Coactivator condensation at super-enhancers links phase separation and gene control

Identification of FLYWCH1 as a regulator of platinum-resistance in epithelial ovarian cancer

Platinum-based combination chemotherapy remains the backbone of first-line treatment for patients with advanced epithelial ovarian cancer (EOC). While most patients initially respond well to the treatment, patients with relapse ultimately develop platinum resistance. This study identified FLYWCH-type zinc finger-containing protein 1 (FLYWCH1) as an important regulator in the resistance development process. We showed that the loss of FLYWCH1 promotes platinum resistance in EOC cells, and the low FLYWCH1 expression is correlated with poor prognosis of EOC patients. In platinum-sensitive cells, FLYWCH1 colocalizes with H3K9me3, but this association is significantly reduced when cells acquire resistance. The suppression of FLYWCH1 induces gene expression changes resulting in the deregulation of pathways associated with resistance. In line with its connection to H3K9me3, FLYWCH1 induces gene silencing in a synthetic reporter assay and the suppression of FLYWCH1 alters H3K9me3 at promoter regions and repeat elements. The loss of FLYWCH1 leads to the derepression of LTR and Alu repeats, thereby increasing transcriptional plasticity and driving the resistance development process. Our data highlight the importance of FLYWCH1 in chromatin biology and acquisition of platinum resistance through transcriptional plasticity and propose FLYWCH1 as a potential biomarker for predicting treatment responses in EOC patients.

Biophysical Aspect of Assembly and Regulation of Nuclear Bodies Scaffolded by Architectural RNA

A growing body of evidence suggests that nuclear bodies, condensates of RNAs and proteins within the nucleus, are assembled through liquid-liquid phase separation. Some nuclear bodies, such as paraspeckles, are scaffolded by a class of RNAs known as architectural RNAs. From a materials science perspective, RNAs are categorized as polymers, which have been extensively studied in soft matter physics. While soft matter physics has the potential to provide significant insights, it is not directly applicable because transcription and other biochemical processes differentiate RNAs from other polymers studied in this field. Therefore, an interdisciplinary research fusing molecular biology and soft matter physics offers a powerful approach to studying nuclear bodies. This review introduces the biophysical insights provided by such interdisciplinary research in the assembly and regulation of nuclear bodies.

Small Molecules Targeting the Structural Dynamics of AR-V7 Partially Disordered Proteins Using Deep Ensemble Docking

The extensive conformational dynamics of partially disordered proteins hinders the efficiency of traditional in-silico structure-based drug discovery approaches due to the challenge of screening large chemical spaces of compounds, albeit with an excessive number of transient binding sites, quickly making this problem intractable. In this study, using the monomer of the AR-V7 transcription factor splicing variant related to prostate cancer as a test case, we present a deep ensemble docking pipeline that accelerates the screening of small molecule binders targeting partially disordered proteins at functional regions. By swiftly identifying the conformational ensemble of AR-V7 and reducing the dimension of binding sites by a factor of 90, we identify functionally relevant binding sites along the AR-V7 structural ensemble at phase separation-prone regions that have been experimentally shown to contribute to enhanced transcription activity and the onset of tumor growth. Following this, we combine physics-based molecular docking and multiobjective classification machine learning models to speed up the screening for binders in a larger chemical space able to target these functional multiple binding sites of AR-V7. This step increases the multibinding site hit rate of small molecules by a factor of 17 compared to naive molecular docking. Finally, assessing in atomistic molecular dynamics the effect of a selected binder on AR-V7 dynamics, we find that in the presence of the ChEMBL22003 compound, AR-V7 exhibits less conformational entropy, smaller solvent exposure of phase separation-prone regions, and higher solvent exposure of other protein regions, promoting this compound as a potential AR-V7 phase separation modulator.

Targeting a key disulfide linkage to regulate RIG-I condensation and cytosolic RNA-sensing

Maintaining innate immune homeostasis is critical for preventing infections and autoimmune diseases but effective interventions are lacking. Here we identified C864-C869-mediated intermolecular disulfide-linkage formation as a critical step for human RIG-I activation that can be bidirectionally regulated to control innate immune homeostasis. The viral-stimulated C864-C869 disulfide linkage mediates conjugation of an SDS-resistant RIG-I oligomer, which prevents RIG-I degradation by E3 ubiquitin-ligase MIB2 and is necessary for RIG-I to perform liquid-liquid phase separation to compartmentalize downstream signalsome, thereby stimulating type I interferon signalling. The corresponding C865S 'knock-in' caused an oligomerization defect and liquid-liquid phase separation in mouse RIG-I, which inhibited innate immunity, resulting in increased viral load and mortality in mice. Using unnatural amino acids to generate covalent C864-C869 linkage and the development of an interfering peptide to block C864-C869 residues, we bidirectionally regulated RIG-I activities in human diseases. These findings provide in-depth insights on mechanism of RIG-I activation, allowing for the development of methodologies that hold promising implications in clinics.

Deregulated enhancer-promoter communication in cancer through altered nuclear architecture

Enhancers are critical regulators of gene expression. Structural variations in cancer genomes can lead to enhancer hijacking, where oncogenes are activated by mistargeted enhancer activity. Novel enhancer-promoter interactions may also arise through chromosomal rearrangements that create extrachromosomal DNA elements. Additionally, fusion proteins and other mutation-induced alterations in protein properties can lead to the aberrant assembly of proteins into large complexes on the size scale of 0.1-1 μm termed onco-condensates. Transcription factors and co-activators accumulate with cis-regulatory elements in these structures, driving oncogenic programs. Here, we review current evidence of how altered genome architecture and macromolecular assembly result in deregulated enhancer-promoter communication. We discuss emerging strategies to exploit these mechanisms for clinical applications.

DNA binding and mitotic phosphorylation protect polyglutamine proteins from assembly formation

Polyglutamine (polyQ) expansion is associated with pathogenic protein aggregation in neurodegenerative disorders. However, long polyQ tracts are also found in many transcription factors (TFs), such as FOXP2, a TF implicated in human speech. Here, we explore how FOXP2 and other glutamine-rich TFs avoid unscheduled assembly. Throughout interphase, DNA binding, irrespective of sequence specificity, has a solubilizing effect. During mitosis, multiple phosphorylation events promote FOXP2's eviction from chromatin and supplant the solubilizing function of DNA. Further, human-specific amino acid substitutions linked to the evolution of speech map to a mitotic phospho-patch, the "EVO patch," and reduce the propensity of the human FOXP2 to assemble. Fusing the pathogenic form of Huntingtin to either a DNA-binding domain, a phosphomimetic variant of this EVO patch, or a negatively charged peptide is sufficient to diminish assembly formation, suggesting that hijacking mechanisms governing solubility of glutamine-rich TFs may offer new strategies for treatment of polyQ expansion diseases.

Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution

The dynamic three-dimensional spatial conformations of chromosomes demonstrate complex structural variations across single cells, which plays pivotal roles in modulating single-cell specific transcription and epigenetics landscapes. The high rates of missing contacts in single-cell chromatin contact maps impose significant challenges to reconstruct high-resolution spatial chromatin configurations. We develop a data-driven algorithm, Tensor-FLAMINGO, based on a low-rank tensor completion strategy. Implemented on a diverse panel of single-cell chromatin datasets, Tensor-FLAMINGO generates 10kb- and 30kb-resolution spatial chromosomal architectures across individual cells. Tensor-FLAMINGO achieves superior accuracy in reconstructing 3D chromatin structures, recovering missing contacts, and delineating cell clusters. The unprecedented high-resolution characterization of single-cell genome folding enables expanded identification of single-cell specific long-range chromatin interactions, multi-way spatial hubs, and the mechanisms of disease-associated GWAS variants. Beyond the sparse 2D contact maps, the complete 3D chromatin conformations promote an avenue to understand the dynamics of spatially coordinated molecular processes across different cells.

3D genome folding in epigenetic regulation and cellular memory

The 3D folding of the genome is tightly linked to its epigenetic state which maintains gene expression programmes. Although the relationship between gene expression and genome organisation is highly context dependent, 3D genome organisation is emerging as a novel epigenetic layer to reinforce and stabilise transcriptional states. Whether regulatory information carried in genome folding could be transmitted through mitosis is an area of active investigation. In this review, we discuss the relationship between epigenetic state and nuclear organisation, as well as the interplay between transcriptional regulation and epigenetic genome folding. We also consider the architectural remodelling of nuclei as cells enter and exit mitosis, and evaluate the potential of the 3D genome to contribute to cellular memory.

Is Enhancer Function Driven by Protein-Protein Interactions? From Bacteria to Leukemia

The precise regulation of the transcription of genes is essential for normal development and for the maintenance of life. Aberrant gene expression changes drive many human diseases. Despite this, we still do not completely understand how precise gene regulation is controlled in living systems. Enhancers are key regulatory elements that enable cells to specifically activate genes in response to environmental cues, or in a stage or tissue-specific manner. Any model of enhancer activity needs to answer two main questions: (1) how enhancers are able to identify and act on specific genes and (2) how enhancers influence transcription. To address these points, we first outline some of the basic principles that can be established from simpler prokaryotic systems, then discuss recent work on aberrant enhancer activity in leukemia. We argue that highly specific protein-protein interactions are a key driver of enhancer-promoter proximity, allowing enhancer-bound factors to directly act on RNA polymerase and activate transcription.

Nucleolar protein PEXF controls ribosomal RNA synthesis and pluripotency exit

Maintenance and exit from pluripotency of embryonic stem cells (ESCs) are controlled by highly coordinated processes of protein synthesis and ribosome biogenesis (RiBi). ESCs are characterized by low rates of global protein synthesis and high levels of RiBi. Transient reduction of RiBi is a characteristic molecular event during the exit from pluripotency, of which the regulatory mechanism is unclear. Here, we identify that a previously uncharacterized nucleolar protein, pluripotency exit factor (PEXF), encoded by long noncoding RNA LINC00472, plays a role in the transient reduction of RiBi. PEXF dissociates RNA polymerase I from the rDNA through interaction with the rDNA promoter region in a liquid-liquid phase separation-dependent manner, therefore inhibiting the production of pre-ribosomal RNA, a key component of ribosomes. This finding reveals a potential mechanism of exit from pluripotency gated by ribosome levels in human ESCs.

Conservation of Putative Liquid-Liquid Phase Separating Proteins in Multiple Drug-Resistant Mycobacterium tuberculosis: Role in Host-Pathogen Interactions?

We observed a high proportion of proteins in pathogenic Mycobacterium species that can potentially undergo liquid-liquid phase separation (LLPS) mediated biomolecular condensate formation, compared to nonpathogenic species. These proteins mainly include the PE-PPE and PE-PGRS families of proteins that have nucleic acid and protein-protein binding functions, typical of LLPS proteins. We also mapped identified LLPS proteins in M. tuberculosis (M.tb) drug-resistant databases PubMLST and TBProfiler, based upon the WHO 2023 catalogue of resistance-associated mutations. High sequence conservation of LLPS-associated proteins in various multiple drug-resistant M.tb isolates points to their potentially important role in virulence and host-pathogen interactions during pathogenic evolution. This analysis provides a perspective on the role of protein phase separation in the evaluation of M.tb pathogenesis and offers avenues for future research aimed at developing innovative strategies to combat M.tb infection.

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

Most human transcription factor (TF) genes encode multiple protein isoforms differing in DNA-binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators," both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.

Three- and four-stranded nucleic acid structures and their ligands

Nucleic acids have the potential to form not only duplexes, but also various non-canonical secondary structures in living cells. Non-canonical structures play regulatory functions mainly in the central dogma. Therefore, nucleic acid targeting molecules are potential novel therapeutic drugs that can target 'undruggable' proteins in various diseases. One of the concerns of small molecules targeting nucleic acids is selectivity, because nucleic acids have only four different building blocks. Three- and four-stranded non-canonical structures, triplexes and quadruplexes, respectively, are promising targets of small molecules because their three-dimensional structures are significantly different from the canonical duplexes, which are the most abundant in cells. Here, we describe some basic properties of the triplexes and quadruplexes and small molecules targeting the triplexes and tetraplexes.

A transcription coupling model for how enhancers communicate with their target genes

How enhancers communicate with their target genes to influence transcription is an unresolved question of fundamental importance. Current models of the mechanism of enhancer-target gene or enhancer-promoter (E-P) communication are transcription-factor-centric and underappreciate major findings, including that enhancers are themselves transcribed by RNA polymerase II, which correlates with enhancer activity. In this Perspective, we posit that enhancer transcription and its products, enhancer RNAs, are elementary components of enhancer-gene communication. Specifically, we discuss the possibility that transcription at enhancers and at their cognate genes are linked and that this coupling is at the basis of how enhancers communicate with their targets. This model of transcriptional coupling between enhancers and their target genes is supported by growing experimental evidence and represents a synthesis of recent key discoveries.

