Liquid phase condensation in cell physiology and disease

Deciphering the molecular mechanism underlying morphology transition in two-component DNA-protein cophase separation

Nucleic acid and protein co-condensates exhibit diverse morphologies crucial for fundamental cellular processes. Despite many previous studies that advanced our understanding of this topic, several interesting biophysical questions regarding the underlying molecular mechanisms remain. We investigated DNA and human transcription factor p53 co-condensates-a scenario where neither dsDNA nor the protein demonstrates phase-separation behavior individually. Through a combination of experimental assays and theoretical approaches, we elucidated: (1) the phase diagram of DNA-protein co-condensates at a certain observation time, identifying a phase transition between viscoelastic fluid and viscoelastic solid states, and a morphology transition from droplet-like to "pearl chain"-like co-condensates; (2) the growth dynamics of co-condensates. Droplet-like and "pearl chain"-like co-condensates share a common initial critical microscopic cluster size at the nanometer scale during the early stage of phase separation. These findings provide important insights into the biophysical mechanisms underlying multi-component phase separation within cellular environments.

Bioinspired programmable coacervate droplets and self-assembled fibers through pH regulation of monomers

Phase separation and phase transitions pervade the biological domain, where proteins and RNA engage in liquid-liquid phase separation (LLPS), forming liquid-like membraneless organelles. The misregulation or dysfunction of these proteins culminates in the formation of solid aggregates via a liquid-to-solid transition, leading to pathogenic conditions. To decipher the underlying mechanisms, synthetic LLPS has been examined through complex coacervate formation from charged polymers. Nonetheless, temporal control over phase transitions from prebiotically relevant small organic synthons remains largely unexplored. Herein, we propose utilizing pH modulation to regulate the charge of small molecular building blocks, thereby controlling the LLPS process. Through a bio-inspired, enzyme-mediated pH-regulated reaction, we introduce temporal control over both LLPS and the transition from coacervates to supramolecular polymers. Additionally, by incorporating antagonistic pH modulators, we achieve transient LLPS and further temporal regulation of supramolecular polymer disassembly. Our investigation into pH-regulated LLPS provides a new avenue for exploring the stimuli-responsive, dynamic, and transient nature of LLPS.

Fluorescence Loss After Photoactivation (FLAPh): A Pulse-Chase Cellular Assay for Understanding Kinetics and Dynamics of Viral Inclusions

Influenza A virus (IAV) relies on host cellular machinery for replication. Upon infection, the eight genomic segments, independently packed as viral ribonucleoproteins (vRNPs), are released into the cytosol before nuclear import for viral replication. After nucleocytoplasmic transport, the resulting progeny vRNPs reach the cytosol, accumulating in highly mobile and dynamic viral inclusions that display liquid properties. Being sites postulated to support IAV genome assembly, the biophysical properties of IAV inclusions may be critical for function. In agreement, imposing liquid-to-solid transitions was demonstrated to impact viral replication negatively. Therefore, screening for host factors or compounds able to alter the material properties may provide the molecular basis for how influenza genomic complex forms as well as identify novel antivirals. Conventional techniques employed to investigate biomolecular condensates' material properties include fluorescence correlation spectroscopy, raster image correlation spectroscopy, single molecule or microrheology particle tracking, and Fluorescence Recovery After Photobleaching (FRAP). These approaches allow measuring molecular dynamics in systems that do not move very much. However, the analysis of highly mobile intracellular condensates, such as IAV inclusions, poses significant challenges as these structures not only constantly move within the cell but also exchange material, fusing, and dividing, rendering the quantitation of internal rearrangements and diffusion coefficients of molecules within condensates inaccurate. As an alternative, we opted for measuring the kinetics and the exchange of material between IAV inclusions using the Fluorescence Loss After Photoactivation (FLAPh) technique. It involves pulse photoactivation of individual or pools of viral inclusions in the cell, and chasing over time in photoactivated and non-photoactivated regions. This approach is suitable for quantifying the movement and spatial distribution of components within inclusions over time, enabling the determination of both the distance and speed from a specific cellular location. As a result, this method allows the quantification of decay profiles, half-lives, decay constant rate, and mobile and immobile fractions in viral inclusions. It, therefore, enables high throughput screenings for compounds or host factors that affect this dynamism and indirectly allows assessing the material properties of IAV inclusions.

Relevance of Microorganisms in Causing Rain and Snow

Various natural phenomena (such as solar fluctuations, oceanic patterns, volcanic eruptions, and tectonic movements) alongside human activities (including deforestation, CO and CO2 emissions, and desertification) contribute to ongoing climate change and subsequent global warming. However, human actions significantly exacerbate global warming, amplifying its adverse impacts worldwide. With rising temperatures, water evaporation from water bodies and soils intensifies, leading to heightened water scarcity, particularly in drought-prone regions. This scarcity compounds rainfall deficits, posing significant challenges. Precipitation, essential for the biosphere's hydrological cycle, replenishes much of the world's freshwater. It occurs when condensed water vapor in the atmosphere falls back to Earth as rain, drizzle, sleet, graupel, hail, or snow due to gravity. Literature highlights the indispensable role of microbial populations in this process, termed bio-precipitation. This phenomenon begins with microbial colonization on plant surfaces, with colonies subsequently dispersed into the atmosphere by winds, triggering ice crystal formation. Through their ice nucleating property, these microbes facilitate the growth of larger ice crystals, which eventually melt and precipitate as rain or snow. This mechanism aids in nutrient transfer from clouds to soil or vegetation. Pseudomonas syringae stands out as the most notable microorganism exhibiting this ice-nucleation property, serving as the primary source of ice nucleators driving bio-precipitation. Despite limited literature on "rain and snow-causing microorganisms," this review comprehensively explores the conceptual background of bio-precipitation, the involved bioprocesses, and the critical role of bacteria like P. syringae, offering insights into future research directions and patent innovations.

Time-resolved fluorescence of ANS dye as a sensor of proteins LLPS

The explosive growth in the number of works addressing the phase separation of intrinsically disordered proteins has driven both the development of new approaches and the optimization of existing methods for biomolecular condensate visualization. In this work, we studied the potential use of the fluorescent dye ANS as a sensor for liquid-liquid phase separation (LLPS), focusing on visualizing condensates formed by the stress-granules scaffold protein G3BP1. Using fluorescence lifetime imaging microscopy (FLIM), we demonstrated that ANS can accumulate in RNA-induced G3BP1 condensates in aqueous solutions, but not in G3BP1 condensates formed under macromolecular crowding conditions in highly concentrated PEG solutions. We showed that the experimentally determined limiting fluorescence anisotropy (r0'), which characterizes the amplitude of high-frequency intramolecular mobility of ANS in aqueous solutions containing RNA-induced G3BP1 condensates, is half the value observed for ANS in aqueous G3BP1 solutions. Our results demonstrate the feasibility of using time-resolved fluorescence spectroscopy and microscopy of ANS for detecting LLPS of intrinsically disordered proteins in aqueous solutions.

