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Genome-wide transcriptome and epigenome data analysis of kaku4-2 mutant and WT plants

ABSTRACT: We conducted ChIP-seq technology to generate epigenomic profiles of H3K4me3, H3K27me3 and H3K9me2 in Arabidopsis leaves for the mutant (kaku4-2) and wild-type (WT) plants. The results showed that knockdown of KAKU4 has the strongest effect on H3K27me3, followed by H3K9me2, and the least effect on H3K4me3, leading to significant change of chromatin states in Arabidopsis genome. KAKU4 may affect the switch between active and repressive chromatin states, especially knockdown of KAKU4 caused the transition between H3K9me2 and H3K27me3 in some specific PLAD regions. The combination analysis of epigenomic and transcriptomic data between kaku4-2 mutant and WT suggested that KAKU4 may regulate some key biological processes, especially programmed cell death and hormone signaling pathways.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE247174 | GEO | 2024/02/29

REPOSITORIES: GEO

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Project description:The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-4. In plants, timely transition to a flowering state is crucial for successful reproduction5-7. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis8,9. Here, we revealed that bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules of EBS bind H3K27me3 and H3K4me3, respectively. A subset of EBS-associated genes was co-enriched with H3K4me3, H3K27me3, and the Polycomb repressor complex 2 (PRC2). Interestingly, EBS adopts an auto-inhibition mode to mediate its binding preference switch between H3K27me3 and H3K4me3. This binding balance is critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induces EBS-mediated early floral transition. This study identifies a single bivalent chromatin reader capable of recognizing two antagonistic histone marks and reveals a distinct mechanism of interplay between active and repressive chromatin states.The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-4. In plants, timely transition to a flowering state is crucial for successful reproduction5-7. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis8,9. Here, we revealed that bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules of EBS bind H3K27me3 and H3K4me3, respectively. A subset of EBS-associated genes was co-enriched with H3K4me3, H3K27me3, and the Polycomb repressor complex 2 (PRC2). Interestingly, EBS adopts an auto-inhibition mode to mediate its binding preference switch between H3K27me3 and H3K4me3. This binding balance is critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induces EBS-mediated early floral transition. This study identifies a single bivalent chromatin reader capable of recognizing two antagonistic histone marks and reveals a distinct mechanism of interplay between active and repressive chromatin states.v

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Genome-wide transcriptome and epigenome data analysis of kaku4-2 mutant and WT plants

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