The PTM profiling of CTCF reveals the regulation of 3D chromatin structure by O-GlcNAcylation.

CCCTC-binding factor (CTCF), a ubiquitously expressed and highly conserved protein, is known to play a critical role in chromatin structure. Post-translational modifications (PTMs) diversify the functions of protein to regulate numerous cellular processes. However, the effects of PTMs on the genome-wide binding of CTCF and the organization of three-dimensional (3D) chromatin structure have not been fully understood. In this study, we uncovered the PTM profiling of CTCF and demonstrated that CTCF can be O-GlcNAcylated and arginine methylated. Functionally, we demonstrated that O-GlcNAcylation inhibits CTCF binding to chromatin. Meanwhile, deficiency of CTCF O-GlcNAcylation results in the disruption of loop domains and the alteration of chromatin loops associated with cellular development. Furthermore, the deficiency of CTCF O-GlcNAcylation increases the expression of developmental genes and negatively regulates maintenance and establishment of stem cell pluripotency. In conclusion, these results provide key insights into the role of PTMs for the 3D chromatin structure.

Precise prediction of phase-separation key residues by machine learning.

Understanding intracellular phase separation is crucial for deciphering transcriptional control, cell fate transitions, and disease mechanisms. However, the key residues, which impact phase separation the most for protein phase separation function have remained elusive. We develop PSPHunter, which can precisely predict these key residues based on machine learning scheme. In vivo and in vitro validations demonstrate that truncating just 6 key residues in GATA3 disrupts phase separation, enhancing tumor cell migration and inhibiting growth. Glycine and its motifs are enriched in spacer and key residues, as revealed by our comprehensive analysis. PSPHunter identifies nearly 80% of disease-associated phase-separating proteins, with frequent mutated pathological residues like glycine and proline often residing in these key residues. PSPHunter thus emerges as a crucial tool to uncover key residues, facilitating insights into phase separation mechanisms governing transcriptional control, cell fate transitions, and disease development.

[Role of Liquid-Liquid Phase Separation in Cell Fate Transition and Diseases].

Liquid-liquid phase separation (LLPS), a novel mechanism of the organization and formation of cellular structures, plays a vital role in regulating cell fate transitions and disease pathogenesis and is gaining widespread attention. LLPS may lead to the assemblage of cellular structures with liquid-like fluidity, such as germ granules, stress granules, and nucleoli, which are classic membraneless organelles. These structures are typically formed through the high-concentration liquid aggregation of biomacromolecules driven by weak multivalent interactions. LLPS is involved in regulating various intracellular life activities and its dysregulation may cause the disruption of cellular functions, thereby contributing to the pathogenesis and development of neurodegenerative diseases, infectious diseases, cancers, etc. Herein, we summarized published findings on the LLPS dynamics of membraneless organelles in physiological and pathological cell fate transition, revealing their crucial roles in cell differentiation, development, and various pathogenic processes. This paper provides a fresh theoretical framework and potential therapeutic targets for LLPS-related studies, opening new avenues for future research.

Photo-Induced, Phenylhydrazine-Promoted Transition-Metal-Free Dehalogenation of Aryl Fluorides, Chlorides, Bromides, and Iodides.

In this study, we present a straightforward and highly effective photo-triggered hydrogenation method for aryl halides, devoid of transition-metal catalysts. Through the synergistic utilization of light, PhNHNH2, and a base, we have successfully initiated the desired radical-mediated hydrogenation process. Remarkably, utilizing mild reaction conditions, a wide range of aryl halides, including fluorides, chlorides, bromides, and iodides, can be selectively transformed into their corresponding (hetero)arene counterparts, with exceptional yields. Additionally, this approach demonstrates a remarkable compatibility with diverse functional groups and heterocyclic compounds, highlighting its versatility and potential for use in various chemical transformations.

Simultaneous profiling of chromatin architecture and transcription in single cells.

