinc finger protein, localizes in the quiescent centre and the ground tissue, and regulates tissue boundaries and asymmetric cell division by delimiting SHORT-ROOT movement"
Activity of transcription factor JACKDAW is essential for SHR/SCR-dependent activation of SCARECROW and MAGPIE and is modulated by reciprocal interactions with MAGPIE, SCARECROW and SHORT ROOT.
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JKD activates SCR and MGP promoter reporters in protoplasts.
"Transient expression of LUC reporter genes with the proximal sequences upstream from the ATG codon of SCR and MGP in protoplasts were activated by JKD"
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JKD binds SCR and MGP promoter sequences in yeast one-hybrid.
"Yeast one-hybrid analysis showed that JKD binds to the SCR and MGP promoter sequences"
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JKD directly regulates SCR and MGP with SHR, SCR and MGP.
"Our findings suggest that JKD directly regulates SCR and MGP expression in cooperation with SHR, SCR and MGP"
DELLA protein functions as a transcriptional activator through the DNA binding of the indeterminate domain family proteins.
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IDDs bind DELLA and the SCL3 promoter.
"we identified five members of indeterminate domain (IDD) protein family which bind physically to both DELLA and the promoter sequence of the GA-positive regulator SCARECROW-LIKE 3 (SCL3)"
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IDDs act as transcriptional scaffolds for the DELLA and SCL3 coregulators.
"These results suggest that the coregulators DELLA and SCL3, using IDDs as transcriptional scaffolds for DNA binding, antagonistically regulate the expression of their downstream targets to control the GA signaling pathway"
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Loss of AtIDD10 (JKD) increases endodermal periclinal division.
"lack of AtIDD10 causes a defect in DELLA-mediated feedback, thus resulting in increased cell division"
Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tissue Boundaries by Confining the Cell Fate Regulator SHORT-ROOT and Contributing to Fate Specification.
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BIRDs constrain SHR spread via nuclear retention and regulate SHR targets SCR and CYCD6.
"constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6"
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BIRDs tether and regulate transcriptional competence of SHR complexes.
"BIRD proteins promote formative divisions and tissue specification in the Arabidopsis thaliana root meristem ground tissue by tethering and regulating transcriptional competence of SHORT-ROOT complexes"
Transcriptional control of tissue formation throughout root development.
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JKD and BIB promote SHR nuclear retention and, with MGP and NUC, are required for formative divisions.
"JKD and BALD-IBIS regulate SHR movement by promoting its nuclear retention, and cooperatively with MAGPIE (MGP) and NUTCRACKER (NUC) are required for the formative divisions that pattern the ground tissue into cortex and endodermis"
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BLJ, JKD and SCR are essential for SHR to carry out ground tissue patterning.
"These results indicate that BLJ, JKD, and SCR are essential for SHR to carry out ground tissue patterning"
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JKD direct targets were identified by ChIP-seq.
"Among the BIRDs, we focused on BLJ and JKD because they have a specific role in ground tissue establishment and identified their direct targets through chromatin immunoprecipitation (ChIP) followed by sequencing"
Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD.
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SHR-SCR bind JKD ZF3-ZF4 and function as transcription cofactors.
"SHR-SCR function as transcription cofactors by binding to the third and fourth ZFs, (ZF3-ZF4) of JKD"
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JKD ZF1-ZF3 mediate DNA binding within the JKD-SHR-SCR complex.
"the ZF1-ZF2-ZF3 of JKD in the JKD-SHR-SCR complex is involved in DNA binding"
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SHR-SCR binds JKD ZF3-ZF4 with 124 nM affinity.
"relatively high affinity of the SHR-SCR complex to MGP ZF3-ZF4 (the KD value of 36 nM) and JKD ZF3-ZF4 (124 nM)"
In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots.
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In vivo FRET-FLIM shows cell-type-specific higher-order complexes of SHR, SCR and JKD.
"three fully functional fluorescently tagged cell fate regulators establish cell-type-specific interactions at endogenous expression levels and can form higher order complexes"
INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves.
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IDD binding sites in the SCR promoter are crucial for SCR expression.
"mutation of the -340 bp sequence eliminated most of the promoter activity, indicating that this sequence was indispensable for SCR expression"
An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants.
Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth.
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SHR and SCR directly activate CYCD6;1 at the formative division.
"Coincident with the onset of a specific formative division, SHR and SCR directly activate a D-type cyclin"