Chromatin Regulation through Ubiquitin and Ubiquitin-like Histone Modifications

Abstract

Chromatin functions are influenced by the addition, removal, and recognition of histone post-translational modifications (PTMs). Ubiquitin and ubiquitin-like (UBL) PTMs on histone proteins can function as signaling molecules by mediating protein-protein interactions. Fueled by the identification of novel ubiquitin and UBL sites and the characterization of the writers, erasers, and readers, the breadth of chromatin functions associated with ubiquitin signaling is emerging. Here, we highlight recently appreciated roles for histone ubiquitination in DNA methylation control, PTM crosstalk, nucleosome structure, and phase separation. We also discuss the expanding diversity and functions associated with histone UBL modifications. We conclude with a look toward the future and pose key questions that will drive continued discovery at the interface of epigenetics and ubiquitin signaling.

Keywords: DNA methylation; epigenetics; histones; phase separation; post-translational modifications; ubiquitin-like modifications; ubiquitination.

Figure 1 –. Regulators of histone ubiquitination.

Ubiquitin writers, erasers, and readers are organized by their associated histone targets and specific lysine residues when known. Unk; histone association is known but target lysine is not defined. Colored boxes correspond to the color of each histone in the nucleosome (PDB ID 5NL0). See also Online Supplemental Information Table S1 for references, data on E2 usage by E3 ligases, and E2 enzymes capable of E3-independent histone ubiquitination.

Figure 2 –. Ubiquitin-dependent regulation of DNA methylation maintenance.

(left) The E3 ligase UHRF1 writes multiple mono-ubiquitin sites on histone H3 and PAF15, (middle) both of which can bind to the ubiquitin interacting motif (UIM) in the replication foci targeting sequence (RFTS) of the DNMT1 maintenance DNA methyltransferase. Engagement of ubiquitinated proteins by the DNMT1 UIM enhances DNMT1’s catalytic activity to facilitate maintenance methylation. While longer H3 peptides used for crystallization (as indicated in the Figure), only residues 2–20 and 2–19 were resolved for H3K18ubK23ub and H3K9me3K18K23ub, respectively. (right) The DUB USP7 is potentially involved in DNA methylation regulation by controlling stability of other DNA methylation regulators and by directly removing H3 and other ubiquitin marks read by DNMT1. The indicated USP7 inhibitors are in various stages of preclinical evaluation.

Figure 3 -. Structural insights into ubiquitin-like proteins and nucleosomal ubiquitin.

(a) Cartoon representations of ubiquitin and ubiquitin-like domain secondary structure (upper), and electrostatic potential (lower). Alignment was performed by command cealign in PyMOL and electrostatic potential was calculated using the APBS module in PyMOL. Units are given in energy per charge (k, Boltzmann constant; T, temperature in Kelvin; e, charge of an electron). Only single UBL units are shown for ISG15 and FAT10. PDB IDs used in order of appearance are 1UBQ, 5IA7, 1NDD, 6GF1, 1Z2M, 1P0R, 4WJQ, 1WM2, 1U4A. (b) Structures of nucleosomes containing ubiquitinated histones were aligned based on the histone and DNA; H2Aub nucleosomes (upper), H2Bub nucleosomes (lower). PDB IDs for each ubiquitin are indicated by color and the nucleosome core particle is from PDB 6PX1.