Histone H2B Deacylation Selectivity: Exploring Chromatin’s Dark Matter with an Engineered Sortase

Wang, Zhipeng A.; Whedon, Samuel D.; Wu, Mingxuan; Wang, Siyu; Brown, Edward A.; Anmangandla, Ananya; Regan, Liam; Lee, Kwang-Woon; Du, Jianfeng; Hong, Jun Young; Fairall, Louise; Kay, Taylor; Lin, Hening; Zhao, Yingming; Schwabe, John W. R.; Cole, Philip A.

doi:10.1021/jacs.1c13555

Cited by 35 publications

(31 citation statements)

References 40 publications

(74 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…8a-b ). H2BNTac is increased by class I deacetylases inhibitors in vivo and HDAC1/2 can deacetylate it in vitro 19,29 . We tagged endogenous HDAC1/2 with GFP-FKBP 12F36V , depleted HDAC1/2- GFP-FKBP 12F36V using the dTAG approach 30 , and confirmed that H2BNTac is deacetylated by HDAC1/2 ( Extended Data Fig.…”

Section: Resultsmentioning

confidence: 99%

A unique H2B acetylation signature marks active enhancers and predicts their target genes

Narita

Higashijima

Kilic

et al. 2022

Preprint

View full text Add to dashboard Cite

Chromatin features are widely used for genome-scale mapping of enhancers. However, discriminating active enhancers from other cis-regulatory elements, predicting enhancer strength, and identifying their target genes remains challenging. Here we establish histone H2B N-terminus multisite lysine acetylation (H2BNTac) as a genuine signature of active enhancers. H2BNTac prominently marks candidate active enhancers and their target promoters and discriminates them from ubiquitously active promoters. Two mechanisms afford the distinct H2BNTac specificity. (1) Unlike H3K27ac, H2BNTac is specifically catalyzed by CBP/p300. (2) H2A-H2B, but not H3-H4, are rapidly exchanged through transcription-induced nucleosome remodeling. H2BNTac-positive candidate enhancers show a high validation rate in orthogonal enhancer activity assays, and a vast majority of endogenously active enhancers are marked by H2BNTac and H3K27ac. Notably, H2BNTac intensity predicts enhancer strength and outperforms the current state-of-the-art models in predicting enhancer target genes. These findings have broad implications for generating fine-grained enhancer maps and modeling enhancer-dependent gene regulation.

show abstract

Section: Resultsmentioning

confidence: 99%

A unique H2B acetylation signature marks active enhancers and predicts their target genes

Narita

Higashijima

Kilic

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“… 120 Most recently this approach has been used by Wang et al in combination with a HPXTG-specific sortase to generate a wide range of engineered histone H2B variants with complexly modified N-termini. 121 …”

Section: Substrate Engineering To Enhance Product Yieldmentioning

confidence: 99%

Challenges in the use of sortase and other peptide ligases for site-specific protein modification

2022

View full text Add to dashboard Cite

show abstract

“…A recent study showed that, out of six HDAC1-containing nuclear complexes, only the mitotic deacetylase complex (MiDAC) and the arginine-glutamic acid dipeptide repeats (RERE) could remove K(L-la) marks from histone H2B lysine 11 (H2BK11) on nucleosomes in vitro. 24 Importantly, HDAC1-3 are targets of approved cancer chemotherapy and histone K(L-la) accumulation might therefore be involved in the observed epigenetic effects of HDAC inhibitors. 4,25 Sirtuins 1 and 2 are poor delactylases on peptide substrates, with catalytic efficiencies ~1000 times lower than that of HDAC3, 26 but they can remove K(L-la) modifications from histones upon extended incubation times.…”

