Combinatorial Histone Readout by the Dual Plant Homeodomain (PHD) Fingers of Rco1 Mediates Rpd3S Chromatin Recruitment and the Maintenance of Transcriptional Fidelity

Abstract

The plant homeodomain (PHD) finger is found in many chromatin-associated proteins and functions to recruit effector proteins to chromatin through its ability to bind both methylated and unmethylated histone residues. Here, we show that the dual PHD fingers of Rco1, a member of the Rpd3S histone deacetylase complex recruited to transcribing genes, operate in a combinatorial manner in targeting the Rpd3S complex to histone H3 in chromatin. Although mutations in either the first or second PHD finger allow for Rpd3S complex formation, the assembled complexes from these mutants cannot recognize nucleosomes or function to maintain chromatin structure and prevent cryptic transcriptional initiation from within transcribed regions. Taken together, our findings establish a critical role of combinatorial readout in maintaining chromatin organization and in enforcing the transcriptional fidelity of genes.

Shaping the cellular landscape with Set2/SETD2 methylation

“…Eaf3 contains a chromo domain that recognizes H3K36me2/3 [90–94], and Rco1 contains a dual plant homeodomain (PHD) finger motif that is necessary for chromatin engagement [95] and a homo-dimerization domain [96]. Both PHD fingers are essential for chromatin binding and Rpd3S function, and both domains prefer to bind the unmodified N-terminus of H3 [97]. Interestingly, Rco1 exists as a dimer within the Rpd3S complex, adding two additional chromatin contacts to the complex [96].…”

“…Like Set2, Rpd3S can be recruited to chromatin via the phosphorylated CTD of RNAPII, specifically the Ser2/Ser5 dually phosphorylated form [98, 99]. However, without Eaf3 binding to H3K36me2/3, or without the PHD fingers of Rco1, the Rpd3S complex is catalytically inactive [95, 97]. Recent work has suggested that H3K36me stimulates a conformational change in Rpd3S that increases its affinity for chromatin, perhaps stimulating its enzymatic activity [100].…”

“…Without proper spacing, and even with proper H3K36me, the affinity of Rpd3S for chromatin is decreased to a degree where the naturally low binding affinity of Eaf3 for H3K36me2/3 is not able to sufficiently engage nucleosomes and stimulate Rpd3’s deacetylase activity. Further, Rpd3S also depends on the PHD fingers in Rco1 to maintain its localization on chromatin [95, 97]. If any of these conditions are not met, the net result is increased histone acetylation in gene bodies.…”

The Paralogous Histone Deacetylases Rpd3 and Rpd31 Play Opposing Roles in Regulating the White-Opaque Switch in the Fungal Pathogen Candida albicans

“…In contrast, ScRpd3S only decorates coding regions and employs Ser5-phosphorylated polymerase II and Set2-methylated histone H3 to suppress intragenic transcription (46). Interestingly, a recent report shows that the dual PHD fingers of ScRco1 recognize the unmodified N terminus of H3, which restricts the recruitment of ScRpd3S to promoter histones normally carrying H3K4me3 marks (47). Of note, CaRco1 also contains two PHD fingers, and all residues critical for ScRco1 function are conserved in CaRco1 (see Fig.…”

Molecular structures guide the engineering of chromatin

“…The arrangement of nucleosomes and histone PTMs at genomic target regions influences the function of multivalent PTM-binding proteins. The combined contribution of the PHD finger domain in Rco1 and the chromodomain in Eaf3 direct the histone deacetylase complex Rpd3S to active loci that are enriched H3K36me ( 58 , 110 ). Hu et al .…”