Ubiquitous MEIS transcription factors actuate lineage-specific transcription to establish cell fate

Control of gene expression is commonly mediated by distinct combinations of transcription factors (TFs). This cooperative action allows the integration of multiple biological signals at regulatory elements, resulting in highly specific gene expression patterns. It is unclear whether combinatorial binding is also necessary to bring together TFs with distinct biochemical functions, which collaborate to effectively recruit and activate RNA polymerase II. Using a cardiac differentiation model, we find that the largely ubiquitous homeodomain proteins MEIS act as actuators, fully activating transcriptional programs selected by lineage-restricted TFs. Combinatorial binding of MEIS with lineage-enriched TFs, GATA, and HOX, provides selectivity, guiding MEIS to function at cardiac-specific enhancers. In turn, MEIS TFs promote the accumulation of the methyltransferase KMT2D to initiate lineage-specific enhancer commissioning. MEIS combinatorial binding dynamics, dictated by the changing dosage of its partners, drive cells into progressive stages of differentiation. Our results uncover tissue-specific transcriptional activation as the result of ubiquitous actuator TFs harnessing general transcriptional activator at tissue-specific enhancers, to which they are directed by binding with lineage- and domain-specific TFs.

The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus

A fertilized egg is initially transcriptionally silent and relies on maternally provided factors to initiate development. For embryonic development to proceed, the oocyte-inherited cytoplasm and the nuclear chromatin need to be reprogrammed to create a permissive environment for zygotic genome activation (ZGA). During this maternal-to-zygotic transition (MZT), which is conserved in metazoans, transient totipotency is induced and zygotic transcription is initiated to form the blueprint for future development. Recent technological advances have enhanced our understanding of MZT regulation, revealing common themes across species and leading to new fundamental insights about transcription, mRNA decay and translation.

Synergistic and antagonistic activities of IRF8 and FOS enhancer pairs during an immune-cell fate switch

Cell fate instructive genes tend to be regulated by large clusters of enhancers. Whether and how individual enhancers within such clusters cooperate in regulating gene expression is poorly understood. We have previously developed a computational method, SEGCOND, which identifies hubs that we termed Putative Transcriptional Condensates (PTCs), consisting of enhancer clusters and associated target genes. Here, we use SEGCOND to identify PTCs in a CEBPA-induced B-cell-to-macrophage transdifferentiation system. We find that PTCs are enriched for highly expressed, lineage-restricted genes and associate with BRD4, a component of transcriptional condensates. Further, we performed single and combinatorial deletions of enhancers within two PTCs active during induced transdifferentiation, harboring IRF8 and FOS. Two enhancers within the IRF8 PTC were found to provide a backup mechanism when combined, safeguarding IRF8 expression and efficient transdifferentiation. Unexpectedly, two individual enhancers within the FOS PTC antagonize each other on day 1 of transdifferentiation, delaying the conversion of B-cells into macrophages and reducing FOS expression, while on day 7, they cooperate to increase FOS levels induced cells. Our results reveal complex, differentiation-stage-specific interactions between individual enhancers within enhancer clusters.

Beyond equilibrium: roles of RNAs in condensate control

Membraneless subcompartments organize various activities in the cell nucleus. Some of them are formed through phase separation that is driven by the polymeric and multivalent nature of biomolecules. Here, we discuss the role of RNAs in regulating nuclear subcompartments. On the one hand, chromatin-associated RNA molecules may act as binding platforms that recruit molecules to specific genomic loci. On the other hand, RNA molecules may act as multivalent scaffolds that stabilize biomolecular condensates. The active production and processing of RNAs inside of nuclear subcompartments drives them out of thermodynamic equilibrium and thereby modulates their properties. Accordingly, RNA content and transcriptional activity appear as key determinants of the biophysical and functional nature of nuclear substructures.

An eRNA transcription checkpoint for diverse signal-dependent enhancer activation programs

The evidence that signal- and ligand-dependent pathways function by activating regulatory enhancer programs suggests that a 'checkpoint' strategy may underline activation of many diversely regulated enhancers. Here we report a molecular mechanism common to several acute signal- and ligand-dependent enhancer activation programs based on release of a shared enhancer RNA (eRNA) transcription checkpoint. It requires recruitment of a DNA-dependent protein kinase catalytic subunit (DNA-PKcs)-phosphorylated RING finger repressor (Krüppel-associated box)-associated protein 1 (KAP1) as a modulator, inhibiting its association with 7SK and E3 small ubiquitin-like modifier (SUMO) ligase activity on the CDK9 subunit of positive transcription elongation factor b (P-TEFb). This facilitates formation of an activated P-TEFb complex, licensing eRNA elongation. Overcoming this checkpoint for signal-dependent enhancer activation occurs in diverse pathways, including estrogen receptor-α, NF-κB-regulated proinflammatory stimulation, androgen receptor and neuronal depolarization. Therefore, a specific strategy required to convert a basal state enhancer P-TEFb complex to an active state to release a conserved checkpoint is apparently employed by several functionally important signal-regulated regulatory enhancers to implement the instructions of the endocrine and paracrine system.

Regulation of 3D genome organization during T cell activation

Within the three-dimensional (3D) nuclear space, the genome organizes into a series of orderly structures that impose important influences on gene regulation. T lymphocytes, crucial players in adaptive immune responses, undergo intricate transcriptional remodeling upon activation, leading to differentiation into specific effector and memory T cell subsets. Recent evidence suggests that T cell activation is accompanied by dynamic changes in genome architecture at multiple levels, providing a unique biological context to explore the functional relevance and molecular mechanisms of 3D genome organization. Here, we summarize recent advances that link the reorganization of genome architecture to the remodeling of transcriptional programs and conversion of cell fates during T cell activation and differentiation. We further discuss how various chromatin architecture regulators, including CCCTC-binding factor and several transcription factors, collectively modulate the genome architecture during this process.

Liquid-liquid phase separation in cell physiology and cancer biology: recent advances and therapeutic implications

Liquid-liquid phase separation (LLPS) is a pivotal biophysical phenomenon that plays a critical role in cellular organization and has garnered significant attention in the fields of molecular mechanism and pathophysiology of cancer. This dynamic process involves the spontaneous segregation of biomolecules, primarily proteins and nucleic acids, into condensed, liquid-like droplets under specific conditions. LLPS drives the formation of biomolecular condensates, which are crucial for various cellular functions. Increasing evidences link alterations in LLPS to the onset and progression of various diseases, particularly cancer. This review explores the diverse roles of LLPS in cancer, highlighting its underlying molecular mechanisms and far-reaching implications. We examine how dysregulated LLPS contributes to cancer development by influencing key processes such as genomic instability, metabolism, and immune evasion. Furthermore, we discuss emerging therapeutic strategies aimed at modulating LLPS, underscoring their potential to revolutionize cancer treatment.

Selective phase separation of transcription factors is driven by orthogonal molecular grammar

Protein production is critically dependent on gene transcription rates, which are regulated by RNA polymerase and a large collection of different transcription factors (TFs). How these transcription factors selectively address different genes is only partially known. Recent discoveries show that the differential condensation of separate TF families through phase separation may contribute to selectivity. Here we address this by conducting phase separation studies on six TFs from three different TF families with residue-scale coarse-grained molecular dynamics simulations. Our exploration of ternary TF phase diagrams reveals four dominant sticker motifs and two orthogonal driving forces that dictate the resultant condensate morphology, pointing to sequence-dependent orthogonal molecular grammar as a generic molecular mechanism that drives selective transcriptional condensation in gene expression.

