Cryoelectron tomography reveals the multiplex anatomy of condensed native chromatin and its unfolding by histone citrullination

Chromatin compaction by Polycomb group proteins revisited

The chromatin compaction activity of Polycomb group proteins has traditionally been considered essential for transcriptional repression. However, there is very little information on how Polycomb group proteins compact chromatin at the molecular level and no causal link between the compactness of chromatin and transcriptional repression. Recently, a more complete picture of Polycomb-dependent chromatin architecture has started to emerge, owing to advanced methods for imaging and chromosome conformation capture. Discoveries into Polycomb-driven phase separation add another layer of complexity. Recent observations generally imply that Polycomb group proteins modulate chromatin structure at multiple scales to reduce its dynamics and segregate it from active domains. Hence, it is reasonable to hypothesise that Polycomb group proteins maintain the energetically favourable state of compacted chromatin, rather than actively compact it.

Liquid-liquid phase separation (LLPS) in DNA and chromatin systems from the perspective of colloid physical chemistry

DNA is a highly charged polyelectrolyte and is prone to associative phase separation driven by the presence of multivalent cations, charged surfactants, proteins, polymers and colloids. The process of DNA phase separation induced by positively charged species is often called DNA condensation. Generally, it refers to either intramolecular DNA compaction (coil-globule transition) or intermolecular DNA aggregation with macroscopic phase separation, but the formation of a DNA liquid crystalline system is also displayed. This has traditionally been described by polyelectrolyte theory and qualitative (Flory-Huggins-based) polymer theory approaches. DNA in the cell nucleus is packed into chromatin wound around the histone octamer (a protein complex comprising two copies each of the four histone proteins H2A, H2B, H3 and H4) to form nucleosomes separated by linker DNA. During the last decade, the phenomenon of the formation of biomolecular condensates (dynamic droplets) by liquid-liquid phase separation (LLPS) has emerged as a generally important mechanism for the formation of membraneless organelles from proteins, nucleic acids and their complexes. DNA and chromatin droplet formation through LLPS has recently received much attention by in vitro as well as in vivo studies that established the importance of this for compartmentalisation in the cell nucleus. Here, we review DNA and chromatin LLPS from a general colloid physical chemistry perspective. We start with a general discussion of colloidal phase separation in aqueous solutions and review the original (pre-LLPS era) work on DNA (macroscopic) phase separation for simpler systems with DNA in the presence of multivalent cations and well-defined surfactants and colloids. Following that, we discuss and illustrate the similarities of such macroscopic phase separation with the general behaviour of LLPS droplet formation by associative phase separation for DNA-protein systems, including chromatin; we also note cases of segregative association. The review ends with a discussion of chromatin LLPS in vivo and its physiological significance.

Beyond the tail: the consequence of context in histone post-translational modification and chromatin research

The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.

Combining per-particle cryo-ET and cryo-EM single particle analysis to elucidate heterogeneous DNA-protein organization

Cryo-electron microscopy single particle analysis (cryo-EM SPA) and cryo-electron tomography (cryo-ET) have historically been employed as distinct approaches for investigating molecular structures of disparate sample types, focusing on highly purified biological macromolecules and in situ cellular contexts, respectively. However, these techniques offer inherently complementary structural insights that, when combined, provide a more comprehensive understanding of complex biological systems. For example, if both techniques are applied to the same purified biological macromolecules, cryo-ET has the ability to resolve highly flexible yet strong signal features on an individual target molecule which will not be preserved in the high-resolution cryo-EM SPA results. In this review, we highlight recent achievements utilizing such applications to unveil new insights into the chromatin assembly and activities of DNA-protein assemblies. This convergence of cryo-EM SPA and cryo-ET holds great promise for elucidating new structural aspects of these essential molecular processes.