Molecule of the Month: Histone Ubiquitination and Deubiquitination Complexes

In each of our cells, the roughly two meters of DNA making up our genome is wrapped around proteins called histones, enabling the high level of compaction required to fit inside the nucleus. The basic organizational unit of our genome is the nucleosome, which contains DNA wrapped around a protein core containing four distinct histones. These proteins are not simply passive spools, however. Histones are decorated with many different chemical marks that influence which genes are active and which remain silent. Among the most consequential of these marks is the covalent attachment of a small protein called ubiquitin.

Ubiquitin is perhaps most famous for flagging damaged or unwanted proteins for destruction by the proteasome. But when a single ubiquitin is attached to histones, the consequences are entirely different: rather than tagging the histone for destruction, the monoubiquitin tag acts as a molecular signal that changes how the chromosome is read.

Attaching ubiquitin to a histone (or any other protein) requires a chain of three enzymes working in sequence: an E1 activating enzyme, an E2 conjugating enzyme, and an E3 ubiquitin ligase that brings the ubiquitin-loaded E2 enzyme into contact with the correct lysine on the correct protein. There are estimated to be over 600 E3 ligases in the human genome that are highly specialized for different classes of protein substrates.

Although there are many lysines on histones that can be monoubiquitinated, two sites have been found to be particularly important. Monoubiquitination of histone H2A at lysine 119 (H2AK119) is a hallmark of silenced genes. It is placed there by the polycomb repressive complex 1 (PRC1), an E3 ubiquitin ligase and a key regulator of developmental genes. When PRC1 tags H2AK119, it helps keep developmental switches in the "off" position, ensuring, for example, that liver cells do not accidentally start producing proteins needed only in neurons. The PRC1 ubiquitination module, from pdb_00004r8p and shown on the right, shows Ring1B and Bmi1 (yellow), the catalytic RING domain pair that act together as the E3 ubiquitin ligase, clamped to the nucleosome surface, with the E2 enzyme UbcH5c (orange) positioned directly above H2AK119.

A second major site of monoubiquitination is histone H2B at lysine 120 (H2BK120). This mark has the opposite effect: it is found on actively transcribed genes and helps transcription machinery access DNA. The E3 ligase that places this activating mark is called Bre1 in yeast and RNF20-RNF40 in humans, and is shown in the figure on the right (pdb_00008ieg and pdb_00008t3y, yellow). The E2 enzyme, called Rad6, is shown in orange. Similarly to PRC1, the RING domains of Bre1 ensure precise positioning adjacent to the H2BK120 site. Both PRC1 and Bre1-Rad6 interact with a negatively charged acidic patch on the H2A/H2B surface of the nucleosome, a "landing pad" used by many other chromatin regulators.

Just as important as placing ubiquitin marks is removing them so that the cell can turn genes on and off as needed, for example, during different stages of development. The protein complexes responsible for removing ubiquitins are known as deubiquitinases, or DUBs. Histone DUBs are proteases that must act with extraordinary selectivity, severing only the isopeptide bond linking a single ubiquitin molecule to a specific lysine residue on a specific histone.

The SAGA DUB module removes the active transcription mark on H2BK120. SAGA is a large co-activator complex involved in the activation of hundreds of genes. Buried within it is a four-protein DUB subcomplex (shown on the left, pdb_00004zux) that precisely removes ubiquitin from H2B. Recognition of its nucleosome substrate is mediated by the interaction of a zinc finger on the SAGA DUB with the nucleosome acidic patch. This interaction positions the catalytic subunit directly above the ubiquitin attached to H2BK120.

Removing ubiquitin from H2AK119 involves different DUB complexes. One of these, called PR-DUB, is composed of the catalytic enzyme BAP1 and a regulatory partner from the ASXL family. PR-DUB removes ubiquitin from H2AK119 when it is not needed, preventing inappropriate gene silencing. Intriguingly, both BAP1 and ASXL1 are among the most frequently mutated proteins in human cancers, making this complex a major subject of medical research. The structure of PR-DUB (shown on the left, pdb_00008h1t and also in pdb_00008svf) revealed that ASXL1 pulls the tail of H2A away from the nucleosome surface to expose the ubiquitin for cleavage, providing an explanation of how PR-DUB targets only the ubiquitin ligated to H2AK119 and ignores the other ubiquitin marks on the same nucleosome.