Formation, chemical evolution and solidification of the dense liquid phase of calcium (bi)carbonate

Metal carbonates, which are ubiquitous in the near-surface mineral record, are a major product of biomineralizing organisms and serve as important targets for capturing anthropogenic CO2 emissions. However, pathways of carbonate mineralization typically diverge from classical predictions due to the involvement of disordered precursors, such as the dense liquid phase (DLP), yet little is known about DLP formation or solidification processes. Using in situ methods we report that a highly hydrated bicarbonate DLP forms via liquid-liquid phase separation and transforms into hollow hydrated amorphous CaCO3 particles. Acidic proteins and polymers extend DLP lifetimes while leaving the pathway and chemistry unchanged. Molecular simulations suggest that the DLP forms via direct condensation of solvated Ca²+⋅(HCO3-)2 complexes that react due to proximity effects in the confined DLP droplets. Our findings provide insight into CaCO3 nucleation that is mediated by liquid-liquid phase separation, advancing the ability to direct carbonate mineralization and elucidating an often-proposed complex pathway of biomineralization.

Mechanical Remodeling of Nuclear Biomolecular Condensates

Organism health relies on cell proliferation, migration, and differentiation. These universal processes depend on cytoplasmic reorganization driven notably by the cytoskeleton and its force-generating motors. Their activity generates forces that mechanically agitate the cell nucleus and its interior. New evidence from reproductive cell biology revealed that these cytoskeletal forces can be tuned to remodel nuclear membraneless compartments, known as biomolecular condensates, and regulate their RNA processing function for the success of subsequent cell division that is critical for fertility. Both cytoskeletal and nuclear condensate reorganization are common to numerous physiological and pathological contexts, raising the possibility that mechanical remodeling of nuclear condensates may be a much broader mechanism regulating their function. Here, we review this newfound mechanism of condensate remodeling and venture into the contexts of health and disease where it may be relevant, with a focus on reproduction, cancer, and premature aging.

CRISPR/Cas Enzyme Catalysis in Liquid-Liquid Phase-Separated Systems

The clustered regularly interspaced palindromic repeats (CRISPR) /CRISPR-associated proteins (Cas) system is the immune system in bacteria and archaea and has been extensively applied as a critical tool in bioengineering. Investigation of the mechanisms of catalysis of CRISPR/Cas systems in intracellular environments is essential for understanding the underlying catalytic mechanisms and advancing CRISPR-based technologies. Here, the catalysis mechanisms of CRISPR/Cas systems are investigated in an aqueous two-phase system (ATPS) comprising PEG and dextran, which simulated the intracellular environment. The findings revealed that nucleic acids and proteins tended to be distributed in the dextran-rich phase. The results demonstrated that the cis-cleavage activity of Cas12a is enhanced in the ATPS, while its trans-cleavage activity is suppressed, and this finding is further validated using Cas13a. Further analysis by increasing the concentration of the DNA reporter revealed that this phenomenon is not attributed to the slow diffusion of the reporter, and explained why Cas12a and Cas13a do not randomly cleave nucleic acids in the intracellular compartment. The study provides novel insights into the catalytic mechanisms of CRISPR/Cas systems under physiological conditions and may contribute to the development of CRISPR-based molecular biological tools.

Regulation and function of endoplasmic reticulum autophagy in neurodegenerative diseases

The endoplasmic reticulum, a key cellular organelle, regulates a wide variety of cellular activities. Endoplasmic reticulum autophagy, one of the quality control systems of the endoplasmic reticulum, plays a pivotal role in maintaining endoplasmic reticulum homeostasis by controlling endoplasmic reticulum turnover, remodeling, and proteostasis. In this review, we briefly describe the endoplasmic reticulum quality control system, and subsequently focus on the role of endoplasmic reticulum autophagy, emphasizing the spatial and temporal mechanisms underlying the regulation of endoplasmic reticulum autophagy according to cellular requirements. We also summarize the evidence relating to how defective or abnormal endoplasmic reticulum autophagy contributes to the pathogenesis of neurodegenerative diseases. In summary, this review highlights the mechanisms associated with the regulation of endoplasmic reticulum autophagy and how they influence the pathophysiology of degenerative nerve disorders. This review would help researchers to understand the roles and regulatory mechanisms of endoplasmic reticulum-phagy in neurodegenerative disorders.

Neurological Diseases can be Regulated by Phase Separation

Several neurological diseases arise from abnormal protein aggregation within neurones and this is closely regulated by phase separation. One such is motor neurone disease and aberrant aggregation of superoxide dismutase. Again these events are regulated by electrical forces that are examined.

Ruthenium(II) Lipid-Mimics Drive Lipid Phase Separation to Arouse Autophagy-Ferroptosis Cascade for Photoimmunotherapy

Lipid-mediated phase separation is crucial for the formation of lipophilic spontaneous domain to regulate lipid metabolism and homeostasis, furtherly contributing to multiple cell death pathways. Herein, a series of Ru(II) lipid-mimics based on short chains or midchain lipids are developed. Among them, Ru-LipM with two dodecyl chains significantly induces natural lipid phase separation via hydrocarbon chain-melting phase transitions. Accompanied by the aggregation of Ru-LipM-labeled lipophilic membrane-less compartments, most polyunsaturated lipids are increased and the autophagic flux is retarded with the adaptor protein sequestosome 1 (p62). Upon low-dose irradiation, Ru-LipM further drives ferritinophagy, providing an additional source of labile iron and rendering cells more sensitive to ferroptosis. Meanwhile, the peroxidation of polyunsaturated lipids occurs due to the deactivation of glutathione peroxidase 4 (GPX4) and the overexpression of acyl-CoA synthetase long-chain family member 4 (ACSL4), leading to the immunogenic ferroptosis. Ultimately, both innate and adaptive immunity are invigorated, indicating the tremendous antitumor capability of Ru-LipM in vivo. This study presents an unprecedented discovery of small molecules capable of inducing and monitoring lipid phase separation, thereby eliciting robust immune responses in living cells. It provides a biosimulation strategy for constructing efficient metal-based immune activators.

