The Arabidopsis epigenetic regulator ICU11 as an accessory protein of Polycomb Repressive Complex 2

Abstract

Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification ofArabidopsisINCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs).ICU11encodes a 2-oxoglutarate–dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of theArabidopsisepigenome. To investigate its primary molecular function we identified theArabidopsis FLOWERING LOCUS C(FLC) as a direct target and foundicu11disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization.icu11prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site inFLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states atFLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states.

H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots

“…In addition, our results indicate that chromatin accessibility can be further reduced by EMF1. This plant-specific protein has been shown to associate with PRC2 and to be required for H3K27me3 marking 19,[21][22][23][24][25] . Accordingly, loss of EMF1 function affected H3K27me3 levels but not H2AK121ub.…”

“…However, recent data showed that EMF1 co-purifies with PRC2 (refs. [21][22][23] ) and is required for H3K27me3 marking 19,24,25 . Likewise, LHP1 was proposed to perform similar function to Drosophila PRC1 component Polycomb (Pc) 26,27 ; however, LHP1 also co-purifies with PRC2 (refs.…”

“…Likewise, LHP1 was proposed to perform similar function to Drosophila PRC1 component Polycomb (Pc) 26,27 ; however, LHP1 also co-purifies with PRC2 (refs. [21][22][23] ) and is involved in maintenance/spreading of H3K27me3 (ref. 21 ) but dispensable for H2AK121ub marking 28 .…”

Post-Embryonic Phase Transitions Mediated by Polycomb Repressive Complexes in Plants

“…EOL1 physically interacts with LHP1 and CLF, and together they mediate the deposition of H3K27me3, suggesting that EOL1 assists with the activities of PRC1 and PRC2 [ 98 ]. INCURVATA11 ( ICU11 ), encoding a 2-oxoglutarate-dependent dioxygenase, has been reported to have histone demethylation activity in other organisms [ 99 , 100 ]. In Arabidopsis , the icu11 mutant resembles clf leaves by having upward curly leaves.…”

“…Mutations in icu11 and its close paralog cupuliformis2 ( cp2 )result in flowering without any vegetative growth, mimicking emf1 or emf2 mutants [ 100 ]. ICU11 robustly interacts with PRC2 core components and binds to the nucleation region of FLC to mediate the demethylation of H3K36me3 (an active marker at FLC ) ( Figure 4 b), suggesting that it controls the switch between H3K36me3 and H3K27me3 at FLC [ 99 ]. Together, ALP1, EOL1, ICU11, and CP2 are accessory proteins of PRC2.…”