The Transcription and H3K4me3 Methylation Levels of Many SAGs Are Upregulated in jmj16-1. The Transcription and H3K4me3 Methylation Levels of Many SAGs.

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The Transcription and H3K4me3 Methylation Levels of Many SAGs Are Upregulated in jmj16-1. The Transcription and H3K4me3 Methylation Levels of Many SAGs Are Upregulated in jmj16-1. (A) Venn diagram showing the overlap among genes that are transcriptionally upregulated in jmj16-1, H3K4me3 hypermethylated genes in jmj16-1, and JMJ16-HA–associated genes. (B) Venn diagram showing the overlap among SAGs from Arabidopsis LSD 2.0, H3K4me3 hypermethylated genes in jmj16-1 and JMJ16-HA-associated genes. (C) Venn diagram showing the significant overlap (Fisher’s exact test, P value = 9.64e-178) between the 370 targets from (A) and the 325 targets from (B). (D) Normalized read density of H3K4me3 ChIP-seq signals at the TSS of JMJ16 target genes in Col-0 and jmj16-1. (E) Normalized read density of JMJ16-HA ChIP-seq signals in the gene bodies of JMJ16 target genes and the same number of randomly selected genes. (F) Heatmaps of the gene body regions of JMJ16 target genes ranked by H3K4me3 levels in jmj16-1, showing concordant pattern of ChIP-seq signals of JMJ16-HA and H3K4me3 in Col-0 and jmj16-1. (G) and (K) Genome tracks of RNA-seq, anti-H3K4me3, and anti-HA ChIP-seq data for WRKY53(G) and SAG201(K) loci in Col-0, jmj16-1, and JMJ16-HA plants. Structures of WRKY53 and SAG201. R1 and R2, specific regions used for ChIP-qPCR analysis. Y axis value means normalized read counts. (H) and (L) RT-qPCR analysis of WRKY53(H) and SAG201(L) expression levels. eIF4a was used as an internal control. Error bars = ±sd (n = 3). Significant difference between Col-0 and jmj16-1 was determined by Student’s t test (****P < 0.0001). (I) and (M) ChIP-qPCR analysis of H3K4me3 methylation status at the WRKY53(I) and SAG201(M) loci. Anti-H3 and actin were used as internal references for ChIP-qPCR. Significant difference between Col-0 and jmj16-1 was determined by Student’s t test (****P < 0.0001). (J) and (N) ChIP-qPCR analysis of the association of JMJ16-HA with the WRKY53(J) and SAG201(N) locus. Specific primers corresponding to the WRKY53 R1 region and SAG201 R2 region were used in the ChIP-qPCR analysis. Actin was used as an internal control. Different letters indicate significant differences among genotypes based on one-way ANOVA with Tukey’s honestly significant difference test (P < 0.0001). Leaves 5 and 6 of 5-week–old long-day-grown Col-0, jmj16-1, and JMJ16-HA plants were used for RNA-seq, ChIP-seq, qRT-PCR, or ChIP-qPCR analyses. Error bars = ±sd (n = 3). Peng Liu et al. Plant Cell 2019;31:430-443 ©2019 by American Society of Plant Biologists