A PWWP Domain-Containing Protein Targets the NuA3 Acetyltransferase Complex via Histone H3 Lysine 36 trimethylation to Coordinate Transcriptional Elongation at Coding Regions

Abstract

Post-translational modifications of histones, such as acetylation and methylation, are differentially positioned in chromatin with respect to gene organization. For example, although histone H3 is often trimethylated on lysine 4 (H3K4me3) and acetylated on lysine 14 (H3K14ac) at active promoter regions, histone H3 lysine 36 trimethylation (H3K36me3) occurs throughout the open reading frames of transcriptionally active genes. The conserved yeast histone acetyltransferase complex, NuA3, specifically binds H3K4me3 through a plant homeodomain (PHD) finger in the Yng1 subunit, and subsequently catalyzes the acetylation of H3K14 through the histone acetyltransferase domain of Sas3, leading to transcription initiation at a subset of genes. We previously found that Ylr455w (Pdp3), an uncharacterized proline-tryptophan-tryptophan-proline (PWWP) domain-containing protein, copurifies with stable members of NuA3. Here, we employ mass-spectrometric analysis of affinity purified Pdp3, biophysical binding assays, and genetic analyses to classify NuA3 into two functionally distinct forms: NuA3a and NuA3b. Although NuA3a uses the PHD finger of Yng1 to interact with H3K4me3 at the 5-end of open reading frames, NuA3b contains the unique member, Pdp3, which regulates an interaction between NuA3b and H3K36me3 at the transcribed regions of genes through its PWWP domain. We find that deletion of PDP3 decreases NuA3-directed transcription and results in growth defects when combined with transcription elongation mutants, suggesting NuA3b acts as a positive elongation factor. Finally, we determine that NuA3a, but not NuA3b, is synthetically lethal in combination with a deletion of the histone acetyltransferase GCN5, indicating NuA3b has a specialized role at coding regions that is independent of Gcn5 activity. Collectively, these studies define a new form of the NuA3 complex that associates with H3K36me3 to effect transcriptional elongation. MS data are available via ProteomeXchange with identifier PXD001156. Molecular & Cellular

Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae

“…The NuA3 histone acetyltransferase complex contains three histone PTM binding domains: the Yng1 PHD finger, the Pdp3 PWWP domain, and the Taf14 YEATS domain; which show specificity for H3K4me1/2/3, H3K36me3, and H3K9ac/ H3K9cr, respectively (Taverna et al 2006;Gilbert et al 2014;Shanle et al 2015;Andrews et al 2016) (Table S1). To determine the relative contribution of each histone PTM in targeting the NuA3 complex, we reasoned that histone PTMs that promote the interaction of NuA3 with chromatin would colocalize with Sas3.…”

“…Yng1 contains a PHD finger which binds to H3K4 mono-, di-, and trimethylation, with binding affinity increasing with the number of methyl groups (Martin et al 2006;Taverna et al 2006;Shi et al 2007). Pdp3 contains a PWWP domain, which recognizes H3K36me3 (Gilbert et al 2014). Taf14, through its YEATS domain, binds to acetylated (H3K9ac) and crotonylated (H3K9cr) histone H3K9 (Shanle et al 2015;Andrews et al 2016).…”

A role for histone acetylation in regulating transcription elongation

“…Gcn5 is the HAT activity-containing subunit of the evolutionary conserved SAGA complex, and related ADA and SLIK complexes, which can acetylate histones H3 and H2B [18,19]. Two functionally distinct NuA3 complexes have been identified, NuA3a and b, which contain domains that have affinities for histone modifications found at gene promoters and ORFs respectively [20]. The SAGA complex has been mapped to the upstream activating sequences (UASs) of most Pol II transcribed genes, and has been proposed to act as a general cofactor for all Pol II transcription [21,22].…”

PWWP domains and their modes of sensing DNA and histone methylated lysines

“…5). Mutations of the residues that compose the aromatic cage abolish methylated histone peptide binding (Wang et al 2009Vezzoli et al 2010;Maltby et al 2012;Smolle et al 2012;Wen et al 2014;Gilbert et al 2014;Guo et al 2014). Moreover, this aromatic cage is a common molecular architecture found in members of the Royal superfamily.…”

“…These results first established a functional role for the PWWP domain as a methyl-lysine reader motif involved in epigenetic regulation. After the discovery that Pdp1 PWWP recognizes H4K20me1, many other PWWP domains were shown to exhibit methylated histone-binding activity, including those of BRPF1 (Vezzoli et al 2010;Wu et al 2011), DNMT3a (Dhayalan et al 2010), BRPF2 (Wu et al 2011), HDGF2 (Wu et al 2011), WHSC1 (Wu et al 2011), WHSC1L1 (Wu et al 2011), LEDGF/p75 (Pradeepa et al 2012;Eidahl et al 2013;van Nuland et al 2013), Ioc4 (Maltby et al 2012;Smolle et al 2012), ZMYND11 Wang et al 2014;Guo et al 2014), and Pdp3 (Gilbert et al 2014).…”