Analysis of histone ubiquitylation by MSL1/MSL2 proteins in vitro

The role of RING finger proteins in chromatin remodeling and biological functions

Mammalian DNA duplexes are highly condensed with different components, including histones, enabling chromatin formation. Chromatin remodeling is involved in multiple biological processes, including gene transcription regulation and DNA damage repair. Recent research has highlighted the significant involvement of really interesting new gene (RING) finger proteins in chromatin remodeling, primarily attributed to their E3 ubiquitin ligase activities. In this review, we highlight the pivotal role of RING finger proteins in chromatin remodeling and provide an overview of their capacity to ubiquitinate specific histones, modulate ATP-dependent chromatin remodeling complexes and interact with various histone post-translational modifications. We also discuss the diverse biological effects of RING finger protein-mediated chromatin remodeling and explore potential therapeutic strategies for targeting these proteins.

Histone Modifications, Internucleosome Dynamics, and DNA Stresses: How They Cooperate to “Functionalize” Nucleosomes

Tight packaging of DNA in chromatin severely constrains DNA accessibility and dynamics. In contrast, nucleosomes in active chromatin state are highly flexible, can exchange their histones, and are virtually “transparent” to RNA polymerases, which transcribe through gene bodies at rates comparable to that of naked DNA. Defining mechanisms that revert nucleosome repression, in addition to their value for basic science, is of key importance for the diagnosis and treatment of genetic diseases. Chromatin activity is largely regulated by histone posttranslational modifications, ranging from small chemical groups up to the yet understudied “bulky” ubiquitylation and sumoylation. However, it is to be revealed how histone marks are “translated” to permissive or repressive changes in nucleosomes: it is a general opinion that histone modifications act primarily as “signals” for recruiting the regulatory proteins or as a “neutralizer” of electrostatic shielding of histone tails. Here, we would like to discuss recent evidence suggesting that histone ubiquitylation, in a DNA stress–dependent manner, can directly regulate the dynamics of the nucleosome and their primary structure and can promote nucleosome decomposition to hexasome particles or additionally stabilize nucleosomes against unwrapping. In addition, nucleosome repression/ derepression studies are usually performed with single mononucleosomes as a model. We would like to review and discuss recent findings showing that internucleosomal interactions could strongly modulate the dynamics and rearrangements of nucleosomes. Our hypothesis is that bulky histone modifications, nucleosome inherent dynamics, internucleosome interactions, and DNA torsions could act in cooperation to orchestrate the formation of different dynamic states of arrayed nucleosomes and thus promote chromatin functionality and diversify epigenetic programming methods.

"Direct" and "Indirect" Effects of Histone Modifications: Modulation of Sterical Bulk as a Novel Source of Functionality

The chromatin-regulatory principles of histone post-translational modifications (PTMs) are discussed with a focus on the potential alterations in chromatin functional state due to steric and mechanical constraints imposed by bulky histone modifications such as ubiquitin and SUMO. In the classical view, PTMs operate as recruitment platforms for histone "readers," and as determinants of chromatin array compaction. Alterations of histone charges by "small" chemical modifications (e.g., acetylation, phosphorylation) could regulate nucleosome spontaneous dynamics without globally affecting nucleosome structure. These fluctuations in nucleosome wrapping can be exploited by chromatin-processing machinery. In contrast, ubiquitin and SUMO are comparable in size to histones, and it seems logical that these PTMs could conflict with canonical nucleosome organization. An experimentally testable hypothesis that by adding sterical bulk these PTMs can robustly alter nucleosome primary structure is proposed. The model presented here stresses the diversity of mechanisms by which histone PTMs regulate chromatin dynamics, primary structure and, hence, functionality.

The intrinsic stability of H2B-ubiquitylated nucleosomes and their in vitro assembly/disassembly by histone chaperone NAP1

BACKGROUND

Apart the gene-regulatory functions as docking sites for histone 'readers', some histone modifications could directly affect nucleosome structure. The H2BK34-ubiquitylation deposited by MOF-MSL complex, increases nucleosome dynamics in vitro and promotes donation of one H2A/H2B dimer to histone acceptors.

METHODS

We evaluated temperature-depended stability of H2BK34-ubiquitylated nucleosomes under 'physiological' ionic conditions in the presence or absence of histone acceptor, and examined assembly and disassembly of ubiquitylated nucleosomes in vitro by recombinant mouse NAP1.

RESULTS

H2BK34ub modification is sufficient to promote selective eviction of only one H2A/H2B dimer independently of histone-binding agents. Despite the robust H2A/H2B dimer-displacement effect of mNAP1 with the H2BK34ub (but not unmodified) nucleosomes, NAP1 could assemble symmetrically- or asymmetrically ubiquitylated nucleosomes under 'physiological' conditions in vitro.

CONCLUSIONS AND GENERAL SIGNIFICANCE

The increased mobility of one nucleosomal H2A/H2B dimer is an intrinsic nucleosome destabilizing property of H2BK34 ubiquitylation that has the intranucleosome bases. The ability of NAP to reasonably efficiently assemble H2BK34-ubiquitylated nucleosomes supposes a potential mechanism for deposition/distribution of H2BK34ub mark in the MOF-MSL independent manner (for example, during histone dimer exchange upon transcription elongation).