Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of HDA6 in 14 days old arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we generated genome-wide HDA6-binding maps of 14 days old arabidopsis. To reveal bound genes by HDA6, chimeric protein HDA6-GFP was expressed under HDA6 promoter in hda6 (HDA6pro:HDA6:GFP/ hda6). ChIP was performed using anti-GFP antibody (ab290; ABCAM), and ChIP DNA were analyzed by Illumina HiSeq 2500.
Project description:We perform genome-wide profiling of H3K9me2 in the Arabidopsis thaliana edm3 mutant. By var-seq, we identified EDM3 as a nuclear-localized protein featuring a single RNA-recognition motif (RRM). Similar to PHD finger-containing histone binding protein EDM2, EDM3 promotes high levels of H3K9me2 at RPP7 and controls transcripts of this NLR gene by suppressing proximal polyadenylation and promoting the synthesis of full-length RPP7-coding mRNAs. Our results showed that EDM3 affects levels of this epigenetic mark at a set of genes and transposons, the vast majority of which also feature EDM2-dependent H3K9me2.
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3K4me2 in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide H3K4me2 levels of 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. ChIP was performed using anti-H3K4me2 antibody (diagenode; C15410035), and ChIP DNA were analyzed by Illumina HiSeq 2500.
Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of H3Ac in 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. By obtaining sequence from chromatin immunoprecipitated DNA, we mapped genome-wide H3AC levels of 14 days old WT, hda6, ldl1/2 and hda6/ldl1/2 arabidopsis. ChIP was performed using anti-H3K9K14Ac antibody (Millipore; 06-599), and ChIP DNA were analyzed by Illumina HiSeq 2500.
Project description:Purpose: Circadian clock in plants temporally coordinates biological processes throughout the day synchronizing gene expression with environmental changes. Here, we examined the genome-wide circadian and diurnal control of Arabidopsis transcriptome using high throughout RNA-seq approach. Methods: Transcriptional and posttranscritional profiles were identified and characterized for Arabidopsis seedlings grown under continuous light or long-day condition (16 h light/8 h dark) for one day (each condition has two biological replicates). Results: We show that rhythmic posttranscriptional regulation is also a significant factor for genome-wide profile of circadian plant transcriptome. Two major posttranscriptioal mechanisms alternative splicing (AS) and alternative polyadenylation (APA) show circadian rhythmicity, resulting from the oscillation in the genes invovled in AS and APA. Conclusions: Arabidopsis circadian clock not only controls the transcription of genes, but also affects their posttranscriptional regulation through regulating AS and APA.
Project description:To understand the role of Arabidopsis histone deacetylase HDA6 in plant cold acclimation, we have employed transcriptional profiling of the hda6 mutant and its parental line under cold and control conditions to identify genes differentially expressed in the hda6 mutant under cold and control conditions. Aligent’s Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K) were used.
Project description:To understand the role of Arabidopsis histone deacetylase HDA6 in drought tolerance, we have employed transcriptional profiling of the hda6 mutant and its parental line under drought and control conditions to identify genes differentially expressed in the hda6 mutant under drought and control conditions. Aligent's Whole Arabidopsis Gene Expression Microarray (Agilent-015059, G2519F, V3, 4x44K) was used.
Project description:Use 3ʹ region extraction and deep sequencing (3'READS) and bioinformatics techniques to profile alternative polyadenylation and gene regulation in plant Arabidopsis thaliana exposed to light and darkness
Project description:To understand the role of Arabidopsis histone deacetylase HDA6 in plant cold acclimation, we have employed transcriptional profiling of the hda6 mutant and its parental line under cold and control conditions to identify genes differentially expressed in the hda6 mutant under cold and control conditions. Aligent’s Whole Arabidopsis Gene Expression Microarray (G2519F, V4, 4x44K) were used. Arabidopsis hda6 mutant axe1-5 and its parental line DR5 were grown in MS agar plates for 2 weeks (16 hours light / 8 hours dark). For cold treated sample, the plants were subjected for cold treatment at 2?C for 3 days (12 hours light / 12 hours dark). Then total RNA was prepared and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.
Project description:To understand the role of Arabidopsis histone deacetylase HDA6 in drought tolerance, we have employed transcriptional profiling of the hda6 mutant and its parental line under drought and control conditions to identify genes differentially expressed in the hda6 mutant under drought and control conditions. Aligent's Whole Arabidopsis Gene Expression Microarray (Agilent-015059, G2519F, V3, 4x44K) was used. Arabidopsis hda6 mutant axe1-5 and its parental line DR5 were grown in soil for 3 weeks (16 hours light / 8 hours dark). For drought-treated sample, the plants were subjected to drought by withhelding water supply for indicated days. Then total RNA was prepared from the above-ground tissue and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.