A Simple Method for Generating Light-induced Clusters of Transcription Factors: Effects on the Nuclear Distribution of OCT4 and on its Interactions With Chromatin

In recent years, a wealth of evidence revealed that many transcription-related molecules concentrate in membrane less nuclear compartments which are now recognized as relevant for transcription regulation. However, many aspects of this relationship remain unclear partly due to the experimental challenges of manipulating the distribution of transcription factors (TFs) in a controlled fashion. Here, we introduce a simple procedure to generate in live cells light-induced clusters (LICs) of TFs labeled with Janelia Fluor® probes through the HaloTag. When irradiated with the appropriate laser, the photooxidation/photobleaching of fluorescent molecules leads to the formation of a cluster which grows by incorporating other TF molecules, some through weak interactions. While the method was mostly tested with OCT4, other TFs such as SOX2 and the hormone-stimulated glucocorticoid receptor also form LICs. Relevantly, the inactive receptor in stem cells fails to form LICs suggesting that the process requires certain TF conformations and/or cellular contexts. Finally, we show that the recruitment of OCT4 to large LICs lowers its nucleoplasmic concentration and modifies both the overall distribution of the TF and its interactions with chromatin. In contrast, the generation of smaller LICs triggers the dissolution of nearby natural condensates of OCT4 but does not affect its nucleoplasmic concentration and OCT4-chromatin interactions. These results suggest that OCT4 condensates act as reservoirs, buffering variations in the nucleoplasmic concentration of this TF. This new method could be a valuable tool for exploring the relation between TFs distribution, landscape of interactions with chromatin and transcriptional output.

Hypoxia-induced phase separation of ZHX2 alters chromatin looping to drive cancer metastasis

Hypoxia and dysregulated phase separation can both activate oncogenic transcriptomic profiles. However, whether hypoxia regulates transcription-associated phase separation remains unknown. Here, we find that zinc fingers and homeoboxes 2 (ZHX2) undergoes phase separation in response to hypoxia, promoting their occupancy on chromatin and activating a cluster of oncogene transcription that is enriched by metastatic genes distinct from the targets of hypoxia-inducible factor (HIF) and pathologically relevant to breast cancer. Hypoxia induces ZHX2 phase separation via a proline-rich intrinsically disordered region (IDR), enhancing phosphorylation of ZHX2 at S625 and S628 that incorporates CCCTC-binding factor (CTCF) in condensates to alter chromatin looping, consequently driving metastatic gene transcription and cancer metastasis. Our findings provide significant insight into oncogene activation and suggest a phase-separation-based therapeutic strategy for cancer.

Microphase separation produces interfacial environment within diblock biomolecular condensates

The phase separation of intrinsically disordered proteins is emerging as an important mechanism for cellular organization. However, efforts to connect protein sequences to the physical properties of condensates, that is, the molecular grammar, are hampered by a lack of effective approaches for probing high-resolution structural details. Using a combination of multiscale simulations and fluorescence lifetime imaging microscopy experiments, we systematically explored a series of systems consisting of diblock elastin-like polypeptides (ELPs). The simulations succeeded in reproducing the variation of condensate stability upon amino acid substitution and revealed different microenvironments within a single condensate, which we verified with environmentally sensitive fluorophores. The interspersion of hydrophilic and hydrophobic residues and a lack of secondary structure formation result in an interfacial environment, which explains both the strong correlation between ELP condensate stability and interfacial hydrophobicity scales, as well as the prevalence of protein-water hydrogen bonds. Our study uncovers new mechanisms for condensate stability and organization that may be broadly applicable.

Studies on Gene Enhancer with KSHV mini-chromatin

Kaposi's sarcoma-associated herpesvirus (KSHV) genome contains a terminal repeats (TR) sequence. Previous studies demonstrated that KSHV TR functions as a gene enhancer for inducible lytic gene promoters. Gene enhancers anchor bromodomain-containing protein 4 (BRD4) at specific genomic region, where BRD4 interacts flexibly with transcription-related proteins through its intrinsically disordered domain and exerts transcription regulatory function. Here, we generated recombinant KSHV with reduced TR copy numbers and studied BRD4 recruitment and its contributions to the inducible promoter activation. Reducing the TR copy numbers from 21 (TR21) to 5 (TR5) strongly attenuated viral gene expression during de novo infection and impaired reactivation. The EF1α promoter encoded in the KSHV BAC backbone also showed reduced promoter activity, suggesting a global attenuation of transcription activity within TR5 latent episomes. Isolation of reactivating cells confirmed that the reduced inducible gene transcription from TR-shortened DNA template and is mediated by decreased efficacies of BRD4 recruitment to viral gene promoters. Separating the reactivating iSLK cell population from non-responders showed that reactivatable iSLK cells harbored larger LANA nuclear bodies (NBs) compared to non-responders. The cells with larger LANA NBs, either due to prior transcription activation or TR copy number, supported KSHV reactivation more efficiently than those with smaller LANA NBs. With auxin-inducible LANA degradation, we confirmed that LANA is responsible for BRD4 occupancies on latent chromatin. Finally, with purified fluorescence-tagged proteins, we demonstrated that BRD4 is required for LANA to form liquid-liquid phase-separated dots. The inclusion of TR DNA fragments further facilitated the formation of larger BRD4-containing LLPS in the presence of LANA, similar to the "cellular enhancer dot" formed by transcription factor-DNA bindings. These results suggest that LANA binding to TR establishes an enhancer domain for infected KSHV episomes. The strength of this enhancer, regulated by TR length or transcription memory, determines the outcome of KSHV replication.

Importance

Gene enhancers are genomic domains that regulate frequency and duration of transcription burst at gene promoters, with BRD4 playing a critical role in their enhancer functions. KSHV latent mini-chromosome also contains an enhancer domain made with multiple copies of 801 bp identical repeat DNA fragments, terminal repeats. Here, we utilized manipulable mini-scale chromatins with convenient inducible KSHV reactivation to systematically examine the association between enhancer strength and the outcome of inducible promoter activation. This study illustrated the amount of BRD4 recruitment at the enhancer associated with frequencies of BRD4 distribution to the inducible promoters during KSHV reactivation and, therefore, KSHV lytic replication. Recruitment of BRD4 to the TR is specifically regulated by KSHV latent protein, LANA. KSHV evolves clever enhancer elements designed to be regulated by the KSHV own latent protein, LANA.

