Structural insights into the π-π-π stacking mechanism and DNA-binding activity of the YEATS domain

Klein, Brianna J.; Vann, Kendra R.; Andrews, Forest H.; Wang, Wesley Wei; Zhang, Jibo; Zhang, Yi; Beloglazkina, Anastasia A.; Mi, Wenyi; Li, Yuanyuan; Li, Haitao; Shi, Xiaobing; Kutateladze, Andrei G.; Strahl, Brian D.; Liu, Wenshe Ray; Kutateladze, Tatiana G.

doi:10.1038/s41467-018-07072-6

Cited by 49 publications

(58 citation statements)

References 36 publications

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“…Though future work is warranted, these findings offer a new avenue to pinpoint the role of benzoyl-CoA metabolism in gene regulation and beyond. Moreover, our structural studies provide key insights into molecular engineering of preference-switched acylation readers, an intriguing strategy that has been adopted to explore the functional importance of histone modification and its readout ( 51 , 52 ).…”

Section: Discussionmentioning

confidence: 99%

Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins

Ren

Zhou

Xue

et al. 2020

Nucleic Acids Research

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Histone modifications and their functional readout serve as an important mechanism for gene regulation. Lysine benzoylation (Kbz) on histones is a recently identified acylation mark associated with active transcription. However, it remains to be explored whether putative readers exist to recognize this epigenetic mark. Here, our systematic binding studies demonstrated that the DPF and YEATS, but not the Bromodomain family members, are readers for histone Kbz. Co-crystal structural analyses revealed a ‘hydrophobic encapsulation’ and a ‘tip-sensor’ mechanism for Kbz readout by DPF and YEATS, respectively. Moreover, the DPF and YEATS family members display subtle yet unique features to create somewhat flexible engagements of different acylation marks. For instance, YEATS2 but not the other YEATS proteins exhibits best preference for Kbz than lysine acetylation and crotonylation due to its wider ‘tip-sensor’ pocket. The levels of histone benzoylation in cultured cells or in mice are upregulated upon sodium benzoate treatment, highlighting its dynamic regulation. In summary, our work identifies the first readers for histone Kbz and reveals the molecular basis underlying Kbz recognition, thus paving the way for further functional dissections of histone benzoylation.

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Section: Discussionmentioning

confidence: 99%

Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins

Ren

Zhou

Xue

et al. 2020

Nucleic Acids Research

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“…When OD reached to 0.6, H3 expression was induced at 37 °C by adding 0.5 mM IPTG, 0.2% (w/v) l -arabinose and 5 mM AcK into cell culture. Cells were harvested 6 h after induction, and purified in the same steps as previously reported 51 . The whole procedure of CrK ( N -ε-crotonyl- l -lysine) incorporation into the K14 position of histone H3 was identical with AcK incorporation, except that pEVOL-MmPylRS-384W vector was used, and 1 mM of CrK ( N -ε-crotonyl- l -lysine) was added into 2YT medium after induction.…”

Section: Methodsmentioning

confidence: 99%

Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation

et al. 2019

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Acetylation of histone H3K23 has emerged as an essential posttranslational modification associated with cancer and learning and memory impairment, yet our understanding of this epigenetic mark remains insufficient. Here, we identify the native MORF complex as a histone H3K23-specific acetyltransferase and elucidate its mechanism of action. The acetyltransferase function of the catalytic MORF subunit is positively regulated by the DPF domain of MORF (MORFDPF). The crystal structure of MORFDPF in complex with crotonylated H3K14 peptide provides mechanistic insight into selectivity of this epigenetic reader and its ability to recognize both histone and DNA. ChIP data reveal the role of MORFDPF in MORF-dependent H3K23 acetylation of target genes. Mass spectrometry, biochemical and genomic analyses show co-existence of the H3K23ac and H3K14ac modifications in vitro and co-occupancy of the MORF complex, H3K23ac, and H3K14ac at specific loci in vivo. Our findings suggest a model in which interaction of MORFDPF with acylated H3K14 promotes acetylation of H3K23 by the native MORF complex to activate transcription.

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“…The AF9 YEATS domain can bind to several K Cr marks on histone H3 (K9, K18, K27) as well as K Pr and K Bu marks [105], while Taf14 binds preferentially to H3K9 Cr [106] and YEATS2 to H3K27 Cr [107]. Using a mutated version of TAF14 designed to selectively bind H3K9 Cr over H3K9 Ac ; Klein et al [108] were able to show that there may be a differential requirement of H3K9 Ac and H3K9 Cr in the expression of TAF14-regulated genes. More recently it has been suggested that the YEATS domain of GAS41 is a pH-dependent reader of H3K122 Succ [109], hinting that there may be a further expansion of the reading capabilities of the YEATS domain family (reviewed in [110]).…”

Section: Physiological Roles Of Diverse Acylationsmentioning

confidence: 99%

Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription

Barnes

English

Cowley

2019

Essays in Biochemistry

173

142

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Packaging the long and fragile genomes of eukaryotic species into nucleosomes is all well and good, but how do cells gain access to the DNA again after it has been bundled away? The solution, in every species from yeast to man, is to post-translationally modify histones, altering their chemical properties to either relax the chromatin, label it for remodelling or make it more compact still. Histones are subject to a myriad of modifications: acetylation, methylation, phosphorylation, ubiquitination etc. This review focuses on histone acylations, a diverse group of modifications which occur on the ε-amino group of Lysine residues and includes the well-characterised Lysine acetylation. Over the last 50 years, histone acetylation has been extensively characterised, with the discovery of histone acetyltransferases (HATs) and histone deacetylases (HDACs), and global mapping experiments, revealing an association of hyperacetylated histones with accessible, transcriptionally active chromatin. More recently, there has been an explosion in the number of unique short chain ‘acylations’ identified by MS, including: propionylation, butyrylation, crotonylation, succinylation, malonylation and 2-hydroxyisobutyrylation. These novel modifications add a range of chemical environments to histones, and similar to acetylation, appear to accumulate at transcriptional start sites and correlate with gene activity.

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Structural insights into the π-π-π stacking mechanism and DNA-binding activity of the YEATS domain

Cited by 49 publications

References 36 publications

Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins

Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins

Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation

Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription

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