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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MGP expression depends on SHR and SCR; JKD and MGP regulate the SHR/SCR range of action.
"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"
Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis.
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 the MGP promoter with SHR and SCR.
"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 (including AtIDD3/MGP) 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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AtIDD3 acts positively in GA signalling (IDD3-SRDX).
"supported the possibility that AtIDD3 is positively involved in GA signaling"
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IDDs are DNA-binding 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"
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 retain SHR in nuclei and regulate SCR and CYCD6.
"constraining SHORT-ROOT spread through nuclear retention and transcriptional regulation of key downstream SHORT-ROOT targets, including SCARECROW and CYCLIND6"
Transcriptional control of tissue formation throughout root development.
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MGP, with JKD, BIB and NUC, is required for formative ground-tissue 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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MGP is a direct SHR target.
"Our network indicated that SCR, BLJ, JKD, MGP, and NUC are direct targets of SHR"
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Cortex marker expression requires JKD, MGP and NUC.
"Expression of cortex-specific markers required at least JKD, MGP, and NUC"
Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD.
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MGP ZF1-ZF3 bind DNA, ZF3-ZF4 bind SHR-SCR.
"of the four ZFs of MGP and possibly JKD, ZF1, ZF2 and ZF3 are responsible for DNA binding, while ZF3 and ZF4 are involved in SHR binding"
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MGP ZF1-4 binds the IDD consensus with 50 nM affinity.
"Our DNA binding assay using this consensus sequence with ZFs of MGP showed high affinity (KD value of 50 nM) for ZF1-4 (all four ZFs)"
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SHR-SCR binds MGP ZF3-ZF4 with 36 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)"
Enhanced Y1H assays for Arabidopsis.
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eY1H TF-promoter interactions for stele-expressed promoters.
"We identified 158 interactions with 13 stele-expressed promoters, many of which occur physically or are regulatory in planta"
Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.
Transcriptional regulation of nitrogen-associated metabolism and growth.
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Y1H nitrogen-metabolism transcriptional network.
"Here we present a transcriptional regulatory network and twenty-one transcription factors that regulate the architecture of root and shoot systems in response to changes in nitrogen availability"
A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis.
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Y1H PXY-mediated vascular transcriptional network.
"Here, we mapped a putative PXY-mediated transcriptional regulatory network comprising 690 transcription factor-promoter interactions in Arabidopsis"
CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.
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Massively multiplexed Y2H map of Arabidopsis TF interactions.
"uncovering a network of 8,577 interactions among 1,453 transcription factors"