From genes to patterns: a framework for modeling the emergence of embryonic development from transcriptional regulation

Understanding embryonic patterning, the process by which groups of cells are partitioned into distinct identities defined by gene expression, is a central challenge in developmental biology. This complex phenomenon is driven by precise spatial and temporal regulation of gene expression across many cells, resulting in the emergence of highly organized tissue structures. While similar emergent behavior is well understood in other fields, such as statistical mechanics, the regulation of gene expression in development remains less clear, particularly regarding how molecular-level gene interactions lead to the large-scale patterns observed in embryos. In this study, we present a modeling framework that bridges the gap between molecular gene regulation and tissue-level embryonic patterning. Beginning with basic chemical reaction models of transcription at the single-gene level, we progress to model gene regulatory networks (GRNs) that mediate specific cellular functions. We then introduce phenomenological models of pattern formation, including the French Flag and Temporal Patterning/Speed Regulation models, and integrate them with molecular/GRN realizations. To facilitate understanding and application of our models, we accompany our mathematical framework with computer simulations, providing intuitive and simple code for each model. A key feature of our framework is the explicit articulation of underlying assumptions at each level of the model, from transcriptional regulation to tissue patterning. By making these assumptions clear, we provide a foundation for future experimental and theoretical work to critically examine and challenge them, thereby improving the accuracy and relevance of gene regulatory models in developmental biology. As a case study, we explore how different strategies for integrating enhancer activity affect the robustness and evolvability of GRNs that govern embryonic pattern formation. Our simulations suggest that a two-step regulation strategy, enhancer activation followed by competitive integration at the promoter, ensures more standardized integration of new enhancers into developmental GRNs, highlighting the adaptability of eukaryotic transcription. These findings shed new light on the transcriptional mechanisms underlying embryonic patterning, while the overall modeling framework serves as a foundation for future experimental and theoretical investigations.

BmNPV interacts with super-enhancer regions of the host chromatin to hijack cellular transcription machinery

Effective transcriptional activation relies on the spatial interaction between specific DNA elements. DNA interactions have also been observed between DNA viruses and their hosts, with limited understanding of the involved details. Baculovirus is a representative species of DNA virus and has been reported to interact with the host genome in our previous study. However, the biological significance of the baculovirus-host trans-species DNA interaction and its underlying mechanisms remain elusive. Here, using Bombyx mori nucleopolyhedrovirus (BmNPV) as the model virus, we combine epigenome, transcriptome, and biochemical assays to investigate the baculovirus-host DNA interaction. Our data show that BmNPV hijacks the transcriptional regulatory capacity of host super-enhancers (SEs) by physically interacting with these regions on the host genome. This results in the usurpation of the activating capacity of an SE-binding transcription factor GATA by the virus, thereby impairing the SE-induced specific transcriptional activation of the target antiviral genes. Moreover, the hijacked regulatory capacity is spread on BmNPV genome through cis-interaction of viral DNA, leading to enhanced viral gene expression. Overall, our results provide novel insights into the intricate interplay of viruses with host gene expression regulatory networks and broaden the vision in the mechanisms of viral exploitation on cellular machinery.

In silico nanoscope to study the interplay of genome organization and transcription regulation

In eukaryotic genomes, regulated access and communication between cis-regulatory elements (CREs) are necessary for enhancer-mediated transcription of genes. The molecular framework of the chromatin organization underlying such communication remains poorly understood. To better understand it, we develop a multiscale modeling pipeline to build near-atomistic models of the 200 kb Nanog gene locus in mouse embryonic stem cells comprising nucleosomes, transcription factors, co-activators, and RNA polymerase II-mediator complexes. By integrating diverse experimental data, including protein localization, genomic interaction frequencies, cryo-electron microscopy, and single-molecule fluorescence studies, our model offers novel insights into chromatin organization and its role in enhancer-promoter communication. The models equilibrated by high-performance molecular dynamics simulations span a scale of ∼350 nm, revealing an experimentally consistent local and global organization of chromatin and transcriptional machinery. Our models elucidate that the sequence-regulated chromatin accessibility facilitates the recruitment of transcription regulatory proteins exclusively at CREs, guided by the contrasting nucleosome organization compared to other regions. By constructing an experimentally consistent near-atomic model of chromatin in the cellular environment, our approach provides a robust framework for future studies on nuclear compartmentalization, chromatin organization, and transcription regulation.

Cancer-associated mutation at glycine 400 in TIP60 disrupt its phase separation property and catalytic activity resulting in compromised DNA damage repair function of the cell

TIP60 is a tumor suppressor with histone acetyltransferase (HAT) activity, playing a crucial role in regulating chromatin architecture by acetylating histones to enhance accessibility for other regulatory factors. Its function is vital for several key cellular processes, including DNA damage repair, apoptosis, and autophagy. While the downregulation of TIP60 has been associated with various cancers, the effects of naturally occurring mutations in TIP60 on its function in malignancies remain poorly understood. In this study, we explored how cancer-related mutations in TIP60 impact its structure and function. Several deleterious and destabilizing missense mutations were identified and analyzed for structural changes. Molecular dynamics simulations revealed alterations in protein conformational stability and radius of gyration due to these mutations, supported by significant changes in TIP60's solvent accessibility and intramolecular hydrogen bonding. Biochemical assays with recombinant proteins showed a loss of catalytic activity in the G400W mutant. Live cell imaging indicated abnormal localization of the G400W mutant within the nucleus. Additionally, we observed aberrant phase separation of TIP60 caused by the G400W mutation. Notably, the G400W mutation impairs TIP60's catalytic function, preventing effective DNA repair and leaving the genome vulnerable to further mutations. Our findings highlight cancer-associated mutations in TIP60 that may contribute to the molecular mechanisms underlying cancer initiation and progression.

Both the transcriptional activator, Bcd, and repressor, Cic, form small mobile oligomeric clusters

Transcription factors play an essential role in pattern formation during early embryo development, generating a strikingly fast and precise transcriptional response that results in sharp gene expression boundaries. To characterize the steps leading up to transcription, we performed a side-by-side comparison of the nuclear dynamics of two morphogens, a transcriptional activator, Bicoid (Bcd), and a transcriptional repressor, Capicua (Cic), both involved in body patterning along the anterior-posterior axis of the early Drosophila embryo. We used a combination of fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, and single-particle tracking to access a wide range of dynamical timescales. Despite their opposite effects on gene transcription, we find that Bcd and Cic have very similar nuclear dynamics, characterized by the coexistence of a freely diffusing monomer population with a number of oligomeric clusters, which range from low stoichiometry and high mobility clusters to larger, DNA-bound hubs. Our observations are consistent with the inclusion of both Bcd and Cic into transcriptional hubs or condensates, while putting constraints on the mechanism by which these form. These results fit in with the recent proposal that many transcription factors might share a common search strategy for target gene regulatory regions that makes use of their large unstructured regions, and may eventually help explain how the transcriptional response they elicit can be at the same time so fast and so precise.