The three-dimensional structure of chromatin plays a crucial role in development and disease, both of which are associated with transcriptional changes. However, given the heterogeneity in single-cell chromatin architecture and transcription, the regulatory relationship between the three-dimensional chromatin structure and gene expression is difficult to explain based on bulk cell populations. Here we develop a single-cell, multimodal, omics method allowing the simultaneous detection of chromatin architecture and messenger RNA expression by sequencing (single-cell transcriptome sequencing (scCARE-seq)). Applying scCARE-seq to examine chromatin architecture and transcription from 2i to serum single mouse embryonic stem cells, we observe improved separation of cell clusters compared with single-cell chromatin conformation capture. In addition, after defining the cell-cycle phase of each cell through chromatin architecture extracted by scCARE-seq, we find that periodic changes in chromatin architecture occur in parallel with transcription during the cell cycle. These findings highlight the potential of scCARE-seq to facilitate comprehensive analyses that may boost our understanding of chromatin architecture and transcription in the same single cell.

Electronic Beam Steering Metamaterial Antenna with Dual-Tuned Mode of Liquid Crystal Material.

In this study, a dual-tuned mode of liquid crystal (LC) material was proposed and adopted on reconfigurable metamaterial antennas to expand the fixed-frequency beam-steering range. The novel dual-tuned mode of the LC is composed of double LC layers combined with composite right/left-handed (CRLH) transmission line theory. Through a multi-separated metal layer, the double LC layers can be loaded with controllable bias voltage independently. Therefore, the LC material exhibits four extreme states, among which the permittivity of LC can be varied linearly. On the strength of the dual-tuned mode of LC, a CRLH unit cell is elaborately designed on three-layer substrates with balanced dispersion values under arbitrary LC state. Then five CRLH unit cells are cascaded to form an electronically controlled beam-steering CRLH metamaterial antenna on a downlink Ku satellite communication band with dual-tuned characteristics. The simulated results demonstrate that the metamaterial antenna features' continuous electronic beam-steering capacity from broadside to -35° at 14.4 GHz. Furthermore, the beam-steering properties are implemented in a broad frequency band from 13.8 GHz to 17 GHz, with good impedance matching. The proposed dual-tuned mode can make the regulation of LC material more flexible and enlarge the beam-steering range simultaneously.

A decade of liver organoids: Advances in disease modeling.

Liver organoids are three-dimensional cellular tissue models in which cells interact to form unique structures in culture. During the past 10 years, liver organoids with various cellular compositions, structural features, and functional properties have been described. Methods to create these advanced human cell models range from simple tissue culture techniques to complex bioengineering approaches. Liver organoid culture platforms have been used in various research fields, from modeling liver diseases to regenerative therapy. This review discusses how liver organoids are used to model disease, including hereditary liver diseases, primary liver cancer, viral hepatitis, and nonalcoholic fatty liver disease. Specifically, we focus on studies that used either of two widely adopted approaches: differentiation from pluripotent stem cells or epithelial organoids cultured from patient tissues. These approaches have enabled the generation of advanced human liver models and, more importantly, the establishment of patient-tailored models for evaluating disease phenotypes and therapeutic responses at the individual level.

The dynamics of three-dimensional chromatin organization and phase separation in cell fate transitions and diseases.

Cell fate transition is a fascinating process involving complex dynamics of three-dimensional (3D) chromatin organization and phase separation, which play an essential role in cell fate decision by regulating gene expression. Phase separation is increasingly being considered a driving force of chromatin folding. In this review, we have summarized the dynamic features of 3D chromatin and phase separation during physiological and pathological cell fate transitions and systematically analyzed recent evidence of phase separation facilitating the chromatin structure. In addition, we discuss current advances in understanding how phase separation contributes to physical and functional enhancer-promoter contacts. We highlight the functional roles of 3D chromatin organization and phase separation in cell fate transitions, and more explorations are required to study the regulatory relationship between 3D chromatin organization and phase separation. 3D chromatin organization (shown by Hi-C contact map) and phase separation are highly dynamic and play functional roles during early embryonic development, cell differentiation, somatic reprogramming, cell transdifferentiation and pathogenetic process. Phase separation can regulate 3D chromatin organization directly, but whether 3D chromatin organization regulates phase separation remains unclear.

Apoptotic vesicles inherit SOX2 from pluripotent stem cells to accelerate wound healing by energizing mesenchymal stem cells.