Ageing drop by drop: Disturbance of the membrane-less organelle biogenesis as an aging hallmark

Despite extensive research, the features associated with the aging phenotype are not all-inclusive and need to be updated on a regular basis to incorporate new findings. We propose to include the dysfunction of membrane-less organelle (MLO) as a new aging hallmark. Special scaffold proteins with a high degree of intrinsic disorder drive the formation of MLOs via the liquid-liquid phase separation (LLPS) process. Aberrant behavior of MLOs was shown to be associated with the pathogenesis of many neurodegenerative diseases. In this work, we challenge the aging through bidirectional bioinformatics analysis of human proteins found in Granulome consisting of 7264 protein and Ageome containing 1624 aging-related proteins. The analysis indicates the interconnectivity of MLOs and aging. Approximately 67 % of the Ageome are presented in Granulome thereby constituting the Intersectome that include 1084 proteins showing an enrichment significantly higher than for the random datasets of the same size. Furthermore, for proteins in 10 representative MLOs, we analyzed in detail molecular functions, association with the already known aging hallmarks, and the roles in MLO formation (scaffold, client, or regulator). Cumulatively, our results strengthen the hypothesis that the dysfunction of MLOs can serve as a potent new aging hallmark.

Quantitative Spatial Analysis of Chromatin Biomolecular Condensates using Cryo-Electron Tomography

Phase separation is an important mechanism to generate certain biomolecular condensates and organize the cell interior. Condensate formation and function remain incompletely understood due to difficulties in visualizing the condensate interior at high resolution. Here we analyzed the structure of biochemically reconstituted chromatin condensates through cryo-electron tomography. We found that traditional blotting methods of sample preparation were inadequate, and high-pressure freezing plus focused ion beam milling was essential to maintain condensate integrity. To identify densely packed molecules within the condensate, we integrated deep learning-based segmentation with novel context-aware template matching. Our approaches were developed on chromatin condensates, and were also effective on condensed regions of in situ native chromatin. Using these methods, we determined the average structure of nucleosomes to 6.1 and 12 Å resolution in reconstituted and native systems, respectively, and found that nucleosomes form heterogeneous interaction networks in both cases. Our methods should be applicable to diverse biochemically reconstituted biomolecular condensates and to some condensates in cells.

Liquid-liquid phase separation of tau and α-synuclein: A new pathway of overlapping neuropathologies

Liquid-liquid phase separation (LLPS) is a critical phenomenon that leads to the formation of liquid-like membrane-less organelles within cells. Advances in our understanding of condensates reveal their significant roles in biology and highlight how their dysregulation may contribute to disease. Recent evidence indicates that the high protein concentration in coacervates may lead to abnormal protein aggregation associated with several neurodegenerative diseases. The presence of condensates containing multiple amyloidogenic proteins may play a role in the co-deposition and comorbidity seen in neurodegeneration. This review first provides a brief overview of the physicochemical bases and molecular determinants of LLPS. It then summarizes our understanding of Tau and α-synuclein (AS) phase separation, key proteins in Alzheimer's and Parkinson's diseases. By integrating recent findings on complex Tau and AS coacervation, this article offers a fresh perspective on how LLPS may contribute to the pathological overlap in neurodegenerative disorders and provide a novel therapeutic target to mitigate or prevent such conditions.

Cellular Function of a Biomolecular Condensate Is Determined by Its Ultrastructure

Biomolecular condensates play key roles in the spatiotemporal regulation of cellular processes. Yet, the relationship between atomic features and condensate function remains poorly understood. We studied this relationship using the polar organizing protein Z (PopZ) as a model system, revealing how its material properties and cellular function depend on its ultrastructure. We revealed PopZ's hierarchical assembly into a filamentous condensate by integrating cryo-electron tomography, biochemistry, single-molecule techniques, and molecular dynamics simulations. The helical domain drives filamentation and condensation, while the disordered domain inhibits them. Phase-dependent conformational changes prevent interfilament contacts in the dilute phase and expose client binding sites in the dense phase. These findings establish a multiscale framework that links molecular interactions and condensate ultrastructure to macroscopic material properties that drive cellular function.

TFEB Phase Separation Mediates the Amelioration Effect of Intermittent Fasting on Inflammatory Colitis

Intermittent fasting (IF) has been shown to ameliorate inflammation including DSS-induced colitis. It is well known that autophagy can limit inflammation and TFEB is a master transcriptional factor that regulates the processes of autophagy. However, whether TFEB is involved in the regulation of IF-mediated amelioration of inflammation and its mechanism remained unclear. In this study, we found that IF ameliorated DSS-induced colitis and induced TFEB. Nutrition deprivation induced TFEB puncta formation, which processes the characteristics of liquid-liquid phase separation (LLPS) showed by fluorescence recovery after photobleaching (FRAP) assay and 1,6-hexanediol treatment. We found the 24-33 amino acids of Coiled-Coil (CC) domain located in N terminus is essential for TFEB phase separation. Deletion of 24-33 amino acids within the CC domain inhibited TFEB-mediated target gene expression. In addition, we found transcription co-activators, EP300 and MED1, co-localized with TFEB condensate to formed a transcriptional hub that promotes the efficient expression of target genes. More importantly, TFEB inhibitor with ability to suppress TFEB puncta formation abolished the IF-mediated amelioration of DSS colitis. Together, these findings revealed a critical role of TFEB phase separation in the regulation of its transcriptional activity and anti-inflammatory functions induced by IF.

Nuclear Structure, Size Regulation, and Role in Cell Migration

The nucleus serves as a pivotal regulatory and control hub in the cell, governing numerous aspects of cellular functions, including DNA replication, transcription, and RNA processing. Therefore, any deviations in nuclear morphology, structure, or organization can strongly affect cellular activities. In this review, we provide an updated perspective on the structure and function of nuclear components, focusing on the linker of nucleoskeleton and cytoskeleton complex, the nuclear envelope, the nuclear lamina, and chromatin. Additionally, nuclear size should be considered a fundamental parameter for the cellular state. Its regulation is tightly linked to environmental changes, development, and various diseases, including cancer. Hence, we also provide a concise overview of different mechanisms by which nuclear size is determined, the emerging role of the nucleus as a mechanical sensor, and the implications of altered nuclear morphology on the physiology of diseased cells.

RNA-dependent RNA polymerase of predominant human norovirus forms liquid-liquid phase condensates as viral replication factories

Many viral proteins form biomolecular condensates via liquid-liquid phase separation (LLPS) to support viral replication and evade host antiviral responses, and thus, they are potential targets for designing antivirals. In the case of nonenveloped positive-sense RNA viruses, forming such condensates for viral replication is unclear and less understood. Human noroviruses (HuNoVs) are positive-sense RNA viruses that cause epidemic and sporadic gastroenteritis worldwide. Here, we show that the RNA-dependent RNA polymerase (RdRp) of pandemic GII.4 HuNoV forms distinct condensates that exhibit all the signature properties of LLPS with sustained polymerase activity and the capability of recruiting components essential for viral replication. We show that such condensates are formed in HuNoV-infected human intestinal enteroid cultures and are the sites for genome replication. Our studies demonstrate the formation of phase-separated condensates as replication factories in a positive-sense RNA virus, which plausibly is an effective mechanism to dynamically isolate RdRp replicating the genomic RNA from interfering with the ribosomal translation of the same RNA.