Coarse-Grained Model of Disordered RNA for Simulations of Biomolecular Condensates

Protein-RNA condensates are involved in a range of cellular activities. Coarse-grained molecular models of intrinsically disordered proteins have been developed to shed light on and predict single-chain properties and phase separation. An RNA model compatible with such models for disordered proteins would enable the study of complex biomolecular mixtures involving RNA. Here, we present a sequence-independent coarse-grained, two-beads-per-nucleotide model of disordered, flexible RNA based on a hydropathy scale. We parametrize the model, which we term CALVADOS-RNA, using a combination of bottom-up and top-down approaches to reproduce local RNA geometry and intramolecular interactions based on atomistic simulations and in vitro experiments. The model semiquantitatively captures several aspects of RNA-RNA and RNA-protein interactions. We examined RNA-RNA interactions by comparing calculated and experimental virial coefficients and nonspecific RNA-protein interaction by studying the reentrant phase behavior of protein-RNA mixtures. We demonstrate the utility of the model by simulating the formation of mixed condensates consisting of the disordered region of MED1 and RNA chains and the selective partitioning of disordered regions from transcription factors into these and compare the results to experiments. Despite the simplicity of our model, we show that it captures several key aspects of protein-RNA interactions and may therefore be used as a baseline model to study several aspects of the biophysics and biology of protein-RNA condensates.

Protein codes promote selective subcellular compartmentalization

Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. In this study, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. We developed a protein language model, ProtGPS, that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in the nucleolus. ProtGPS identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code but also a previously unrecognized code governing their distribution to diverse subcellular compartments.

Activation and memory of the heat shock response is mediated by prion-like domains of sensory HSFs in Arabidopsis

Plants are able to sense and remember heat stress. An initial priming heat stress enables plants to acclimate so that they are able to survive a subsequent higher temperature. The heat shock transcription factors (HSFs) play a crucial role in this process, but the mechanisms by which plants sense heat stress are not well understood. By comprehensively analyzing the binding targets of all the HSFs, we found that HSFs act in a network, with upstream sensory HSFs acting in a transcriptional cascade to activate downstream HSFs and protective proteins. The upstream sensory HSFs are activated by heat at the protein level via a modular prion-like domain (PrD) structure. PrD1 enables HSF sequestration via chaperone binding, allowing release under heat shock. Activated HSFs are recruited into transcriptionally active foci via PrD2, enabling the formation of DNA loops between heat-responsive promoters and enhancer motifs, boosting gene expression days after a priming heat stress. The ability of HSFs to respond rapidly to heat via a protein phase-change response is likely a conserved mechanism in eukaryotes.

CTCF-mediated 3D chromatin sets up the gene expression program in the male germline

Spermatogenesis is a unidirectional differentiation process that generates haploid sperm, but how the gene expression program that directs this process is established is largely unknown. Here we determine the high-resolution three-dimensional (3D) chromatin architecture of mouse male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin dictates the gene expression program required for spermatogenesis. In undifferentiated spermatogonia, CTCF-mediated chromatin interactions between meiosis-specific super-enhancers (SEs) and their target genes precede activation of these SEs on autosomes. These meiotic SEs recruit the master transcription factor A-MYB (MYBL1) in meiotic spermatocytes, which strengthens their 3D contacts and instructs a burst of meiotic gene expression. We also find that at the mitosis-to-meiosis transition, the germline-specific Polycomb protein SCML2 facilitates the resolution of chromatin loops that are specific to mitotic spermatogonia. Moreover, SCML2 and A-MYB help shape the unique 3D chromatin organization of sex chromosomes during meiotic sex chromosome inactivation. We propose that CTCF-mediated 3D chromatin organization regulates epigenetic priming that directs unidirectional differentiation, thereby determining the cellular identity of the male germline.

Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies

Transcriptional dysregulation is a hallmark of cancer initiation and progression, driven by genetic and epigenetic alterations. Enhancer reprogramming has emerged as a pivotal driver of carcinogenesis, with cancer cells often relying on aberrant transcriptional programs. The advent of high-throughput sequencing technologies has provided critical insights into enhancer reprogramming events and their role in malignancy. While targeting enhancers presents a promising therapeutic strategy, significant challenges remain. These include the off-target effects of enhancer-targeting technologies, the complexity and redundancy of enhancer networks, and the dynamic nature of enhancer reprogramming, which may contribute to therapeutic resistance. This review comprehensively encapsulates the structural attributes of enhancers, delineates the mechanisms underlying their dysregulation in malignant transformation, and evaluates the therapeutic opportunities and limitations associated with targeting enhancers in cancer.

The mechanobiology of biomolecular condensates

The central goal of mechanobiology is to understand how the mechanical forces and material properties of organelles, cells, and tissues influence biological processes and functions. Since the first description of biomolecular condensates, it was hypothesized that they obtain material properties that are tuned to their functions inside cells. Thus, they represent an intriguing playground for mechanobiology. The idea that biomolecular condensates exhibit diverse and adaptive material properties highlights the need to understand how different material states respond to external forces and whether these responses are linked to their physiological roles within the cell. For example, liquids buffer and dissipate, while solids store and transmit mechanical stress, and the relaxation time of a viscoelastic material can act as a mechanical frequency filter. Hence, a liquid-solid transition of a condensate in the force transmission pathway can determine how mechanical signals are transduced within and in-between cells, affecting differentiation, neuronal network dynamics, and behavior to external stimuli. Here, we first review our current understanding of the molecular drivers and how rigidity phase transitions are set forth in the complex cellular environment. We will then summarize the technical advancements that were necessary to obtain insights into the rich and fascinating mechanobiology of condensates, and finally, we will highlight recent examples of physiological liquid-solid transitions and their connection to specific cellular functions. Our goal is to provide a comprehensive summary of the field on how cells harness and regulate condensate mechanics to achieve specific functions.

