Ballare, C. | Search bioRxiv

bioRxiv2023

Alternative splicing decouples local from global PRC2 activity

The Polycomb repressive complex 2 (PRC2) mediates epigenetic maintenance of gene silencing in eukaryotes via methylation of histone H3 at lysine 27 (H3K27). This complex interacts with sets of accessory factors to form two distinct subtypes, PRC2.1 and PRC2.2, that differ in their actions and chromatin targeting mechanisms. The underlying molecular mechanisms orchestrating PRC2 assembly are not yet fully understood. Here, we report that alternative splicing (AS) of the PRC2 core component SUZ12 generates an uncharacterised isoform SUZ12-S, which co-exists with the canonical SUZ12-L isoform in the same cell in virtually all tissues and developmental stages. We show that SUZ12-S drives PRC2.1 subtype formation and favours PRC2 dimerisation. While SUZ12-S is necessary and sufficient to ensure correct repression of Polycomb target genes via promoter-proximal H3K27me3 deposition, SUZ12-L is needed for maintaining global H3K27 methylation levels. Lastly, we show that mouse embryonic stem cells (ESCs) lacking either of the two isoforms have a slower exit from pluripotency upon differentiation stimulus. Our findings thus reveal a physiological mechanism regulating PRC2 assembly and higher-order interactions, with impacts on H3K27 methylation and gene repression.

molecular biology↗

bioRxiv2023

Long noncoding RNA-mediated epigenetic regulation of auxin-related genes controlling shade avoidance syndrome in Arabidopsis thaliana

The long noncoding RNA (lncRNA) AUXIN-REGULATED PROMOTER LOOP (APOLO) recognizes a subset of target loci across the Arabidopsis thaliana genome by forming RNA-DNA hybrids (R-loop) and modulating local three-dimensional chromatin conformation. Here we show that APOLO is involved in regulating the shade avoidance syndrome (SAS) by dynamically modulating the expression of key factors. In response to far-red (FR) light, the expression of APOLO anticorrelates with its target BRANCHED1 (BRC1), a master regulator of shoot branching in Arabidopsis thaliana. APOLO deregulation results in BRC1 transcriptional repression and an increase in the number of branches. APOLO transcriptional accumulation fine-tunes the formation of a repressive chromatin loop encompassing the BRC1 promoter, which normally occurs only in leaves as well as in a late response to FR treatment in axillary buds. In addition, our data reveal that APOLO participates in leaf hyponasty, in agreement with its previously reported role in the control of auxin homeostasis through direct modulation of YUCCA2 (auxin synthesis), PID and WAG2 (auxin efflux). We found that direct application of APOLO RNA to leaves results in a rapid increase in auxin accumulation that is associated with changes in the response of the plants to FR light. Collectively, our data support the view that lncRNAs coordinate the shade avoidance syndrome in Arabidopsis thaliana and shed light on the potential of lncRNAs as bioactive exogenous molecules. Deploying exogenous RNAs that modulate plant-environment interactions are important new tools for sustainable agriculture.

plant biology↗