Identification of HDA15-PIF1 as a Key Repression Module Directing the Transcriptional Network of Seed Germination in the Dark
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE96848 | GEO | 2017/03/22
SECONDARY ACCESSION(S): PRJNA379933
REPOSITORIES: GEO
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Project description:Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. This SuperSeries is composed of the SubSeries listed below.
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Project description:Elucidating direct roles of natural variation in biological processes has been challenging due to the difficulty in dissecting the causal role of a gene in traits displaying continuous variation. The decision of a seed to germinate is an easily quantifiable binary choice, which makes it an ideal phenotype to assess the contribution of natural variation in adaptation of plants to begin their lifecycle under optimal conditions. seeds must integrate a complex array of environmental signals to begin their lifecycle under optimal conditions. Light availability is a crucial environmental stimulus that promotes germination in many small seed plant species including Arabidopsis thaliana. Upon perception of light by photoreceptors, phytohormones act as internal signals to coordinate germination but the karrikin (KAR) signalling pathway through the HTL/KAI2 receptor is thought to play a rudimentary role in Arabidopsis germination (REF). Here we show that the AtHTL/KAI2 pathway is required and sufficient to promote germination under low light conditions. Activation of the AtHTL/KAI2 receptor by nanomolar Karrikin2 (KAR2) concentrations or inactivation of SMAX1 bypass the light requirement for germination. By performing a screen of A. thaliana accessions that can germinate under low light conditions, we identified an accession from Afghanistan (Ara-1) which misexpressed AtKAI2/HTL and had a nearly identical transcriptional signature to the activation of AtKAI2 upon addition of KAR2 in the reference accession. Our data suggest that AtKAI2 is a central regulator of germination in natural Arabidopsis populations in response to light availability, to optimize germination timing in their ecological niche.
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Project description:This SuperSeries is composed of the following subset Series:; GSE3783: Trichostatin A (TSA) inhibition of histone deacetylase in Arabiodopsis thaliana; GSE3784: Seed germination in presence and absence of histone deaceatylase inhibitor, Trichostain A (TSA). Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. Experiment Overall Design: Refer to individual Series
2008-06-12 | E-GEOD-3799 | biostudies-arrayexpress
Project description:Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. Keywords: histone deacetylase inbibition, developmental effects
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