LncRNAs chaperoning dynamic protein condensates in cancer cells

In this issue of Molecular Cell, Sun et al. reveal that the long non-coding RNA (lncRNA) DNAJC3-AS1 plays a dual role in maintaining the rRNA processing function of fibrillarin (FBL) in cancer cells. It promotes FBL condensation while preventing abnormal aggregation, offering new therapeutic insights for cancer treatment by targeting lncRNAs involved in the regulation of FBL condensation.

lncRNAs maintain the functional phase state of nucleolar prion-like protein to facilitate rRNA processing

Liquid-to-solid phase transition of proteins with prion-like domains (PLDs) has been associated with neurodegenerative diseases and aging. High protein concentration is one important aspect triggering the transition; however, several prion-like proteins, including fibrillarin (FBL), an important phase-separated protein in the nucleolus for pre-rRNA processing, show relatively high expression levels in certain cells, especially cancer cells, without obvious phase transitions and growth arrest. How cells maintain prion-like protein proteostasis is still unknown. Here, we attempt to answer the question, with FBL as an example. We find that lncRNA DNAJC3-AS1 can buffer the behavior of FBL condensation and maintain the state and function of fibrillar component/dense fibrillar component (FC/DFC) units in human cell lines through two mechanisms, not only facilitating FBL condensation but also inhibiting excessive aggregation by binding multiple PLDs and partially blocking their interactions. We propose that lncRNAs could supply buffered systems to sustain functional phase states of prion-like proteins.

Thermophilic Behavior of Heat-Dissociative Coacervate Droplets

In exploring the genesis of life, liquid-liquid phase-separated coacervate droplets have been proposed as primitive protocells. Within the hydrothermal hypothesis, these droplets would emerge from molecule-rich hot fluids and thus be subjected to temperature gradients. Investigating their thermophoretic behavior can provide insights into protocell footprints in thermal landscapes, advancing our understanding of life's origins. Here, we report the thermophilic behavior of heat-dissociative droplets, contrary to the intuition that heat-associative condensates would prefer hotter areas. This aspect implies the preferential presence of heat-dissociative primordial condensates near hydrothermal environments, facilitating molecular incorporation and biochemical syntheses. Additionally, our investigations reveal similarities between thermophoretic and electrophoretic motions, dictated by molecular redistribution within droplets due to their fluid nature, which necessitates revising current electrophoresis frameworks for surface charge characterization. Our study elucidates how coacervate droplets navigate thermal and electric fields, reveals their thermal-landscape-dependent molecular characteristics, and bridges foundational theories of early life: the hydrothermal and condensate-as-protocell hypotheses.

An integrated machine learning approach delineates an entropic expansion mechanism for the binding of a small molecule to α-synuclein

The mis-folding and aggregation of intrinsically disordered proteins (IDPs) such as α-synuclein (αS) underlie the pathogenesis of various neurodegenerative disorders. However, targeting αS with small molecules faces challenges due to the lack of defined ligand-binding pockets in its disordered structure. Here, we implement a deep artificial neural network-based machine learning approach, which is able to statistically distinguish the fuzzy ensemble of conformational substates of αS in neat water from those in aqueous fasudil (small molecule of interest) solution. In particular, the presence of fasudil in the solvent either modulates pre-existing states of αS or gives rise to new conformational states of αS, akin to an ensemble-expansion mechanism. The ensembles display strong conformation-dependence in residue-wise interaction with the small molecule. A thermodynamic analysis indicates that small-molecule modulates the structural repertoire of αS by tuning protein backbone entropy, however entropy of the water remains unperturbed. Together, this study sheds light on the intricate interplay between small molecules and IDPs, offering insights into entropic modulation and ensemble expansion as key biophysical mechanisms driving potential therapeutics.

Optogenetic Tools for Regulating RNA Metabolism and Functions

RNA molecules play a vital role in linking genetic information with various cellular processes. In recent years, a variety of optogenetic tools have been engineered for regulating cellular RNA metabolism and functions. These highly desirable tools can offer non-intrusive control with spatial precision, remote operation, and biocompatibility. Here, we would like to review these currently available approaches that can regulate RNAs with light: from non-genetically encodable chemically modified oligonucleotides to genetically encoded RNA aptamers that recognize photosensitive small-molecule or protein ligands. Some key applications of these optogenetic tools will also be highlighted to illustrate how they have been used for regulating all aspects of the RNA life cycle: from RNA synthesis, maturation, modification, and translation to their degradation, localization, and phase separation control. Some current challenges and potential practical utilizations of these RNA optogenetic tools will also be discussed.

Recent Technologies on 2D and 3D Imaging Flow Cytometry

Imaging flow cytometry is a technology that performs microscopy image analysis of cells within flow cytometry and allows high-throughput, high-content cell analysis based on their intracellular molecular distribution and/or cellular morphology. While the technology has been available for a couple of decades, it has recently gained significant attention as technical limitations for higher throughput, sorting capability, and additional imaging dimensions have been overcome with various approaches. These evolutions have enabled imaging flow cytometry to offer a variety of solutions for life science and medicine that are not possible with conventional flow cytometry or microscopy-based screening. It is anticipated that the extent of applications will expand in the upcoming years as the technology becomes more accessible through dissemination. In this review, we will cover the technical advances that have led to this new generation of imaging flow cytometry, focusing on the advantages and limitations of each technique.

Chromatin folding through nonuniform motorization by responsive motor proteins

Chromatin is partially structured through the effects of biological motors. "Swimming motors" such as RNA polymerases and chromatin remodelers are thought to act differentially on the active parts of the genome and the stored inactive part. By systematically expanding the many-body master equation for chromosomes driven by swimming motors, we show that this nonuniform aspect of motorization leads to heterogeneously folded conformations, thereby contributing to chromosome compartmentalization.

Nucleo-cytoplasmic environment modulates spatiotemporal p53 phase separation

Liquid-liquid phase separation of various transcription factors into biomolecular condensates plays an essential role in gene regulation. Here, using cellular models and in vitro studies, we show the spatiotemporal formation and material properties of p53 condensates that might dictate its function. In particular, p53 forms liquid-like condensates in the nucleus of cells, which can bind to DNA and perform transcriptional activity. However, cancer-associated mutations promote misfolding and partially rigidify the p53 condensates with impaired DNA binding ability. Irrespective of wild-type and mutant forms, the partitioning of p53 into cytoplasm leads to the condensate formation, which subsequently undergoes rapid solidification. In vitro studies show that abundant nuclear components such as RNA and nonspecific DNA promote multicomponent phase separation of the p53 core domain and maintain their liquid-like property, whereas specific DNA promotes its dissolution into tetrameric functional p53. This work provides mechanistic insights into how the life cycle and DNA binding properties of p53 might be regulated by phase separation.

