The CHD3 Remodeler PICKLE Promotes Trimethylation of Histone H3 Lysine 27

Abstract

CHD3 proteins are ATP-dependent chromatin remodelers that contribute to repression of developmentally regulated genes in both animal and plant systems. In animals, this repression has been linked to a multiple subunit complex, Mi-2/NuRD, whose constituents include a CHD3 protein, a histone deacetylase, and a methylCpG-binding domain protein. In Arabidopsis, PICKLE (PKL) codes for a CHD3 protein that acts during germination to repress expression of seed-associated genes. Repression of seed-associated traits is promoted in pkl seedlings by the plant growth regulator gibberellin (GA). We undertook a microarray analysis to determine how PKL and GA act to promote the transition from seed to seedling. We found that PKL and GA act in separate pathways to repress expression of seed-specific genes. Comparison of genomic datasets revealed that PKL-dependent genes are enriched for trimethylation of histone H3 lysine 27 (H3K27me3), a repressive epigenetic mark. Chromatin immunoprecipitation studies demonstrate that PKL promotes H3K27me3 in both germinating seedlings and in adult plants but do not identify a connection between PKLdependent expression and acetylation levels. Taken together, our analyses illuminate a new pathway by which CHD3 remodelers contribute to repression in eukaryotes.The transition from inert seed to growing seedling marks the culmination of a remarkable transformation in developmental identity and transcriptional programs. During seed formation, numerous genes are expressed that contribute to establishment of the body plan, laying down of storage reserves, and desiccation tolerance (1, 2). Many of these genes are widely expressed in the developing seed only to be silenced by the time the seed germinates, often for the remainder of the life cycle of the plant (3). Although several key regulators have been identified that activate various seed transcriptional programs, such as the LEAFY COTY-LEDON (LEC) genes and ABSCISIC ACID-INSENSITIVE3 (ABI3) (4, 5), relatively little is known about the mechanisms that ensure that these programs are restricted to developing seeds. This repression is critical for subsequent stages of plant development. In particular, continued expression of LEC genes leads to continued expression of seed-specific programs and substantial alteration of seedling development (6 -8).PICKLE (PKL) has previously been shown to play a significant role in repression of seed-associated genes. In pkl plants, many seed-associated traits continue to be expressed after germination, including accumulation of seed storage reserves and the ability to undergo somatic embryogenesis (9, 10). Primary roots of pkl seedlings that continue to express seed-associated developmental programs stop elongating and adopt a green tuberous phenotype referred to as the "pickle root" phenotype. PKL codes for a predicted ATP-dependent chromatin remodeling factor in the CHD3 family (11,12). In animal systems, CHD3 proteins are a component of the Mi-2/NuRD complex (13-16). This complex includes several other proteins, in...

CHD3 Proteins and Polycomb Group Proteins Antagonistically Determine Cell Identity in Arabidopsis

“…This is consistent with earlier observations by others [23]. Because we failed to detect direct binding of PKL to any of the up-regulated genes, we conclude that increased expression of these genes in pkl is an indirect effect.…”

The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci

“…One of the mechanisms by which PKL represses gene expression is by promoting H3K27me3 deposition [45, 46]. The level of H3K9me2 is tightly linked to non-CG DNA methylation [13].…”

A transcriptional view on somatic embryogenesis

“…The pkl mutant seedlings retain embryonic traits after germination and produce somatic embryos from a number of seedling tissues, coinciding with de‐repression of the LEC genes (Henderson et al., 2004; Ogas, Kaufmann, Henderson, & Somerville, 1999). CHD3 proteins are associated with histone deacetylases in animals (Torchy, Hamiche, & Klaholz, 2015), but loss of PKL in plants was found to affect global H3K27me3 levels, also at the LEC1 and LEC2 loci, rather than acetylation levels (Zhang et al., 2008). However, HDAC activity has also been shown to be required for certain pkl phenotypes in plants (Fukaki, Taniguchi, & Tasaka, 2006), and TSA treatment could to a certain extent mimic pkl phenotypes in arabidopsis calli (Furuta et al., 2011), suggesting that PKL may function by guiding both H3K27me3 and histone deacetylation.…”