Histone acylations and chromatin dynamics: concepts, challenges, and links to metabolism

Abstract

In eukaryotic cells, DNA is tightly packed with the help of histone proteins into chromatin. Chromatin architecture can be modified by various post-translational modifications of histone proteins. For almost 60 years now, studies on histone lysine acetylation have unraveled the contribution of this acylation to an open chromatin state with increased DNA accessibility, permissive for gene expression. Additional complexity emerged from the discovery of other types of histone lysine acylations. The acyl group donors are products of cellular metabolism, and distinct histone acylations can link the metabolic state of a cell with chromatin architecture and contribute to cellular adaptation through changes in gene expression. Currently, various technical challenges limit our full understanding of the actual impact of most histone acylations on chromatin dynamics and of their biological relevance. In this review, we summarize the state of the art and provide an overview of approaches to overcome these challenges. We further discuss the concept of subnuclear metabolic niches that could regulate local CoA availability and thus couple cellular metabolisms with the epigenome.

Keywords: acylation; chromatin; histones; metabolism; microdomains.

Figure 1. Overview of lysine acylations on core histones and their role in chromatin compaction

(A) Increasing histone acylation levels can contribute to opening up chromatin. (B) Identified lysine acylation sites in the four core histones (Sabari et al, ; Barnes et al, ; Zhang et al, 2019a). Lysines within the N‐terminal histone tail are in bold. Selected acylations and their chemical nature are depicted (hydrophobic: blue, polar: gray, acidic: red). Abbreviations: ac—acetylation, pr—propionylation, bu—butyrylation, cr—crotonylation, bz—benzoylation, hib—2‐hydroxyisobutyrylation, bhb—β‐hydroxybutyrylation, la—lactylation, mal—malonylation, succ—succinylation, glu—glutarylation.

Figure 2. Overview of potential impacts of acylations on chromatin and exemplary in vitro approaches to study them

(A) Generation of “designer” chromatin with site‐specific acylations. The genetic code expansion approach uses an AcKRS/ tRNA_CUA pair (top panel). The incorporation of an acyl‐lysine (shown as example here: propionyl‐lysine, Kpr) at site‐specifically installed amber codons (UAG) leads to the synthesis of acylated histones. During native chemical ligation (bottom panel), the thioester of an acylated peptide (e.g., histone N‐terminus) is linked to the cysteine of the truncated histone core. Acylated histones and remaining core histones can be used to refold octamers and assemble “designer” chromatin on DNA templates. (B) Impact on nucleosome stability. FRET approaches with fluorescent dye pairs, e.g., on the DNA (yellow and pink star) allow for the quantification of nucleosome disassembly. (C) Effects of histone acylations on DNA‐histone interaction strength and nucleosome stability can be measured in an optical tweezer setup, where mononucleosomes or nucleosomal arrays can be clamped between two beads (light gray). Within an optical trap, a pulling force (F) on the lower bead displaces the upper bead in the optical trap. (D) Changes of histone tail flexibility upon lysine acylations can be studied, e.g., by NMR experiments assessing the conformation of the tails (shown here: acylated (Kpr) versus unmodified histone tail). (E) DNA origami (a nanoscale folding of DNA to create three‐dimensional shapes such as tweezers) with a flexible hinge region can be used to study the interaction between attached nucleosomes. Nucleosome interaction is reflected in a closed conformation of the DNA origami and can be quantified. (F) Specific reader proteins. Schematic interaction study using an acylated mononucleosome as a bait. Interaction partners can be identified and quantified via MS. Their interaction affinity can further be analyzed by, e.g., isothermal titration calorimetry (ITC). (G) Role of acylation in transcription. Schematic of in vitro transcription assay in which chromatin is assembled on a plasmid. The direct and indirect effects of different lysine acylations on transcriptional efficiency can be studied in a well‐controlled system.

Figure 3. Metabolic subnuclear niches

Droplet or aggregate formation within the nucleus could locally increase concentrations of metabolic enzymes, CoAs, and histone acyltransferases, thus promoting local histone acylations. The locus‐ or domain‐specific microenvironment might further help to recruit (or retain) specific readers, transcription factors as well as the transcriptional machinery. Shown here is a putative metabolic niche (with symbols for nucleosomes, metabolic enzymes, and chromatin modifiers) in which crotonyl‐CoA, succinyl‐CoA, ACSS2, and α‐KGDH are enriched. HATs such as GCN5 (KAT2A) or p300 (KAT3B) can use these CoAs to succinylate (Ksucc) and crotonylate (Kcr) histones (purple) within the niche. Unmodified exemplary nucleosomes outside the niche are shown in gray.