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Series GSE122454 Query DataSets for GSE122454
Status Public on Mar 19, 2020
Title AT-hook transcription factors repress petiole growth by antagonizing PIF4 [RNA-seq]
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary As sessile organisms, plants rely heavily on growth and developmental plasticity to respond to external challenges threatening their survival. Strict regulation of growth in organs such as hypocotyls and petioles enables plants to respond optimally to varying environmental conditions, such as changes in light and temperature, while also ensuring that resources are not needlessly wasted on unnecessary growth. Studies performed in Arabidopsis thaliana have established the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factor family as key positive regulators of growth, particularly in hypocotyls and petioles. In this study, we identify members of the AT-HOOK MOTIF NUCLEAR LOCALIZED (AHL) family, including SUPPRESSOR OF PHYTOCHROME B4-#3 (SOB3), as repressors of PIF4-mediated petiole elongation. Specifically, we found that high levels of SOB3 lead to a short-petiole phenotype similar to that conferred by removal of PIF4. Conversely, the dominant-negative sob3-6 mutant has long petioles, a phenotype which is dependent on PIF4. Additionally, we show that AHLs repress the expression of many PIF-activated genes, including a number involved in hormone-mediated promotion of growth and a subset of which are directly bound by both SOB3 and PIFs. Taken together these results suggest that AHLs repress petiole growth by antagonizing PIF-mediated transcriptional activation of growth-promoting genes, including ARABIDOPSIS THALIANA HOMEOBOX PROTEIN 2 (ATHB2), BRASSINOSTEROID INSENSITIVE 1 (BRI1), INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19), PIN-FORMED 3 (PIN3), SMALL AUXIN UP RNA 24 (SAUR24), and YUCCA8 (YUC8). Elucidating a mechanism by which positive and negative growth factors influence growth in petioles achieves a critical first step towards understanding the gene regulatory networks which modulate leaf growth in response to the environment.
Overall design Identification of AHL and PIF regulated genes in juvenile rosettes of Arabidopsis. RNA-seq was performed in triplicate for WT Col-0, sob3-6, SOB3-D, and pif4 pif5 pif7. Processed data available for download are parts per million mapped tags (ppm) for each transcript.
Contributor(s) Favero DS, Sugimoto K
Citation(s) 32197081
Submission date Nov 13, 2018
Last update date Jun 05, 2020
Contact name David Seth Favero
Phone +81-45-503-9575
Organization name RIKEN
Department CSRS
Lab Keiko Sugimoto
Street address 1-7-22 Suehirocho, Tsurumi-ku
City Yokohama
State/province International
ZIP/Postal code 230-0045
Country Japan
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (12)
GSM3466740 Col-0 RNA-seq replicate 1
GSM3466741 Col-0 RNA-seq replicate 2
GSM3466742 Col-0 RNA-seq replicate 3
This SubSeries is part of SuperSeries:
GSE122456 AT-hook transcription factors repress petiole growth by antagonizing PIF4
BioProject PRJNA505275
SRA SRP168419

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE122454_RAW.tar 2.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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