PICNIC accurately predicts condensate-forming proteins regardless of their structural disorder across organisms

Biomolecular condensates are membraneless organelles that can concentrate hundreds of different proteins in cells to operate essential biological functions. However, accurate identification of their components remains challenging and biased towards proteins with high structural disorder content with focus on self-phase separating (driver) proteins. Here, we present a machine learning algorithm, PICNIC (Proteins Involved in CoNdensates In Cells) to classify proteins that localize to biomolecular condensates regardless of their role in condensate formation. PICNIC successfully predicts condensate members by learning amino acid patterns in the protein sequence and structure in addition to the intrinsic disorder. Extensive experimental validation of 24 positive predictions in cellulo shows an overall ~82% accuracy regardless of the structural disorder content of the tested proteins. While increasing disorder content is associated with organismal complexity, our analysis of 26 species reveals no correlation between predicted condensate proteome content and disorder content across organisms. Overall, we present a machine learning classifier to interrogate condensate components at whole-proteome levels across the tree of life.

Actin polymerization counteracts prewetting of N-WASP on supported lipid bilayers

Cortical condensates, transient punctate-like structures rich in actin and the actin nucleation pathway member Neural Wiskott-Aldrich syndrome protein (N-WASP), form during activation of the actin cortex in the Caenorhabditis elegans oocyte. Their emergence and spontaneous dissolution is linked to a phase separation process driven by chemical kinetics. However, the mechanisms that drive the onset of cortical condensate formation near membranes remain unexplored. Here, using a reconstituted phase separation assay of cortical condensate proteins, we demonstrate that the key component, N-WASP, can collectively undergo surface condensation on supported lipid bilayers via a prewetting transition. Actin partitions into the condensates, where it polymerizes and counteracts the N-WASP prewetting transition. Taken together, the dynamics of condensate-assisted cortex formation appear to be controlled by a balance between surface-assisted condensate formation and polymer-driven condensate dissolution. This opens perspectives for understanding how the formation of complex intracellular structures is affected and controlled by phase separation.

Phase separation of chimeric antigen receptor promotes immunological synapse maturation and persistent cytotoxicity

Major challenges of chimeric antigen receptor (CAR)-T cell therapy include poor antigen sensitivity and cell persistence. Here, we report a solution to these issues by exploiting CAR phase separation. We found that incorporation of an engineered T cell receptor CD3ε motif, EB6I, into the conventional 28Z or BBZ CAR induced self-phase separation through cation-π interactions. EB6I CAR formed a mature immunological synapse with the CD2 corolla to transduce efficient antigen and costimulatory signaling, although its tonic signaling remained low. Functionally, EB6I CAR-T cells exhibited improved signaling and cytotoxicity against low-antigen tumor cells and persistent tumor-killing function. In multiple primary and relapsed murine tumor models, EB6I CAR-T cells exerted better antitumor functions than conventional CAR-T cells against blood and solid cancers. This study thus unveils a CAR engineering strategy to improve CAR-T cell immunity by leveraging molecular condensation and signaling integration.

Liquid-liquid separation in gut immunity

Gut immunity is essential for maintaining intestinal health. Recent studies have identified that intracellular liquid-liquid phase separation (LLPS) may play a significant role in regulating gut immunity, however, the underlying mechanisms remain unclear. LLPS refers to droplet condensates formed through intracellular molecular interactions, which are crucial for the formation of membraneless organelles and biomolecules. LLPS can contribute to the formation of tight junctions between intestinal epithelial cells and influence the colonization of probiotics in the intestine, thereby protecting the intestinal immune system by maintaining the integrity of the intestinal barrier and the stability of the microbiota. Additionally, LLPS can affect the microclusters on the plasma membrane of T cells, resulting in increased density and reduced mobility, which in turn influences T cell functionality. The occurrence of intracellular LLPS is intricately associated with the initiation and progression of gut immunity. This review introduces the mechanism of LLPS in gut immunity and analyzes future research directions and potential applications of this phenomenon.

Endogenous oligomer formation underlies DVL2 condensates and promotes Wnt/β-catenin signaling

Activation of the Wnt/β-catenin pathway crucially depends on the polymerization of dishevelled 2 (DVL2) into biomolecular condensates. However, given the low affinity of known DVL2 self-interaction sites and its low cellular concentration, it is unclear how polymers can form. Here, we detect oligomeric DVL2 complexes at endogenous protein levels in human cell lines, using a biochemical ultracentrifugation assay. We identify a low-complexity region (LCR4) in the C-terminus whose deletion and fusion decreased and increased the complexes, respectively. Notably, LCR4-induced complexes correlated with the formation of microscopically visible multimeric condensates. Adjacent to LCR4, we mapped a conserved domain (CD2) promoting condensates only. Molecularly, LCR4 and CD2 mediated DVL2 self-interaction via aggregating residues and phenylalanine stickers, respectively. Point mutations inactivating these interaction sites impaired Wnt pathway activation by DVL2. Our study discovers DVL2 complexes with functional importance for Wnt/β-catenin signaling. Moreover, we provide evidence that DVL2 condensates form in two steps by pre-oligomerization via high-affinity interaction sites, such as LCR4, and subsequent condensation via low-affinity interaction sites, such as CD2.

Molecular sociology of virus-induced cellular condensates supporting reovirus assembly and replication

Virus-induced cellular condensates, or viral factories, are poorly understood high-density phases where replication of many viruses occurs. Here, by cryogenic electron tomography (cryoET) of focused ion beam (FIB) milling-produced lamellae of mammalian reovirus (MRV)-infected cells, we visualized the molecular organization and interplay (i.e., "molecular sociology") of host and virus in 3D at two time points post-infection, enabling a detailed description of these condensates and a mechanistic understanding of MRV replication within them. Expanding over time, the condensate fashions host ribosomes at its periphery, and host microtubules, lipid membranes, and viral molecules in its interior, forming a 3D architecture that supports the dynamic processes of viral genome replication and capsid assembly. A total of six MRV assembly intermediates are identified inside the condensate: star core, empty and genome-containing cores, empty and full virions, and outer shell particle. Except for star core, these intermediates are visualized at atomic resolution by cryogenic electron microscopy (cryoEM) of cellular extracts. The temporal sequence and spatial rearrangement among these viral intermediates choreograph the viral life cycle within the condensates. Together, the molecular sociology of MRV-induced cellular condensate highlights the functional advantage of transient enrichment of molecules at the right location and time for viral replication.

