The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development

Abstract

Polycomb Group regulation in Arabidopsis (Arabidopsis thaliana) is required to maintain cell differentiation and allow developmental phase transitions. This is achieved by the activity of three PcG repressive complex 2s (PRC2s) and the participation of a yet poorly defined PRC1. Previous results showed that apparent PRC1 components perform discrete roles during plant development, suggesting the existence of PRC1 variants; however, it is not clear in how many processes these components participate. We show that AtBMI1 proteins are required to promote all developmental phase transitions and to control cell proliferation during organ growth and development, expanding their proposed range of action. While AtBMI1 function during germination is closely linked to B3 domain transcription factors VAL1/2 possibly in combination with GT-box binding factors, other AtBMI1 regulatory networks require participation of different factor combinations. Conversely, EMF1 and LHP1 bind many H3K27me3 positive genes up-regulated in atbmi1a/b/c mutants; however, loss of their function affects expression of a different subset, suggesting that even if EMF1, LHP1, and AtBMI1 exist in a common PRC1 variant, their role in repression depends on the functional context.

Figure 1.

Transcriptome analysis of wild type and selected atbmi1 mutants at 10 DAG. A, Volcano plots representing differentially expressed genes in atbmi1 mutants compared to wild type according to a 4-fold change and a P value of 0.05. Green color indicates significantly up-regulated genes and red color significantly down-regulated genes. B, Principal component analysis of the transcriptomes showing that wild type, atbmi1a, and atbmi1b cluster together, whereas atbmi1a/b and atbmi1a/b/c constitute two distinct clusters. C, Differentially expressed genes in the different genotypes, where the number of up- and down-regulated genes is indicated. D, Number of genes that were up-regulated in the different mutants and H3K27me3 marked in wild-type seedlings of the same age (up_K27).

Figure 2.

Genes regulated by AtBMI1A and AtBMI1B. A, Venn diagram showing the number of up_K27 genes that overlap among atbmi1a, atbmi1b, and atbmi1a/b mutants. All overlaps are significant with P < 2.2 × 10⁻¹⁶ and odds ratios >17 according to Fisher’s exact test. B, Expression of levels of genes that were apparently specifically up-regulated in atbmi1a or atbmi1b mutants in the different genotypes.

Figure 3.

Functional redundancy between AtBMI1A/B and AtBMI1C. A, Clustering analysis of genes up_K27 in atbmi1a/b and atbmi1a/b/c mutants. This is a significant overlap with P < 2.2 × 10⁻¹⁶ and an odds ratio >21 according to Fisher’s exact test. B, Expression levels in wild type, atbmi1a/b, and atbmi1a/b/c of genes from the different clusters. The color code represents normalized expression values measured in FPKM.

Figure 4.

Different gene expression patterns of atbmi1a/b weak and strong mutants. A, Venn diagram showing overlap between the genes up_K27 in atbmi1a/b weak and strong mutants. The overlap is significant with P < 2.2 × 10⁻¹⁶ and an odds ratio >15 according to Fisher’s exact test. Some representative TFs in each dataset are indicated. TFs found in the two data sets are highlighter in red. B, Key flowering genes are down-regulated in atbmi1a/b/c mutants. The color code in upper panel represents normalized expression values measured in FPKM.

Figure 5.

Interplay of AtBMI1 proteins with VAL1/2 proteins. A, Venn diagram showing overlap between the genes up_K27 in atbmi1a/b/c and val1/2 mutants. Sequence LOGOs of cis-regulatory elements enriched only in up_K27 atbmi1a/b/c and in atbmi1a/b/c and val1/2 overlapping genes. B, Co-occurrence and overlapping of ABRE/G-box and GT-box at the promoter of AtBMI1/VAL1/2 coregulated genes. P values and percentage in targets and background are indicated.

Figure 6.

AtBMI1, EMF1, and LHP1 regulatory networks. A, Comparison of genes H3K27me3 marked bound by EMF1 and misexpressed in atbmi1a/b/c and with genes up_K27 in atbmi1a/b/c. B, Venn diagram showing up_K27 genes in atbmi1a/b/c and emf1-2. C, Comparison of genes H3K27me3 marked bound by LHP1 and misexpressed in atbmi1a/b/c and with genes up_K27 in atbmi1a/b/c. D, Venn diagram showing up_K27 genes in atbmi1a/b/c and lhp1. Some overlapping and nonoverlapping representative genes are indicated. All these overlaps are significant (P values and Fisher’s exact test results are indicated).

Figure 7.

Role of AtBMI1 proteins in regulating plant development. A, AtBMI1 proteins and PRC2 promote developmental phase transitions by the repression of key regulatory genes. B, AtBMI1 and PRC2 are required to control cell proliferation and differentiation during organ growth and development through the repression of master regulators. C, PRC1 variants differing in component composition and biochemical properties may collaborate with PRC2 activity in regulating phase transitions and different developmental processes throughout plant development. VAL and ASIL1/2 or AL1 to 7 proteins may recruit AtBMI1-containing complexes to target gene promoters by binding the appropriate combination of cis-regulatory elements.