The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing

Abstract

In eukaryotes, heterochromatin regions are typically subjected to transcriptional silencing. DNA methylation has an important role in such silencing and has been studied extensively. However, little is known about how methylated heterochromatin regions are subjected to silencing. We conducted a genetic screen and identified an () mutant that releases heterochromatin silencing in We demonstrated that EPCR1 functions redundantly with its paralog EPCR2 and interacts with PWWP domain-containing proteins (PWWPs), AT-rich interaction domain-containing proteins (ARIDs), and telomere repeat binding proteins (TRBs), thus forming multiple functionally redundant protein complexes named PEAT (WWPs-PCRs-RIDs-RBs). The PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing. In heterochromatin regions, the production of small interfering RNAs (siRNAs) and DNA methylation is repressed by the PEAT complexes. The study reveals how histone deacetylation, heterochromatin condensation, siRNA production, and DNA methylation interplay with each other and thereby maintain heterochromatin silencing.

Arabidopsis YAF9 histone readers modulate flowering time through NuA4‐complex‐dependent H4 and H2A.Z histone acetylation at FLC chromatin

“…Furthermore, our proteomics experiments revealed that Arabidopsis YAF9A interacted with some NuA4-C subunits, and in vivo Co-IP experiments from this work ( Fig. 7d; Dataset S2) and independent pulldown assays involving HAM proteins (Tan et al, 2018) corroborated the interaction with HAM1, consistent with YAF9A being part of this putative HAT complex in plants. Nevertheless, it cannot be ruled out that YAF9 proteins could be nonessential SWR1-C subunits or form part of additional chromatin-remodeling complexes (Zhang et al, 2004).…”

Nuclear encoded photosynthesis genes are specifically controlled by the NuA4 complex

“…1, 2, 3, 5). This unexpected result should be confronted with a recent study showing that, in addition to the pair of EPL1 orthologues described herein, A. thaliana contains two EPL1-related proteins (EPCR) 30 . Despite marginal sequence similarity to EPL1, EPCRs interact physically with HAM1 and HAM2 30 , possibly explaining why essential functions of HAMs and picNuA4 may be completed without AtEPL1.…”

“…In fact, our analysis identified only 5 proteins which show no homology to yeast NuA4 subunits as potential AtEPL1B interactors (Table 1, Supplementary Data 2). Two of these proteins, AOG2 and BRD6, were copurified with A. thaliana NuA4 subunits previously, albeit in much larger pools of additional interactors (Table 1) 24,30,36 . Interestingly, the uncharacterized bromodomain protein BRD6 37 , previously copurified with SWC4 24 and HAM1 30 (Table 1), is orthologous to BRD8, a subunit of the human equivalent of NuA4, the TIP60/p400 complex, according to PANTHER Classification System 38,39 , indicating a possible role as an accessory subunit of the plant NuA4.…”

“…A. thaliana contains two EPL1 orthologues which have been copurified with other plant NuA4 subunits previously 24,30 but have not been studied genetically. In order to investigate the function of AtEPL1, we generated a double T-DNA insertion mutant (later Atepl1-1) by crossing two publicly available lines.…”

Buried in PEAT—discovery of a new silencing complex with opposing activities

“…In this issue of EMBO Journal, Tan et al () describe a new Arabidopsis silencing complex, PEAT. This is a significant discovery because forward genetic screens have been mostly saturated and it is nowadays relatively uncommon to discover a new major silencing factor.…”