Membrane wetting by biomolecular condensates is facilitated by mobile tethers

Biomolecular condensates frequently rely on membrane interactions for localization, recruitment, and chemical substrates. These interactions are often mediated by membrane-anchored tethers, a feature overlooked by traditional wetting models. Using a surface free-energy framework that couples surface tension with tether density, we solve for the contact angle and tether density in a spherical cap geometry, generalizing the Young-Dupré equation. While the contact angle retains its force-balance form, the tether density depends nontrivially on the form and strength of tether-condensate interactions. We solve for this dependence within a simple interaction model, and find a wetting phase diagram with a transition from non-wetting to partial to complete wetting over a biologically realistic parameter range. This work provides a quantitative framework for characterizing condensate-membrane interactions, uncovering potential mechanisms by which membranes mediate cellular organization and function.

YTHDF2 phase separation promotes arsenic-induced keratinocyte transformation in a poly-m6A-dependent manner by inhibiting translational initiation of the key tumor suppressor PTEN

The phase separation of N6-methyladenosine (m6A) binding protein YTHDF2 plays a vital role in arsenic-induced skin damage, and YTHDF2 can bind to m6A-methylated mRNA of tumor suppressor PTEN. However, whether and how YTHDF2 phase separation regulates PTEN involved in arsenic-induced malignant transformation of keratinocytes remains blank. Here, we established arsenite-induced transformation models with stable expression of wild-type YTHDF2 or mutant YTHDF2 protein in vitro and in vivo. We found that the YTHDF2 protein underwent phase separation during arsenite-induced malignant transformation of keratinocytes, and YTHDF2 phase separation promoted the malignant phenotype of keratinocytes. Mechanically, YTHDF2 phase separation reduced PTEN protein levels, which in turn activated the pro-survival AKT signal. The binding of YTHDF2 to multiple m6A sites on PTEN mRNA drove YTHDF2 phase separation, inhibiting PTEN translation initiation and thus reducing PTEN protein levels. YTHDF2 phase separation recruited translation-initiation-factor kinase EIF2AK1 to phosphorylate eIF2α, thereby inhibiting translation initiation of poly-m6A-methylated PTEN mRNA. Furthermore, arsenite-induced oxidative stress triggered YTHDF2 phase separation by increasing m6A levels of PTEN mRNA. Our results demonstrated that YTHDF2 phase separation promotes arsenite-induced malignant transformation by inhibiting PTEN translation in a poly-m6A-dependent manner. This study sheds light on arsenic carcinogenicity from the novel aspect of m6A-mediated YTHDF2 phase separation.

Amino Acid Transfer Free Energies Reveal Thermodynamic Driving Forces in Biomolecular Condensate Formation

The self-assembly of intrinsically disordered proteins into biomolecular condensates shows a dependence on the primary sequence of the protein, leading to sequence-dependent phase separation. Methods to investigate this sequence-dependent phase separation rely on effective residue-level interaction potentials that quantify the propensity for the residues to remain in the dilute phase versus the dense phase. The most direct measure of these effective potentials are the distribution coefficients of the different amino acids between the two phases, but due to the lack of availability of these coefficients, proxies, most notably hydropathy, have been used. However, recent work has demonstrated the limitations of the assumption of hydropathy-driven phase separation. In this work, we address this fundamental gap by calculating the transfer free energies associated with transferring each amino acid side chain analog from the dilute phase to the dense phase of a model biomolecular condensate. We uncover an interplay between favorable protein-mediated and unfavorable water-mediated contributions to the overall free energies of transfer. We further uncover an asymmetry between the contributions of positive and negative charges in the driving forces for condensate formation. The results presented in this work provide an explanation for several non-trivial trends observed in the literature and will aid in the interpretation of experiments aimed at elucidating the sequence-dependent driving forces underlying the formation of biomolecular condensates.

Continuity of Short-Time Dynamics Crossing the Liquid-Liquid Phase Separation in Charge-Tuned Protein Solutions

Liquid-liquid phase separation (LLPS) constitutes a crucial phenomenon in biological self-organization, not only intervening in the formation of membraneless organelles but also triggering pathological protein aggregation, which is a hallmark in neurodegenerative diseases. Employing incoherent quasi-elastic neutron spectroscopy (QENS), we examine the short-time self-diffusion of a model protein undergoing LLPS as a function of phase splitting and temperature to access information on the nanosecond hydrodynamic response to the cluster formation both within and outside the LLPS regime. We investigate the samples as they dissociate into microdroplets of a dense protein phase dispersed in a dilute phase as well as the separated dense and dilute phases obtained from centrifugation. By interpreting the QENS results in terms of the local concentrations in the two phases determined by UV-vis spectroscopy, we hypothesize that the short-time transient protein cluster size distribution is conserved at the transition point while the local volume fractions separate.

Molecular insights into the interaction between a disordered protein and a folded RNA

Intrinsically disordered protein regions (IDRs) are well established as contributors to intermolecular interactions and the formation of biomolecular condensates. In particular, RNA-binding proteins (RBPs) often harbor IDRs in addition to folded RNA-binding domains that contribute to RBP function. To understand the dynamic interactions of an IDR-RNA complex, we characterized the RNA-binding features of a small (68 residues), positively charged IDR-containing protein, Small ERDK-Rich Factor (SERF). At high concentrations, SERF and RNA undergo charge-driven associative phase separation to form a protein- and RNA-rich dense phase. A key advantage of this model system is that this threshold for demixing is sufficiently high that we could use solution-state biophysical methods to interrogate the stoichiometric complexes of SERF with RNA in the one-phase regime. Herein, we describe our comprehensive characterization of SERF alone and in complex with a small fragment of the HIV-1 Trans-Activation Response (TAR) RNA with complementary biophysical methods and molecular simulations. We find that this binding event is not accompanied by the acquisition of structure by either molecule; however, we see evidence for a modest global compaction of the SERF ensemble when bound to RNA. This behavior likely reflects attenuated charge repulsion within SERF via binding to the polyanionic RNA and provides a rationale for the higher-order assembly of SERF in the context of RNA. We envision that the SERF-RNA system will lower the barrier to accessing the details that support IDR-RNA interactions and likewise deepen our understanding of the role of IDR-RNA contacts in complex formation and liquid-liquid phase separation.

TPM4 condensates glycolytic enzymes and facilitates actin reorganization under hyperosmotic stress

Actin homeostasis is fundamental for cell structure and consumes a large portion of cellular ATP. It has been documented in the literature that certain glycolytic enzymes can interact with actin, indicating an intricate interplay between the cytoskeleton and cellular metabolism. Here we report that hyperosmotic stress triggers actin severing and subsequent phase separation of the actin-binding protein tropomyosin 4 (TPM4). TPM4 condensates recruit glycolytic enzymes such as HK2, PFKM, and PKM2, while wetting actin filaments. Notably, the condensates of TPM4 and glycolytic enzymes are enriched of NADH and ATP, suggestive of their functional importance in cell metabolism. At cellular level, actin filament assembly is enhanced upon hyperosmotic stress and TPM4 condensation, while depletion of TPM4 impairs osmolarity-induced actin reorganization. At tissue level, colocalized condensates of TPM4 and glycolytic enzymes are observed in renal tissues subjected to hyperosmotic stress. Together, our findings suggest that stress-induced actin perturbation may act on TPM4 to organize glycolytic hubs that tether energy production to cytoskeletal reorganization.