Billions of cells undergo apoptosis every day in the human body, resulting in the generation of a large number of apoptotic vesicles (apoVs) to maintain organ and tissue homeostasis. However, the characteristics and function of pluripotent stem cell (PSC)-derived apoVs (PSC-apoVs) are largely unknown. In this study, we showed that human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) produced larger numbers of apoVs than human umbilical cord mesenchymal stem cells (UMSCs) do when induced by staurosporine. In addition to expressing the general apoV markers cleaved caspase 3, Annexin V, calreticulin, ALIX, CD63 and TSG101, ESC-apoVs inherited pluripotent-specific molecules SOX2 from ESCs in a caspase 3-dependent manner. Moreover, ESC-apoVs could promote mouse skin wound healing via transferring SOX2 into skin MSCs via activating Hippo signaling pathway. Collectively, these findings reveal that apoVs are capable of inheriting pluripotent molecules from ESCs to energize adult stem cells, suggesting the potential to use PSC-apoVs for clinical applications. STATEMENT OF SIGNIFICANCE: Apoptotic vesicles (apoVs) are essential to maintain organ and tissue homeostasis. However, the characteristics and function of pluripotent stem cell (PSC)-derived apoVs (PSC-apoVs) are largely unknown. This study showed that PSC-apoVs produced 100 times more apoVs than human umbilical cord mesenchymal stem cells (UMSCs). Despite expressing the general apoV makers, PSC-apoVs inherited pluripotent-specific molecule SOX2 from PSCs in a caspase 3-dependent manner. Moreover, PSC-apoVs promote mouse skin wound healing via transferring SOX2 into skin MSCs, thus activating Hippo signaling pathway. These findings reveal that apoVs are capable of inheriting pluripotent molecules from PSCs to energize adult stem cells, thus providing a cell-free strategy for clinical applications of PSCs.

CTCF organizes inter-A compartment interactions through RYBP-dependent phase separation.

Chromatin is spatially organized into three-dimensional structures at different levels including A/B compartments, topologically associating domains and loops. The canonical CTCF-mediated loop extrusion model can explain the formation of loops. However, the organization mechanisms underlying long-range chromatin interactions such as interactions between A-A compartments are still poorly understood. Here we show that different from the canonical loop extrusion model, RYBP-mediated phase separation of CTCF organizes inter-A compartment interactions. Based on this model, we designed and verified an induced CTCF phase separation system in embryonic stem cells (ESCs), which facilitated inter-A compartment interactions, improved self-renewal of ESCs and inhibited their differentiation toward neural progenitor cells. These findings support a novel and non-canonical role of CTCF in organizing long-range chromatin interactions via phase separation.

Estrogen and BRCA1 deficiency synergistically induce breast cancer mutation-related DNA damage.

Estrogen (E2) is crucial for the development of breast cancer caused by BRCA1 mutation, and can increase the DNA damage in BRCA1-deficient cells. However, the mechanisms through which BRCA1 deficiency and E2 synergistically induce DNA damage remains unclear. In this study, we analyzed the distribution of DNA damage in E2-treated BRCA1-deficient cells. We detected DNA lesions in the vicinity of genes that are transcriptionally activated by estrogen receptor-α (ER). Loss of BRCA1 altered chromatin binding by ER, which significantly affected the distribution of DNA damage. Moreover, these changes were associated with the established mutations in BRCA1-mutant breast cancer. Taken together, our findings reveal a new mechanism underlying the DNA damage in breast cancer cells that is synergistically induced by BRCA1 deficiency and E2.

Effect of Different Fertilizations on the Plant-Available Nitrogen in Soil Profile (0-100 cm): A Study on Chinese Cabbage.

