PRC2-Mediated H3K27me3 Contributes to Transcriptional Regulation of FIT-Dependent Iron Deficiency Response

Abstract

Iron is an essential micronutrient for nearly all organisms, but excessive iron can lead to the formation of cytotoxic reactive oxygen species. Therefore, iron acquisition and homeostasis must be tightly regulated. Plants have evolved complex mechanisms to optimize their use of iron, which is one of the most limiting nutrients in the soil. In particular, transcriptional regulation is vital for regulating iron in plants, and much work has revealed the role of transcription factors on this front. Our study adds novel insights to the transcriptional regulation of iron homeostasis in plants by showing that chromatin remodeling via histone 3 lysine 27 trimethylation (H3K27me3) modulates the expression of FIT-dependent genes under iron deficiency. We provide evidence that FIT-dependent iron acquisition genes, IRT1 and FRO2 , as well as FIT itself are direct targets of PRC2-mediated H3K27me3. In the clf mutant, which lacks the predominant H3K27 tri-methyltransferase, induction of FIT , FRO2 , IRT1 , and other FIT-regulated genes in roots is significantly higher under iron deficient conditions than in wild type. Furthermore, we observe that clf mutants are more tolerant to iron deficiency than wild type, indicating that gene expression levels appear to be limiting the plants ability to access iron. We propose that H3K27me3 attenuates the induction of FIT-target genes under iron deficiency and hypothesize that this may serve as a mechanism to restrict the maximum level of induction of iron acquisition genes to prevent iron overload.

Ferroportin 3 is a dual-targeted mitochondrial/chloroplast iron exporter necessary for iron homeostasis in Arabidopsis

“…Staining in the shoots was similar under both iron conditions. This observation corroborates our RT-qPCR results in which FPN3 transcript level was approximately 4.5-fold higher in iron-deficient roots (Figure 3L), and is consistent with transcriptomics studies that reported higher steady state levels of FPN3 transcripts in iron-deficient roots (Mai et al , 2016; Dinneny et al , 2008; Yang et al , 2010; Park et al , 2019; Khan et al , 2018; Buckhout et al , 2009). Meanwhile, the constitutive expression of FPN3 was detected in the shoots regardless of the iron status of the plant (Figure 3I, L).…”

“…We note that our data contradicts the results of Conte et al (2009), who reported the down-regulation of MAR1 expression in low iron conditions by RT-qPCR with whole seedlings. However, multiple transcriptomics datasets corroborate our results and show that FPN3/IREG3 transcript level is higher in wild type roots under iron deficiency (Mai et al , 2016; Dinneny et al , 2008; Yang et al , 2010; Park et al , 2019; Khan et al , 2018; Buckhout et al , 2009) but is not iron-regulated in shoots (Khan et al , 2018; Rodríguez-Celma et al , 2013). The differential expression of FPN3 in roots and shoots under iron-deficient or iron-sufficient conditions (Figure 3G-L) implies that FPN3 might contribute to different physiological roles in roots and shoots.…”

Epigenetic regulation: another layer in plant nutrition

“…Epigenomic studies have associated H3K27me3 enrichment with iron acquisition genes, which led to further investigate the role of CLF in iron homeostasis. 26 CLF was shown to inhibit IRT1, FRO2 and FIT under iron sufficient conditions by H3K27me3 deposition. These marks are removed upon iron starvation allowing the expression of these key genes.…”

“…48 Under iron sufficient conditions two repressive marks, H4R3me2 and H3K27me3, have been shown to repress the expression of genes involved in iron homeostasis. 25,26 H4R3me2 is known to be deposited by SHK1 BINDING PROTEIN 1 (SKB1) which belongs to the protein arginine methyltransferase (PRMTs) family. 49 Microassay analysis performed on the skb1-1 mutant exhibited a higher expression of BHLH transcription factors involved in iron homeostasis.…”

Histone H3 lysine4 trimethylation‐regulated GRF11 expression is essential for the iron‐deficiency response in Arabidopsis thaliana

“…Shk1 BINDING PROTEIN1 (SKB1) negatively regulates Fe homeostasis by catalyzing the symmetric dimethylation of histone H4 argenine3 (H4R3sme2) at the chromatin of bHLH38 , bHLH39 , bHLH100 and bHLH101 (Fan et al ., 2014). In addition, POLYCOMB REPRESSIVE COMPLEX2 (PRC2) mediates histone H3 lysine27 trimethylation (H3K27me3) of the FIT dependent Fe‐deficiency response (Park et al ., 2019) and it also regulates the expression of Fe‐translocation genes in the shoot by specifically targeting YELLOW STRIPE LIKE1 ( YSL1 ) and IRON MAN1 ( IMA1 ) (Park et al ., 2020), and GENERAL CONTROL NON‐REPRESSED PROTEIN5 (GCN5) along with some histone deacetylases (HDACs), especially HDA7, have been reported to regulate the expression of FRD3 , a citrate effluxer for Fe distribution, by modulating its acetylation level in Arabidopsis (Xing et al ., 2015). Moreover, the role of H3K4me3, an activation mark on histone modification, has also been reported where Fe storage genes, FERRITIN1 ( FER1 ), FER3 and FER4 , exhibited an enhanced H3K4me3 level at the promoter region under an Fe‐sufficient condition (Tissot et al ., 2019).…”