Emerging interactions between RNA methylation and chromatin architecture

Epitranscriptomics, the study of chemical modifications of RNA molecules, is increasingly recognized as an important component of gene expression regulation. While the majority of research has focused on N6-methyladenosine (m6A) RNA methylation on mRNAs, emerging evidence has revealed that the m6A modification extends beyond mRNAs to include chromatin-associated RNAs (caRNAs). CaRNAs constitute an important class of RNAs characterized by their interaction with the genome and epigenome. These features allow caRNAs to be actively involved in shaping genome organization. In this review, we bring into focus recent findings of the dynamic interactions between caRNAs and chromatin architecture and how RNA methylation impacts caRNAs' function in this interplay. We highlight several enabling techniques, which were critical for genome-wide profiling of caRNAs and their modifications. Given the nascent stage of the field, we emphasize on the need to address critical gaps in study of these modifications in more relevant biological systems. Overall, these exciting progress have expanded the scope and reach of epitranscriptomics, unveiling new mechanisms that underpin the control of gene expression and cellular phenotypes, with potential therapeutic implications.

Synchronized motion of interface residues for evaluating protein-RNA complex binding affinity: Application to aptamer-mediated inhibition of TDP-43 aggregates

Investigating the binding between proteins and aptamers, such as peptides or RNA molecules, is of crucial importance both for understanding the molecular mechanisms that regulate cellular activities and for therapeutic applications in several pathologies. Here, a new computational procedure, employing mainly docking, clustering analysis, and molecular dynamics simulations, was designed to estimate the binding affinities between a protein and some RNA aptamers, through the investigation of the dynamical behavior of the predicted molecular complex. Using the state-of-the-art software catRAPID, we computationally designed a set of RNA aptamers interacting with the TAR DNA-binding protein 43 (TDP-43), a protein associated with several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). We thus devised a computational protocol to predict the RNA-protein molecular complex, so that the structural and dynamical behavior of such a complex can be investigated through extensive molecular dynamics simulation. We hypothesized that the coordinated and synchronized motion of the protein-binding residues, when in contact with RNA molecule, is a critical requisite in order to have a stable binding. Indeed, we calculated the motion covariance exhibited by the interface residues during molecular dynamics simulation: we tested the results against experimental measurements of binding affinity (in this case, the dissociation constant) for six RNA molecules, resulting in a linear correlation of about 0.9. Our findings suggest that the synchronized movement of interface residues plays a pivotal role in ensuring the stability within RNA-protein complexes, moreover providing insights into the contribution of each interface residue. This promising pipeline could thus contribute to the design of RNA aptamers interacting with proteins.

Drug Discovery for Diseases with High Unmet Need Through Perturbation of Biomolecular Condensates

Biomolecular condensates (BMCs), play significant roles in organizing cellular functions in the absence of membranes through phase separation events involving RNA, proteins, and RNA-protein complexes. These membrane-less organelles form dynamic multivalent weak interactions, often involving intrinsically disordered proteins or regions (IDPs/IDRs). However, the nature of these crucial interactions, how most of these organelles are organized and are functional, remains unknown. Aberrant condensates have been implicated in neurodegenerative diseases and various cancers, presenting novel therapeutic opportunities for small molecule condensate modulators. Recent advancements in optogenetic technologies, particularly Corelet, enable precise manipulation of BMC dynamics within living cells, facilitating high-throughput screening for small molecules that target these complex structures. By elucidating the molecular mechanisms governing BMC formation and function, this innovative approach holds promise to unlock therapeutic strategies against previously "undruggable" protein targets, paving the way for effective interventions in disease.

Recent advances in engineering synthetic biomolecular condensates

Biomolecular condensates are intriguing entities found within living cells. These structures possess the ability to selectively concentrate specific components through phase separation, thereby playing a crucial role in the spatiotemporal regulation of a wide range of cellular processes and metabolic activities. To date, extensive studies have been dedicated to unraveling the intricate connections between molecular features, physical properties, and cellular functions of condensates. This collective effort has paved the way for deliberate engineering of tailor-made condensates with specific applications. In this review, we comprehensively examine the underpinnings governing condensate formation. Next, we summarize the material states of condensates and delve into the design of synthetic intrinsically disordered proteins with tunable phase behaviors and physical properties. Subsequently, we review the diverse biological functions demonstrated by synthetic biomolecular condensates, encompassing gene regulation, cellular behaviors, modulation of biochemical reactions, and manipulation of endogenous protein activities. Lastly, we discuss future challenges and opportunities in constructing synthetic condensates with tunable physical properties and customized cellular functions, which may shed light on the development of new types of sophisticated condensate systems with distinct functions applicable to various scenarios.

A mortality timer based on nucleolar size triggers nucleolar integrity loss and catastrophic genomic instability

Genome instability is a hallmark of aging, with the highly repetitive ribosomal DNA (rDNA) within the nucleolus being particularly prone to genome instability. Nucleolar enlargement accompanies aging in organisms ranging from yeast to mammals, and treatment with many antiaging interventions results in small nucleoli. Here, we report that an engineered system to reduce nucleolar size robustly extends budding yeast replicative lifespan in a manner independent of protein synthesis rate or rDNA silencing. Instead, when nucleoli expand beyond a size threshold, their biophysical properties change, allowing entry of proteins normally excluded from the nucleolus, including the homologous recombinational repair protein Rad52. This triggers rDNA instability due to aberrant recombination, catastrophic genome instability and imminent death. These results establish that nucleolar expansion is sufficient to drive aging. Moreover, nucleolar expansion beyond a specific size threshold is a mortality timer, as the accompanying disruption of the nucleolar condensate boundary results in catastrophic genome instability that ends replicative lifespan.

