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Series GSE94486 Query DataSets for GSE94486
Status Public on Apr 25, 2018
Title A B-ARR-mediated cytokinin transcriptional network directs hormone-cross regulation and shoot development
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary While the biosynthesis, degradation, and signaling pathways for the essential plant hormone cytokinin have been extensively studied, the direct transcriptional targets of B-type ARRs, the key TFs essential for cytokinin action have not been defined. We epitope tagged four B-ARRs (1, 10, 12, and 14) using recombineering techniques and profiled TF binding sites using chromatin immunoprecipitation sequencing (ChIP-seq). The resulting cytokinin transcriptional response network allowed construction of the first cytokinin TF network, identification of numerous direct downstream targets along with the B-ARR-6BA motif and elucidation of one mechanism of activation of WUSCHEL, which requires a high concentration of cytokinin in shoot apical meristem for TF binding.
Overall design we present the profiles of in vivo DNA binding sites for the genetically redundant type-B ARABIDOPSIS RESONSE REGULATORS (B-ARRs): ARR1, ARR10, and ARR12 along with ARR14 using recombineering YFP tagged lines and subsequent chromatin immunoprecipitation sequencing (ChIP-seq) analysis. The expression and genomic protein localization of B-ARRs overlap extensively, demonstrating numerous common targets among the B-ARRs. The negative regulators of cytokinin signaling, the type-A ARRs (A-ARRs), are the top ranked targets of B-ARRs. These findings confirm an immediate negative B-ARR-driven feedback loop in cytokinin signaling. Constructing a cytokinin primary response transcriptional network revealed a recurring theme involving extensive cross-regulation both within the components of the cytokinin pathway and with other plant hormone response pathways.
Contributor(s) Xie M, Chen H, O'Neil R, Huang C, Ecker JR
Citation(s) 29686312
Submission date Feb 03, 2017
Last update date May 15, 2019
Contact name Joseph R Ecker
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (14)
GSM2476318 ARR1.2ypet_etiolated_mock
GSM2476319 ARR1.2Ypet_LD_mock
GSM2476320 ARR1.2ypet_LD_6BA
BioProject PRJNA369824
SRA SRP098817

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Supplementary file Size Download File type/resource
GSE94486_RAW.tar 7.0 Mb (http)(custom) TAR (of BED, DIFF)
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Raw data are available in SRA
Processed data provided as supplementary file

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