Section: L-lactylationmentioning

confidence: 99%

“…3 More recently, we interrogated the activity of HDAC3 using diastereomerically pure substrates and found a clear preference for K(D-bhb) modifications compared to K(L-bhb) in vitro (~12 times higher kcat/KM). 4 Similar to K(L-la), there are multiple deacylases in the cell that are capable of removing K(D/Lbhb); HDAC1-3 and SIRT1/2 show activity on extracted histones, 9 the MiDAC complex presents activity on nucleosomes bearing H2BK11(D-bhb), 24 and HDAC1-3 are the most efficient de-b-hydroxybutyrylases in the cell. 9 However, it is often unclear to what extent these activities serve as regulatory mechanisms of K(D-bhb) modifications in vivo.…”

Section: D-b-hydroxybutyrylationmentioning

confidence: 99%

Chiral Posttranslational Modification to Lysine epsilon-Amino Groups

Moreno–Yruela

Bæk

Monda

et al. 2022

Preprint

View full text Add to dashboard Cite

The sophistication of proteomic analysis has revealed that protein lysine residues are posttranslationally modified by a variety of acyl groups. Protein lysine acetylation regulates metabolism, gene expression, and microtubule formation and has been extensively studied; however, the understanding of the biological significance of other acyl posttranslational modifications (PTMs) is still in its infancy. The acylation of lysine residues is either mediated by acyltransferase ‘writer’ enzymes or through non-enzymatic mechanisms and hydrolase enzymes, termed ‘erasers’, cleave various acyl PTMs to reverse the modified state. We have studied the human lysine deacylase enzymes, comprising the 11 Zn2+-dependent histone deacetylases (HDACs) and the 7 NAD+-consuming sirtuins (SIRTs), over the last decade. We have thus developed selective inhibitors and molecular probes as well as studied the acyl substrate scope of each enzyme using chemically synthesized peptide substrates and photo-crosslinking probes. Recently, we have turned our attention to lysine PTMs containing a stereogenic center, such as -N--hydroxybutyryllysine (Kbhb) and -N-lactyllysine (Kla), that each comprise a pair of mirror image stereoisomers. Both modifications are found on histones, where they affect gene transcription in response to specific metabolic states, and they are found on cytosolic and mitochondrial enzymes involved in fatty acid oxidation (Kbhb) and glycolysis (Kla), respectively. Thus, chiral modifications to lysine side chains give rise to two distinct diastereomeric products, with separate metabolic origins and potentially different activities exhibited by writer and eraser enzymes. Lysine L-lactylation derives from L-lactate, a major energy carrier produced from pyruvate after glycolysis, and it is highly induced by metabolic states such as the Warburg effect. L-Lactate can possibly be activated by acyl-coenzyme A (CoA) synthetases and transferred to lysine residues by histone acetyltransferases such as p300. D-Lactylation, on the other hand, arises primarily from a non-enzymatic reaction with D-lactylglutathione, an intermediate in the glyoxalase pathway. In addition to their distinct origin, we found that both K(L-la) and K(D-la) modifications are erased by HDACs with different catalytic efficiencies. Also, K(L-bhb) and K(D-bhb) arise from different metabolites but depend on interconnected metabolic pathways, while the two stereoisomers of -N-3-hydroxy-3-methylglutaryllysine (Khmg) derive from a single precursor that may then be regulated differently by eraser enzymes. Distinguishing between the individual stereoisomers of PTMs is therefore of crucial importance. In the present Account, we will (1) revisit the long-standing evidence for distinct production and dynamics of enantiomeric forms of chiral metabolites that serve as epsilon-N-acyllysine PTMs and (2) highlight the outstanding questions that arise from the recent literature on chiral lysine PTMs resulting from these metabolites.

show abstract

Histone H2B Deacylation Selectivity: Exploring Chromatin’s Dark Matter with an Engineered Sortase

Cited by 35 publications

References 40 publications

A unique H2B acetylation signature marks active enhancers and predicts their target genes

A unique H2B acetylation signature marks active enhancers and predicts their target genes

Challenges in the use of sortase and other peptide ligases for site-specific protein modification

Chiral Posttranslational Modification to Lysine epsilon-Amino Groups

Contact Info

Product

Resources

About