The landscape of intrinsically disordered proteins in Leishmania parasite: Implications for drug discovery

Proteins that lack three-dimensional structures are known as Intrinsically disordered proteins (IDPs). In this study, we aimed to identify intrinsically disordered proteins in the Leishmania donovani proteome using various predictors that can identify IDPs based on amino acid residues and charge hydropathy. Top identified IDPs are analyzed using STRING, PSP-Hunter, Deep Loc-2.0, and Alpha fold to understand the protein-protein interaction, phase separation, localization, and structural assessment of those proteins. From this study, we found that >50 % of Leishmania donovani proteome has proteins or regions of proteins that are intrinsically disordered with VSL2 score >0.5; most proteins interact with many other proteins with PPI enrichment p-value <1.0e-16. Few proteins, such as Protein phosphatase inhibitor, UMSBP, and Zinc knuckle, have redox-sensitive regions. Functional disorder profiles of identified IDPs showed MoRFs and predicted protein domains. HASPB, UTP11, Nucleolar protein 12, and UMSBP have a high probability of undergoing phase separation. Localization studies showed that most of these proteins are in the cytoplasm and nucleus. Our present study of identifying IDPs in Leishmania proteome yields significant information on druggable targets and can serve as a basis for further studies to identify unexplored pathways.

SERRATE drives phase separation behaviours to regulate m6A modification and miRNA biogenesis

The methyltransferase complex (MTC) deposits N6-adenosine (m6A) onto RNA, whereas the microprocessor produces microRNA. Whether and how these two distinct complexes cross-regulate each other has been poorly studied. Here we report that the MTC subunit B tends to form insoluble condensates with poor activity, with its level monitored by the 20S proteasome. Conversely, the microprocessor component SERRATE (SE) forms liquid-like condensates, which in turn promote the solubility and stability of the MTC subunit B, leading to increased MTC activity. Consistently, the hypomorphic lines expressing SE variants, defective in MTC interaction or liquid-like phase behaviour, exhibit reduced m6A levels. Reciprocally, MTC can recruit the microprocessor to the MIRNA loci, prompting co-transcriptional cleavage of primary miRNA substrates. Additionally, primary miRNA substrates carrying m6A modifications at their single-stranded basal regions are enriched by m6A readers, which retain the microprocessor in the nucleoplasm for continuing processing. This reveals an unappreciated mechanism of phase separation in RNA modification and processing through MTC and microprocessor coordination.

All-Aqueous Embedded 3D Printing for Freeform Fabrication of Biomimetic 3D Constructs

All-aqueous embedded 3D printing, which involves extruding inks in an aqueous bath, has emerged as a transformative platform for the freeform fabrication of 3D constructs with precise control. The use of a supporting bath not only enables the printing of arbitrarily designed 3D constructs but also broadens ink selection for various soft matters, advancing the wide application of this technology. This review focuses on recent progress in the freeform preparation of 3D constructs using all-aqueous embedded 3D printing. It begins by discussing the significance of ultralow interfacial tension in all-liquid embedded printing and highlights the fundamental concepts and properties of all-aqueous system. The review then introduces recent advances in all-aqueous embedded 3D printing and clarifies the key factors affecting printing stability and shape fidelity, aiming to guide expansion and assessment of emerging printing systems used for various representative applications. Furthermore, it proposes the potential scope and applications of this technology, including in vitro models, cytomimetic microreactors, and soft ionic electronics. Finally, the review discusses the challenges facing current all-aqueous embedded 3D printing and offers future perspectives on possible improvements and developments.

PML Nuclear bodies: the cancer connection and beyond

Promyelocytic leukemia (PML) nuclear bodies, membrane-less organelles in the nucleus, play a crucial role in cellular homeostasis. These dynamic structures result from the assembly of scaffolding PML proteins and various partners. Recent crystal structure analyses revealed essential self-interacting domains, while liquid-liquid phase separation contributes to their formation. PML bodies orchestrate post-translational modifications, particularly stress-induced SUMOylation, impacting target protein functions. Serving as hubs in multiple signaling pathways, they influence cellular processes like senescence. Dysregulation of PML expression contributes to diseases, including cancer, highlighting their significance. Therapeutically, PML bodies are promising targets, exemplified by successful acute promyelocytic leukemia treatment with arsenic trioxide and retinoic acid restoring PML bodies. Understanding their functions illuminates both normal and pathological cellular physiology, guiding potential therapies. This review explores recent advancements in PML body biogenesis, biochemical activity, and their evolving biological roles.

From molecular descriptions to cellular functions of intrinsically disordered protein regions

Molecular descriptions of intrinsically disordered protein regions (IDRs) are fundamental to understanding their cellular functions and regulation. NMR spectroscopy has been a leading tool in characterizing IDRs at the atomic level. In this review, we highlight recent conceptual breakthroughs in the study of IDRs facilitated by NMR and discuss emerging NMR techniques that bridge molecular descriptions to cellular functions. First, we review the assemblies formed by IDRs at various scales, from one-to-one complexes to non-stoichiometric clusters and condensates, discussing how NMR characterizes their structural dynamics and molecular interactions. Next, we explore several unique interaction modes of IDRs that enable regulatory mechanisms such as selective transport and switch-like inhibition. Finally, we highlight recent progress in solid-state NMR and in-cell NMR on IDRs, discussing how these methods allow for atomic characterization of full-length IDR complexes in various phases and cellular environments. This review emphasizes recent conceptual and methodological advancements in IDR studies by NMR and offers future perspectives on bridging the gap between in vitro molecular descriptions and the cellular functions of IDRs.

Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin

Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. Non-coding RNA transcripts include a very large number of long noncoding RNAs (lncRNAs). A growing number of identified lncRNAs operate in cellular stress responses, for example in response to hypoxia, genotoxic stress, and oxidative stress. Additionally, lncRNA plays important roles in epigenetic mechanisms operating at chromatin and in maintaining chromatin architecture. Here, we address three lncRNA topics that have had significant recent advances. The first is an emerging role for many lncRNAs in cellular stress responses. The second is the development of high throughput screening assays to develop causal relationships between lncRNAs across the genome with cellular functions. Finally, we turn to recent advances in understanding the role of lncRNAs in regulating chromatin architecture and epigenetics, advances that build on some of the earliest work linking RNA to chromatin architecture.

Calcium ion-triggered liquid-liquid phase separation of silk fibroin and spinning through acidification and shear stress

Many studies try to comprehend and replicate the natural silk spinning process due to its energy-efficient and eco-friendly process. In contrast to spider silk, the mechanisms of how silkworm silk fibroin (SF) undergoes liquid-liquid phase separation (LLPS) concerning the various environmental factors in the silk glands or how the SF coacervates transform into fibers remain unexplored. Here, we show that calcium ions, among the most abundant metal ions inside the silk glands, induce LLPS of SF under macromolecular crowded conditions by increasing both hydrophobic and electrostatic interactions between SF. Furthermore, SF coacervates assemble and further develop into fibrils under acidification and shear force. Finally, we prepare SF fiber using a pultrusion-based dry spinning, mirroring the natural silk spinning system. Unlike previous artificial spinning methods requiring concentrated solutions or harsh solvents, our process uses a less concentrated aqueous SF solution and minimal shear force, offering a biomimetic approach to fiber production.