Abstract
Histone post-translational modifications (PTMs) are critical for processes such as transcription. The more notable among these are the nonacetyl histone lysine acylation modifications such as crotonylation, butyrylation, and succinylation. However, the biological relevance of these PTMs is not fully understood because their regulation is largely unknown. Here, we set out to investigate whether the main histone acetyltransferases in budding yeast, Gcn5 and Esa1, possess crotonyltransferase activity. In vitro studies revealed that the Gcn5-Ada2-Ada3 (ADA) and Esa1-Yng2-Epl1 (Piccolo NuA4) histone acetyltransferase complexes have the capacity to crotonylate histones. Mass spectrometry analysis revealed that ADA and Piccolo NuA4 crotonylate lysines in the N-terminal tails of histone H3 and H4, respectively. Functionally, we show that crotonylation selectively affects gene transcription in vivo in a manner dependent on Gcn5 and Esa1. Thus, we identify the Gcn5- and Esa1-containing ADA and Piccolo NuA4 complexes as bona fide crotonyltransferases that promote crotonylation-dependent transcription.
Highlights
Histone post-translational modifications (PTMs) are critical for processes such as transcription
Because a role for Gcn5 and Esa1 in crotonylation had not been properly described, we examined whether Gcn5 and Esa1 are bona fide writers of this modification in budding yeast
In contrast to a previous report suggesting that crotonylation has a stimulatory effect on transcription [11, 34], we found that transcript levels were both increased and decreased (Table S1, Fig. 4B)
Summary
Because a role for Gcn and Esa in crotonylation had not been properly described, we examined whether Gcn and Esa are bona fide writers of this modification in budding yeast. The Piccolo NuA4 complex displayed robust acetylation activity mainly toward histone H4 (Fig. 2A) [23] This activity depended on the catalytic glutamic acid residue on position 338 in Esa, because changing it to glutamine (Esa1-E338Q) abrogated acetylation, agreeing with previous reports (Fig. 2A) [29, 30]. Crotonate addition increased crotonylation on histone H3 (Fig. 3A) and this was largely dependent on the presence of the yeast acetyl-CoA synthetase enzymes Acs and Acs (Fig. 3A) To further study these crotonate-induced changes, we performed Western blot analysis of H3K9cr H3K14cr and H3K18cr in yeast chromatin following crotonate treatment (Fig. S6). The ADA/SAGA and Piccolo NuA4 complexes are able to directly regulate crotonate-induced transcription independently of histone acetylation
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