Multivalent nucleosome scaffolding by bromodomain and extraterminal domain tandem bromodomains

Promoter-promoter and enhancer-promoter interactions are enriched in histone acetylation and central to chromatin organization in active genetic regions. Bromodomains are epigenetic "readers" that recognize and bind histone acetylation. Bromodomains often exist in tandem or with other reader domains. Cellular knockdown of the bromodomain and extraterminal domain (BET) protein family disrupts chromatin organization, but the mechanisms through which BET proteins preserve chromatin structure are largely unknown. We hypothesize that BET proteins maintain overall chromatin structure by employing their tandem bromodomains to multivalently scaffold acetylated nucleosomes in an intranucleosomal or internucleosomal manner. To test this hypothesis biophysically, we used small-angle X-ray scattering, electron paramagnetic resonance, and Rosetta protein modeling to show that a disordered linker separates BET tandem bromodomain acetylation binding sites by 15 to 157 Å. Most of these modeled distances are sufficient to span the length of a nucleosome (>57 Å). Focusing on the BET family member BRD4, we employed bioluminescence resonance energy transfer and isothermal titration calorimetry to show that BRD4 bromodomain binding of multiple acetylation sites on a histone tail does not increase BRD4-histone tail affinity, suggesting that BET bromodomain intranucleosome binding is not biologically relevant. Using sucrose gradients and amplified luminescent proximity homogeneous (AlphaScreen) assays, we provide the first direct biophysical evidence that BET bromodomains can scaffold multiple acetylated nucleosomes. Taken together, our results demonstrate that BET bromodomains are capable of multivalent internucleosome scaffolding in vitro. The knowledge gained provides implications for how BET bromodomain-mediated acetylated internucleosome scaffolding may maintain cellular chromatin interactions in active genetic regions.

A Minireview on BET Inhibitors: Beyond Bromodomain Targeting

Bromodomain and extra-terminal domain (BET) proteins are epigenetic readers that recognize the histone acetylation code and play a critical role in regulating gene transcription. Dysregulation of BET proteins is associated with a number of pathologies, including cancer, inflammation-related metabolic disorders, etc. BET proteins can also be hijacked by some viruses and mediate latent viral infections, making BET proteins promising targets for therapeutic intervention. Research in this area has mainly focused on bromodomain inhibition, with less attention paid to other domains. Bromodomain inhibitors have great potential as anticancer and anti-inflammatory drug candidates. However, their broad-spectrum impact on transcription and potential cross-reactivity with non-BET bromodomain-containing proteins raise concerns about unforeseen side effects. Non-bromodomain BET inhibitors hold promise for gaining better control over the expression of host and viral genes by targeting different stages of BET-dependent transcriptional regulation. In this review, we discuss recent advances in the development of non-bromodomain BET inhibitors, as well as their potential applications, advantages, and perspectives.

The nuclear poly(A)-binding protein Pab2/PABPN1 promotes heterochromatin assembly through the formation of Pab2 nuclear condensates

The assembly of constitutive heterochromatin is a prerequisite for maintaining genome stability. However, the mechanism of heterochromatin formation has yet to be completely understood. Here, we demonstrate a crucial role of the nuclear poly(A)-binding protein (PABP) Pab2/PABPN1 in promoting constitutive heterochromatin formation in the fission yeast Schizosaccharomyces japonicus. Histone H3 Lys 9 di- and tri-methylation, hallmarks of heterochromatin, are significantly reduced at centromeres in the absence of Pab2. Pab2 forms nuclear condensates through its RNA-recognition motif (RRM) and the intrinsically disordered domain (IDR), both of which bind to centromeric non-coding RNAs. Intriguingly, two key heterochromatin factors, the histone H3 Lys9 methyltransferase Clr4 and the Mi2-type chromatin remodeler Mit1, associate with centromeres in a Pab2-dependent manner. Pab2 interacts with two putative RNA-binding proteins, the ZC3H3 ortholog Red5 and the RBM26·27 ortholog Rmn1, both essential for heterochromatin formation. Deletion of the Pab2 N-terminal region, which disrupts this interaction, largely abolishes Pab2 function, underscoring the importance of this complex. Pab2 also associates and colocalizes with Ppn1 (a PPP1R10 ortholog), a component of the cleavage and polyadenylation specificity factor (CPSF) complex, and ppn1 mutations disrupt constitutive heterochromatin. Notably, both Ppn1 and Rmn1 are able to interact with Clr4. Our findings reveal that Pab2 plays a pivotal role in heterochromatin assembly by forming nuclear condensates through its RRM/IDR, and Pab2 condensates facilitate the recruitment of Clr4 and Mit1 to centromeres, potentially through its binding proteins, Ppn1 and Rmn1. This study provides new insights into the mechanisms underlying heterochromatin formation and highlights the importance of RNA-binding proteins and phase separation in this process.

Disordered Regions of Condensate-promoting Proteins Have Distinct Molecular Signatures Associated with Cellular Function

Disordered regions of proteins play crucial roles in cellular functions through diverse mechanisms. Some disordered regions function by promoting the formation of biomolecular condensates through dynamic multivalent interactions. While many have assumed that interactions among these condensate-promoting disordered regions are non-specific, recent studies have shown that distinct sequence compositions and patterning lead to specific condensate compositions associated with cellular function. Despite in-depth characterization of several key examples, the full chemical diversity of condensate-promoting disordered regions has not been surveyed. Here, we define a list of disordered regions of condensate-promoting proteins to survey the relationship between sequence and function. We find that these disordered regions show amino acid biases associated with different cellular functions. These amino acid biases are evolutionarily conserved in the absence of positional sequence conservation. Overall, our analysis highlights the relationship between sequence features and function for condensate-promoting disordered regions. This analysis suggests that molecular signatures encoded within disordered regions could impart functional specificity.

Biomolecular Condensates in Telomere Maintenance of ALT Cancer Cells

Alternative Lengthening of Telomeres (ALT) pathway is a telomerase-independent mechanism that utilizes homology-directed repair (HDR) to sustain telomere length in specific cancers. Biomolecular condensates, such as ALT-associated promyelocytic leukemia nuclear bodies (APBs), have emerged as critical players in the ALT pathway, supporting telomere maintenance in ALT-positive cells. These condensates bring together DNA repair proteins, telomeric repeats, and other regulatory elements. By regulating replication stress and promoting DNA synthesis, ALT condensates create an environment conducive to HDR-based telomere extension. This review explores recent advancements in ALT, focusing on understanding the role of biomolecular condensates in ALT and how they impact telomere dynamics and stability.

Transcription regulation by biomolecular condensates

Biomolecular condensates regulate transcription by dynamically compartmentalizing the transcription machinery. Classic models of transcription regulation focus on the recruitment and regulation of RNA polymerase II by the formation of complexes at the 1-10 nm length scale, which are driven by structured and stoichiometric interactions. These complexes are further organized into condensates at the 100-1,000 nm length scale, which are driven by dynamic multivalent interactions often involving domain-ligand pairs or intrinsically disordered regions. Regulation through condensate-mediated organization does not supersede the processes occurring at the 1-10 nm scale, but it provides regulatory mechanisms for promoting or preventing these processes in the crowded nuclear environment. Regulation of transcription by transcriptional condensates is involved in cell state transitions during animal and plant development, cell signalling and cellular responses to the environment. These condensate-mediated processes are dysregulated in developmental disorders, cancer and neurodegeneration. In this Review, we discuss the principles underlying the regulation of transcriptional condensates, their roles in physiology and their dysregulation in human diseases.

