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COP1 controls light-dependent chromatin remodeling in Arabidopsis [ChIP-Seq]

ABSTRACT: Light is an environmental factor that influences various aspects of plant development. Phytochromes (phys) as light sensors regulate myriads of downstream genes in response to changes in environmental factors. VIL1 (VIN3-LIKE 1)/VERNALIZATION 5 (VRN5), a Polycomb Repressive Complex 2 (PRC2) - associated protein, mediates vernalization pathway. VIL1 directly interacts with phyB and regulates photomorphogenesis through the formation of repressive chromatin loops at downstream growth-promoting genes in response to light. CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is an E3 ligase for a number of substrates in light signaling, acting as a central repressor of photomorphogenesis. Here, we show that VIL1 is a substrate of COP1 and COP1 degrades VIL1 through the ubiquitin/26S proteosome system (UPS) in the dark. Our study illustrates that COP1 controls light-dependent formation of chromatin loop by regulating the stability of VIL1 and limits a repressive histone modification to fine-tune expressions of growth-promoting genes during photomorphogenesis. We performed Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27me3 in five Arabidopsis genotypes (Col-0, vil1-1, cop1-4, vil1-1cop1-4 and hy5-215).

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE233271 | GEO | 2024/03/06

REPOSITORIES: GEO

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Project description:Although landscapes of several epigenetic marks are now available for Arabidopsis and rice, such profiles remain static and do not provide information about dynamic changes of plant epigenomes in response to developmental or environmental cues. Here we analyzed the effects of light regulation on four epigenetic histone modifications (H3K9ac, H3K9me3, H3K27ac, H3K27me3). Our genome-wide profiling of H3K9ac and H3K27ac revealed that these modifications are gene-specific. In contrast, we found that H3K9me3 and H3K27me3 target genes, but also intergenic-regions and transposable elements. Specific light conditions affected the number of epigenetically modified regions, as well as the overall correlation strength between the presence of specific epigenetic modifications and transcription. Futhermore, we observed that acetylation is an important contributor to light-regulated genome expression not only through its activating action on HY5 and HYH but also on their downstream targets. We found that dynamic acetylation changes in response to light have a major role in the active regulation of photosynthetic gene expression, while H3K27ac and H3K27me3 are major contributors to light regulation of the gibberellin metabolism. We also identified distinct epigenetic patterns in the epigenome of the photomorphogenic mutant cop1-4, suggesting that COP1 might have a role in the establishment of specific epigenetic modifications. Thus, this work provides a dynamic portrait of the variations in histone modifications in response to the plantM-bM-^@M-^Ys changing light environment and strengthens the concept that epigenetic modifications represent another layer of control for light-regulated genes involved in photomorphogenesis. Arabidopsis ecotype Columbia (Col-0) was the genetic background used for this study. Seeds were stratified for two days at 4M-BM-0C, then germinated and grown for five days at 22M-BM-0C in continuous darkness (D). Six hours before harvest, a number of plates were transferred to continuous white light (D to L). The cop1-4 mutant was also used in this study. Seedlings from the different conditions and genotypes were harvested at the same time of day. Chromatin was immunoprecipitated, washed, reverse crosslinked, amplified and hybridized according to AffymetrixM-bM-^@M-^Y Chromatin Immunoprecipitation Assay Protocol Rev.3. Three M-NM-<l of the following antibodies were used: anti-H3K9ac (Upstate 06-942), anti-H3K9me3 (Upstate 07-442), anti-H3K27ac (Upstate 07-360), anti-H3K27me3 (Upstate 07-449), and anti-H3 (Upstate 07-690). Four biological replicates were hybridized to tiling arrays.

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COP1 controls light-dependent chromatin remodeling in Arabidopsis [ChIP-Seq]

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