BioProject

Methylation of H3 lysine 4 (H3K4me) marks transcribed elements of eukaryotic genome, and their distribution alters dynamically through developmental stages and environmental change. More...

Methylation of H3 lysine 4 (H3K4me) marks transcribed elements of eukaryotic genome, and their distribution alters dynamically through developmental stages and environmental change. These dynamic regulations are likely achieved by combinatorial work of H3K4me writers, which multi-cellular organisms carry multiple copies of. To better understand the chromatin targeting mechanisms of H3K4 methyltransferase in plants, here we comparatively characterized the seven H3K4 methyltransferases in model plants Arabidopsis. This work clarified, in combination with previous results, ATX1-5 (TRX/TRR-type methyltransferase) localizes on loci with specific sets of chromatin modifications and DNA motifs. Notably, ATX3 localizes to binding motifs of ASR3 and RAP2.11 transcriptional factors and also directly interacts with those TFs. ATXR7(SET1-type) and ATXR3 (non-canonical H3K4 methyltransferase) seemed co-transcriptional. Interestingly, ATXR3, the major H3K4me3 methyltransferase in Arabidopsis, was not associated with COMPASS, which suggests H3K4me3 regulation in plants and animals is divergent. Our work provides a foundation for understanding the regulation of H3K4 methyltransferases in plants. Overall design: Experimental design; This study contains several data series as described below. 14 ~15 dai seedling of MS plate grown Arabidopsis thaliana were used for all of the data series; 1. ChIP-seq targeting the seven H3K4 methyltransferase proteins in *Arabidopsis thaliana.* Plants expressing epitope (3x-FLAG) tagged ATX1, ATX2, ATX3, ATX4, ATX5, ATXR7 and ATXR3 were generated and their genomic localization were determined in by ChIP-seq. In duplicates for ATX3, ATX4, ATX5 and ATXR3, of which a prior study is unavailable, and single replicate for ATX1, ATX2 and ATXR7, of which ChIP-seq profiles were described previously. 2. H3, H3K4me2 and H3K4me3 ChIP-seq in WT, *atx3-1, atx4/atx5* and *atx3-1/atx4/atx5* mutants, in two replicates. 3. Transcriptome for chromatin-bound, immature RNA in WT and *atxr3* mutant. 4. H3K4me3 ChIP-seq for WT and *cdkc2*. 5. Transcriptome Start Site Sequencing 2 (TSS-seq2) for WT and atxr3 in duplicates. Less...