The aim of this study is to analyze the variations in the plant-available nitrogen (PAN) concentrations in the soil profile. Different fertilizers were applied for Chinese cabbage plantation (CCP) in the experimental fields of the Shunyi region. The treatments used for the comparative analysis are (i) no fertilizer and plantation (NVP), (ii) no fertilizer with CCP (CTP), (iii) fertilization as urea (URP), and (iv) potassium nitrate (KNP) and chicken manure (CMP) with CCP. It was concluded that the yield was significantly high in URP, CMP, and KNP as compared to CTP. In URP, maximum PAN in soil layers 0-60 cm was recorded during crop production and in 60-100 cm after harvesting as compared to other treatments. Significant variations in soil pH and electrical conductivity (EC) for the soil profile (0-100 cm) from the initial values with respect to time and treatments were observed. CMP showed maximum ammonium in the upper layers of 0-60 cm throughout the season, whereas minimum PAN was observed in NVP but increased in lower layers of 60-100 cm. In general, all fertilizers raised the PAN below the soil 60-100 cm which indicates their potential for nitrate leaching (NL).

Comprehensive 3D epigenomic maps define limbal stem/progenitor cell function and identity.

The insights into how genome topology couples with epigenetic states to govern the function and identity of the corneal epithelium are poorly understood. Here, we generate a high-resolution Hi-C interaction map of human limbal stem/progenitor cells (LSCs) and show that chromatin multi-hierarchical organisation is coupled to gene expression. By integrating Hi-C, epigenome and transcriptome data, we characterize the comprehensive 3D epigenomic landscapes of LSCs. We find that super-silencers mediate gene repression associated with corneal development, differentiation and disease via chromatin looping and/or proximity. Super-enhancer (SE) interaction analysis identified a set of SE interactive hubs that contribute to LSC-specific gene activation. These active and inactive element-anchored loop networks occur within the cohesin-occupied CTCF-CTCF loops. We further reveal a coordinated regulatory network of core transcription factors based on SE-promoter interactions. Our results provide detailed insights into the genome organization principle for epigenetic regulation of gene expression in stratified epithelia.

The influence of soil acidification on N2O emissions derived from fungal and bacterial denitrification using dual isotopocule mapping and acetylene inhibition.

Denitrification, as both origins and sinks of N2O, occurs extensively, and is of critical importance for regulating N2O emissions in acidified soils. However, whether soil acidification stimulates N2O emissions, and if so for what reason contributes to stimulate the emissions is uncertain and how the N2O fractions from fungal (ffD) and bacterial (fbD) denitrification change with soil pH is unclear. Thus, a pH gradient (6.2, 7.1, 8.7) was set via manipulating cropland soils (initial pH 8.7) in North China to illustrate the effect of soil acidification on fungal and bacterial denitrification after the addition of KNO3 and glucose. For source partitioning, we used and compared SP/δ18O mapping approach (SP/δ18O MAP) and acetylene inhibition technique combined isotope two endmember mixing model (AIT-IEM). The results showed significantly higher N2O emissions in the acidified soils (pH 6.2 and pH 7.1) compared with the initial soil (pH 8.7). The cumulative N2O emissions during the whole incubation period (15 days) ranged from 7.1 mg N kg-1 for pH 8.7-18.9 mg N kg-1 for pH 6.2. With the addition of glucose, relative to treatments without glucose, this emission also increased with the decrement of pH values, and were significantly stimulated. Similarly, the highest N2O emissions and N2O/(N2O + N2) ratios (rN2O) were observed in the pH 6.2 treatment. But the difference was the highest cumulative N2O + N2 emissions, which were recorded in the pH 7.1 treatment based on SP/δ18O MAP. Based on both approaches, ffD values slightly increased with the acidification of soil, and bacterial denitrification was the dominant pathway in all treatments. The SP/δ18O MAP data indicated that both the rN2O and ffD were lower compared to AIT-IEM. It has been known for long that low pH may lead to high rN2O of denitrification and ffD, but our documentation of a pervasive pH-control of rN2O and ffD by utilizing combined SP/δ18O MAP and AIT-IEM is new. The results of the evaluated N2O emissions by acidified soils are finely explained by high rN2O and enhanced ffD. We argue that soil pH management should be high on the agenda for mitigating N2O emissions in the future, particularly for regions where long-term excessive nitrogen fertilizer is likely to acidify the soils.

Bend family proteins mark chromatin boundaries and synergistically promote early germ cell differentiation.

