dRYBP Counteracts Chromatin-Dependent Activation and Repression of Transcription

Abstract

Chromatin dependent activation and repression of transcription is regulated by the histone modifying enzymatic activities of the trithorax (trxG) and Polycomb (PcG) proteins. To investigate the mechanisms underlying their mutual antagonistic activities we analyzed the function of Drosophila dRYBP, a conserved PcG- and trxG-associated protein. We show that dRYBP is itself ubiquitylated and binds ubiquitylated proteins. Additionally we show that dRYBP maintains H2A monoubiquitylation, H3K4 monomethylation and H3K36 dimethylation levels and does not affect H3K27 trimethylation levels. Further we show that dRYBP interacts with the repressive SCE and dKDM2 proteins as well as the activating dBRE1 protein. Analysis of homeotic phenotypes and post-translationally modified histones levels show that dRYBP antagonizes dKDM2 and dBRE1 functions by respectively preventing H3K36me2 demethylation and H2B monoubiquitylation. Interestingly, our results show that inactivation of dBRE1 produces trithorax-like related homeotic transformations, suggesting that dBRE1 functions in the regulation of homeotic genes expression. Our findings indicate that dRYBP regulates morphogenesis by counteracting transcriptional repression and activation. Thus, they suggest that dRYBP may participate in the epigenetic plasticity important during normal and pathological development.

RYBP stimulates PRC1 to shape chromatin-based communication between Polycomb repressive complexes

“…We were therefore interested to understand the molecular nature of this stimulatory activity, as it could have profound implications for how PRC1 functions in vivo. Interestingly, RYBP has been shown to function as an ubiquitin-binding protein via its zinc finger NZF domain ( Arrigoni et al, 2006 ; Fereres et al, 2014 ). We therefore reasoned that the capacity of RYBP to recognize ubiquitin, perhaps in the form of H2AK119ub1, could account for its stimulatory activity on PRC1.…”

RYBP Is a K63-Ubiquitin-Chain-Binding Protein that Inhibits Homologous Recombination Repair

“…RYBP has a ubiquitin-binding NZF domain. Interestingly, this domain is not required for the assembly of most characterized RYBP-containing complexes and their functions, including transcription (García et al, 1999;Fereres et al, 2014) and apoptosis (Danen-van Oorschot et al, 2004). Using NMR spectroscopy, we determined that this domain binds with higher affinity to K63 than K48 ubiquitin chains.…”

Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancer

“…cPRC1 binds PRC2-mediated H3K27me3 via the chromodomain of Pc (Cao et al 2002;Fischle et al 2003) and is thought to mediate repression through chromatin compaction and loop formation (Francis et al 2004;Entrevan et al 2016;Ogiyama et al 2018). Fly ncPRC1, originally named dRAF (dRing-associated factors), is defined by a core complex composed of Sce, Psc, and Kdm2 but lacks Pc and Ph and can include Rybp (Lagarou et al 2008;Fereres et al 2014). ncPRC1 couples the removal of the active H3K36me2 mark with the deposition of H2AK118ub, whereas cPRC1 lacks appreciable H2A ubiquitylation activity (Lagarou et al 2008).…”