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. 2020 Dec 4;11:6212. doi: 10.1038/s41467-020-20089-0

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a The numbers of up- and down-DEGs identified in the selected mutants. A twofold cutoff was used for the DEG criterion. b The BAH–PHD–CPL2 complex primarily represses low-expression genes. The gene expression levels of up-DEGs were classified into four groups according to their FPKM values in Col-0 mRNA-seq. All the annotated genes serve as controls. c A Venn diagram showing the overlap of up-DEGs between the selected mutants. d A heatmap showing the expression analysis in selected mutants. The genes in the upper and lower panels represent the common 155 up-DEGs and up-DEGs of aipp2-1paipp2-1, respectively. e The distribution of different histone marks in the respective up-DEGs of selected mutants. TTS transcription termination site. f Snapshots showing the expression of the selected target genes. One representative replicate of mRNA-seq and histone ChIP-seq are shown. The adjacent genes with high H3K4me3/low H3K27me3 were also shown as parallel controls. g, h ChIP-qPCR showing the H3K27me3 (g) and H3K4me3 (h) density at the selected target genes. The ChIP signals were normalized to histone H3. The data are means ± S.D. of three technical repeats. One representative result of three biological replicates is shown. The lowercase letters represent the ChIP-qPCR examined regions as shown in f.