Understanding the regulatory networks for germ cell fate specification is necessary to developing strategies for improving the efficiency of germ cell production in vitro. In this study, we developed a coupled screening strategy that took advantage of an arrayed bi-molecular fluorescence complementation (BiFC) platform for protein-protein interaction screens and epiblast-like cell (EpiLC)-induction assays using reporter mouse embryonic stem cells (mESCs). Investigation of candidate interaction partners of core human pluripotent factors OCT4, NANOG, KLF4 and SOX2 in EpiLC differentiation assays identified novel primordial germ cell (PGC)-inducing factors including BEN-domain (BEND/Bend) family members. Through RNA-seq, ChIP-seq, and ATAC-seq analyses, we showed that Bend5 worked together with Bend4 and helped mark chromatin boundaries to promote EpiLC induction in vitro. Our findings suggest that BEND/Bend proteins represent a new family of transcriptional modulators and chromatin boundary factors that participate in gene expression regulation during early germline development.

Protocol to alter a protein's phase separation capacity to control cell fate transitions.

Phase separation of proteins regulates transcription. Here, we present a protocol to manipulate phase separation capacity of a protein. We use this protocol to disrupt phase separation by mutating residues at intrinsically disordered regions (IDRs). Further, we rescue the disabled phase separation by fusing an IDR known to drive phase separation. Phase separation promotes cell fate transitions, whereas disruption of phase attenuates the transitions. The major challenge is how to effectively predict mutation residues. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).

Manipulation of TAD reorganization by chemical-dependent genome linking.

Reorganization of topologically associated domain (TAD) is considered to be a novel mechanism for cell fate transitions. Here, we present a protocol to manipulate TAD via abscisic acid (ABA)-dependent genome linking. We use this protocol to merge two adjacent TADs and evaluate the influence on cell fate transitions. The advantages are that the manipulation does not change the genome and is reversible by withdrawing ABA. The major challenge is how to select linking loci for efficient TAD reorganization. For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).

OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human.

Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). While the protein-protein interactions of core pluripotency factors have been identified in mouse ESCs, their interactome in human ESCs (hESCs) has not to date been explored. Here we mapped the OCT4 interactomes in naïve and primed hESCs, revealing extensive connections to mammalian ATP-dependent nucleosome remodeling complexes. In naïve hESCs, OCT4 is associated with both BRG1 and BRM, the two paralog ATPases of the BAF complex. Genome-wide location analyses and genetic studies reveal that these two enzymes cooperate in a functionally redundant manner in the transcriptional regulation of blastocyst-specific genes. In contrast, in primed hESCs, OCT4 cooperates with BRG1 and SOX2 to promote chromatin accessibility at ectodermal genes. This work reveals how a common transcription factor utilizes differential BAF complexes to control distinct transcriptional programs in naïve and primed hESCs.

Distinguishing N2O and N2 ratio and their microbial source in soil fertilized for vegetable production using a stable isotope method.

Vegetable production systems with excessive nitrogen fertilizer result in severe N2O emission. It is pivotal to identify the source of N2O for reducing N2O emission, but estimating microbial pathways of N2O production is very difficult due to the existence of N2O reduction. A promising tool can address this problem by using δ18O and δ15NSP of N2O to construct a dual isotopocule plot. For ascertaining the microbial pathways of N2O production and consumption in soil fertilized for vegetable production, four treatments were set up: urea (U), half urea and half organic fertilizer (UO), organic fertilizer (O) and no fertilizer (NF), and the experiment was carried out continuously for two years. The δ18O vs. δ15NSP plot method indicated that the nitrification/fungal denitrification was a dominant in N2O emission, and the U treatment was the highest, followed by OU, O and NF in the both years. Among the different treatments, furthermore, the N2O flux had the same trend, whereas the extent of N2O reduction showed an opposite trend. Overall, inorganic fertilizer enhances nitrification/fungal denitrification and hinders reduction of N2O to N2, resulting in a larger amount of N2O emission. However, organic fertilizer increases the contribution of denitrification and greatly improves the extent of N2O reduction, which helps to reduce N2O emission. Therefore, organic fertilizer is crucial to reducing N2O emission by enhancing N2O reduction and should be properly applied in production practice.