Rational design of phytovirucide inhibiting nucleocapsid protein aggregation in tomato spotted wilt virus

Ineffectiveness of managing plant viruses by chemicals has posed serious challenges in crop production. Recently, phase separation has shown to play a key role in viral lifecycle. Using inhibitors that can disturb biomolecular condensates formed by phase separation for virus control has been reported in medical field. However, the applicability of this promising antiviral tactic for plant protection has not been explored. Here, we report an inhibitor, Z9, that targets the tomato spotted wilt virus (TSWV) N protein. Z9 is capable of interacting with the amino acids in the nucleic acid binding region of TSWV N, disrupting the assembly of N and RNA into phase-separated condensates, the reduction of which is detrimental to the stability of the N protein. This study provides a strategy for phase separation-based plant virus control.

Emergent 3D genome reorganization from the stepwise assembly of transcriptional condensates

Transcriptional condensates are clusters of transcription factors, coactivators, and RNA Pol II associated with high-level gene expression, yet how they assemble and function within the cell remains unclear. Here we show that transcriptional condensates form in a stepwise manner to enable both graded and three-dimensional (3D) gene control in the yeast heat shock response. Molecular dissection revealed a condensate cascade. First, the transcription factor Hsf1 clusters upon partial dissociation from the chaperone Hsp70. Next, the coactivator Mediator partitions following further Hsp70 dissociation and Hsf1 phosphorylation. Finally, Pol II condenses, driving the emergent coalescence of HSR genes. Molecular analysis of a series of Hsf1 mutants revealed graded, rather than switch-like, transcriptional activity. Separation-of-function mutants showed that condensate formation can be decoupled from gene activation. Instead, fully assembled HSR condensates promote adaptive 3D genome reconfiguration, suggesting a role of transcriptional condensates beyond gene activation.

Direct ionic stress sensing and mitigation by the transcription factor NFAT5

Rising temperatures and water scarcity caused by climate change are increasingly exposing our cells and tissues to ionic stress, a consequence of elevated cytoplasmic ionic strength that can disrupt protein, organelle, and genome function. Here, we unveil a single-protein mechanism for ionic strength sensing and mitigation in animal cells, one that is notably different from the analogous high osmolarity glycerol kinase cascade in yeast. The Rel family transcription factor NFAT5 directly senses intracellular ionic strength using a C-terminal prion-like domain (PLD). In response to elevated intracellular ionic strength, this PLD is necessary and sufficient to coordinate an adaptive gene expression program by recruiting the transcriptional coactivator BRD4. The purified NFAT5 PLD forms condensates in response to elevated solution ionic strength in vitro, and human NFAT5 alone is sufficient to reconstitute a mammalian transcriptional response to ionic stress in yeast. We propose that ion-sensitive conformational changes in a PLD directly regulate transcription to maintain ionic strength homeostasis in animal cells.

Intrinsically disordered regions as facilitators of the transcription factor target search

Transcription factors (TFs) contribute to organismal development and function by regulating gene expression. Despite decades of research, the factors determining the specificity and speed at which eukaryotic TFs detect their target binding sites remain poorly understood. Recent studies have pointed to intrinsically disordered regions (IDRs) within TFs as key regulators of the process by which TFs find their target sites on DNA (the TF target search). However, IDRs are challenging to study because they can confer specificity despite low sequence complexity and can be functionally conserved despite rapid sequence divergence. Nevertheless, emerging computational and experimental approaches are beginning to elucidate the sequence-function relationship within the IDRs of TFs. Additional insights are informing potential mechanisms underlying the IDR-directed search for the DNA targets of TFs, including incorporation into biomolecular condensates, facilitating TF co-localization, and the hypothesis that IDRs recognize and directly interact with specific genomic regions.

Liquid condensates: a new barrier to loop extrusion?

Liquid-liquid phase separation (LLPS), driven by dynamic, low-affinity multivalent interactions of proteins and RNA, results in the formation of macromolecular condensates on chromatin. These structures are likely to provide high local concentrations of effector factors responsible for various processes including transcriptional regulation and DNA repair. In particular, enhancers, super-enhancers, and promoters serve as platforms for condensate assembly. In the current paradigm, enhancer-promoter (EP) interaction could be interpreted as a result of enhancer- and promoter-based condensate contact/fusion. There is increasing evidence that the spatial juxtaposition of enhancers and promoters could be provided by loop extrusion (LE) by SMC complexes. Here, we propose that condensates may act as barriers to LE, thereby contributing to various nuclear processes including spatial contacts between regulatory genomic elements.

The phenylalanine-and-glycine repeats of NUP98 oncofusions form condensates that selectively partition transcriptional coactivators

Recurrent cancer-causing fusions of NUP98 produce higher-order assemblies known as condensates. How NUP98 oncofusion-driven condensates activate oncogenes remains poorly understood. Here, we investigate NUP98-PHF23, a leukemogenic chimera of the disordered phenylalanine-and-glycine (FG)-repeat-rich region of NUP98 and the H3K4me3/2-binding plant homeodomain (PHD) finger domain of PHF23. Our integrated analyses using mutagenesis, proteomics, genomics, and condensate reconstitution demonstrate that the PHD domain targets condensate to the H3K4me3/2-demarcated developmental genes, while FG repeats determine the condensate composition and gene activation. FG repeats are necessary to form condensates that partition a specific set of transcriptional regulators, notably the KMT2/MLL H3K4 methyltransferases, histone acetyltransferases, and BRD4. FG repeats are sufficient to partition transcriptional regulators and activate a reporter when tethered to a genomic locus. NUP98-PHF23 assembles the chromatin-bound condensates that partition multiple positive regulators, initiating a feedforward loop of reading-and-writing the active histone modifications. This network of interactions enforces an open chromatin landscape at proto-oncogenes, thereby driving cancerous transcriptional programs.

The nuclear pore complex connects energy sensing to transcriptional plasticity in longevity

As the only gateway governing nucleocytoplasmic transport, the nuclear pore complex (NPC) maintains fundamental cellular processes and deteriorates with age. However, the study of age-related roles of single NPC components remains challenging owing to the complexity of NPC composition. Here we demonstrate that the master energy sensor, AMPK, post-translationally regulates the abundance of the nucleoporin NPP-16/NUP50 in response to nutrient availability and energetic stress. In turn, NPP-16/NUP50 promotes transcriptomic activation of lipid catabolism to extend the lifespan of Caenorhabditis elegans independently of its role in nuclear transport. Rather, the intrinsically disordered region (IDR) of NPP-16/NUP50, through direct interaction with the transcriptional machinery, transactivates the promoters of catabolic genes. Remarkably, elevated NPP-16/NUP50 levels are sufficient to promote longevity and metabolic stress defenses. AMPK-NUP50 signaling is conserved to human, indicating that bridging energy sensing to metabolic adaptation is an ancient role of this signaling axis.