mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases

Mitchell, Leslie A.; Huard, Sylvain; Cotrut, Michael; Pourhanifeh-Lemeri, Roghayeh; Steunou, Anne-Lise; Hamza, Akil; Zhou, Hu; Ning, Zhibin; Basu, Amrita; Côté, Jacques; Figeys, Daniel; Baetz, Kristin

doi:10.1073/pnas.1218515110

Cited by 41 publications

(41 citation statements)

References 64 publications

(95 reference statements)

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“…However, enhanced histone acetylation could not rescue all esa1D sds3D phenotypes, suggesting that balanced acetylation of both histone and nonhistone substrates of Esa1 is critical for robust growth in the absence of this essential enzyme. Supporting this idea, in proteomic studies .200 nonhistone substrates have been reported for NuA4 (Lin et al 2009;Mitchell et al 2013), and of these, at least 77 are encoded by essential genes. Substrates include components of the chromatin-remodeling complex RSC (e.g., STH1 and RSC8), proteins involved in ribosome biogenesis (e.g., NOP4 and DBP6), and cytoskeleton and spindle components (e.g., TUB2 and SPC42), whose acetylation state and role in viability in esa1D and esa1D sds3D remain to be tested.…”

Section: Discussionmentioning

confidence: 91%

Bypassing the Requirement for an Essential MYST Acetyltransferase

Torres-Machorro

Pillus

2014

Genetics

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Histone acetylation is a key regulatory feature for chromatin that is established by opposing enzymatic activities of lysine acetyltransferases (KATs/HATs) and deacetylases (KDACs/HDACs). Esa1, like its human homolog Tip60, is an essential MYST family enzyme that acetylates histones H4 and H2A and other nonhistone substrates. Here we report that the essential requirement for ESA1 in Saccharomyces cerevisiae can be bypassed upon loss of Sds3, a noncatalytic subunit of the Rpd3L deacetylase complex. By studying the esa1Δ sds3Δ strain, we conclude that the essential function of Esa1 is in promoting the cellular balance of acetylation. We demonstrate this by fine-tuning acetylation through modulation of HDACs and the histone tails themselves. Functional interactions between Esa1 and HDACs of class I, class II, and the Sirtuin family define specific roles of these opposing activities in cellular viability, fitness, and response to stress. The fact that both increased and decreased expression of the ESA1 homolog TIP60 has cancer associations in humans underscores just how important the balance of its activity is likely to be for human well-being.T HE genetic information of DNA is packed into chromatin, which is predominantly composed of the H3, H4, H2A, and H2B core histone proteins that together with DNA form nucleosomes, the basic subunits of the genome (Kornberg and Lorch 1999). Chromatin structure regulates many cellular processes including gene expression, DNA replication, DNA damage repair, and recombination (Felsenfeld and Groudine 2003). Nucleosomes themselves are tightly regulated by mobilization and positioning that are mediated by ATP-dependent chromatin-remodeling machines (Rando and Winston 2012) and by multiple types of histone posttranslational modifications that include acetylation and many other marks (Campos and Reinberg 2009).Nucleosome acetylation is a highly dynamic modification that is promoted by HATs and removed by HDACs. HATs are classified by sequence into different families (Allis et al. 2007). ESA1/KAT5 belongs to the widely conserved MYST HAT family, named for its founding members (MOZ-YBF2/ SAS3-SAS2-TIP60) (Lafon et al. 2007). Esa1 is an essential HAT in yeast (Smith et al. 1998;Clarke et al. 1999) and the catalytic subunit of two distinct multi-protein complexes: NuA4 and Piccolo (Boudreault et al. 2003). Notably, the human homolog of Esa1 is Tip60, which is also essential in vertebrates and has been linked to multiple human diseases (Squatrito et al. 2006;Avvakumov and Côté 2007;Lafon et al. 2007), thus increasing the relevance of gaining a deeper understanding of essential HAT functions.Esa1 primarily acetylates H4 and H2A in vivo (Clarke et al. 1999;Lin et al. 2008) and regulates the expression of active protein-encoding genes (Reid et al. 2000;Lin et al. 2008). It plays a crucial role in cell cycle progression and ribosomal DNA (rDNA) silencing (Clarke et al. 1999(Clarke et al. , 2006 and is recruited to DNA double-strand breaks (DSBs) to promote damage repair by acetylati...

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Section: Discussionmentioning

confidence: 91%

Bypassing the Requirement for an Essential MYST Acetyltransferase

Torres-Machorro

Pillus

2014

Genetics

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“…Future investigations might benefit from recently developed techniques, such as targeted NGS in large-scale screening and the combination of ChIP and mass spectrometry, to determine the interactome of histone modification writers and readers [96]. Highly sensitive quantitative mass spectrometry may be used as a sensitive and alternative measure, if the dynamics of histone changes must be focused and the amount of available ChIP DNA is limited [97].…”

Section: Discussionmentioning

confidence: 99%

Histone Modification Patterns and Their Responses to Environment

Dai

Wang

2014

Curr Envir Health Rpt

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Histone modifications play important roles in the epigenetic regulation of gene expression. Recent genomewide profiling of histone modifications with deep sequencingbased methods provides novel insights of crosstalk between histone modifications, leading to recent proposals of histone "language" or "web" as an alternative of "code" to appreciate combinatorial modification patterns. Environmental factor-altered histone modifications now may be addressed dynamically and systematically with the recognition and use of these interesting combinatorial patterns.

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“…Although we identified acetylation sites on 27 of these proteins in experiments employing the esa1-ts mutation, none of these sites were defined as Esa1-regulated using our stringent criteria (supplemental Tables S1 and S2). A separate study by Mitchell et al (13), identified 38 proteins acetylated by the Esa1-containing complex NuA4 in vitro. Our analysis identified four of these proteins (Esa1, Eaf3 Epl1, and Yng2 -all members of the NuA4 complex) as having high or medium confidence Esa1-regulated sites.…”

Section: Fig 7 Ada2 Selectively Regulates Gcn5-dependent Acetylationsmentioning

confidence: 99%

“…Although recent efforts have demonstrated that acetylation is a frequent post-translational modification, little is known about the regulation of most of these marks (12)(13)(14)(15). Moreover, although recruitment to chromatin is seen as the key step in acetylation of histone tails, little is known about the mechanism behind non-histone substrate selection.…”

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confidence: 99%

Acetylome Profiling Reveals Overlap in the Regulation of Diverse Processes by Sirtuins, Gcn5, and Esa1

Downey

Johnson

Davey

et al. 2015

Molecular & Cellular Proteomics

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Although histone acetylation and deacetylation machineries (HATs and HDACs) regulate important aspects of cell function by targeting histone tails, recent work highlights that non-histone protein acetylation is also pervasive in eukaryotes. Here, we use quantitative mass-spectrometry to define acetylations targeted by the sirtuin family, previously implicated in the regulation of non-histone protein acetylation. To identify HATs that promote acetylation of these sites, we also performed this analysis in gcn5 (SAGA) and esa1 (NuA4) mutants. We observed strong sequence specificity for the sirtuins and for each of these HATs. Although the Gcn5 and Esa1 consensus sequences are entirely distinct, the sirtuin consensus overlaps almost entirely with that of Gcn5, suggesting a strong coordination between these two regulatory enzymes. Furthermore, by examining global acetylation in an ada2 mutant, which dissociates Gcn5 from the SAGA complex, we found that a subset of Gcn5 targets did not depend on an intact SAGA complex for targeting. Our work provides a framework for understanding how HAT and HDAC enzymes collaborate to regulate critical cellular processes related to growth and division. Molecular & Cellular

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mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases

Cited by 41 publications

References 64 publications

Bypassing the Requirement for an Essential MYST Acetyltransferase

Bypassing the Requirement for an Essential MYST Acetyltransferase

Histone Modification Patterns and Their Responses to Environment

Acetylome Profiling Reveals Overlap in the Regulation of Diverse Processes by Sirtuins, Gcn5, and Esa1

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