Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network.

The embryonic stem (ES) cell transcriptional and chromatin-modifying networks are critical for self-renewal maintenance. However, it remains unclear whether these networks functionally interact and, if so, what factors mediate such interactions. Here, we show that WD repeat domain 5 (Wdr5), a core member of the mammalian Trithorax (trxG) complex, positively correlates with the undifferentiated state and is a regulator of ES cell self-renewal. We demonstrate that Wdr5, an "effector" of H3K4 methylation, interacts with the pluripotency transcription factor Oct4. Genome-wide protein localization and transcriptome analyses demonstrate overlapping gene regulatory functions between Oct4 and Wdr5. The Oct4-Sox2-Nanog circuitry and trxG cooperate in activating transcription of key self-renewal regulators, and furthermore, Wdr5 expression is required for the efficient formation of induced pluripotent stem (iPS) cells. We propose an integrated model of transcriptional and epigenetic control, mediated by select trxG members, for the maintenance of ES cell self-renewal and somatic cell reprogramming.

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.

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.

[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.

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.

Hippo-YAP signaling controls lineage differentiation of mouse embryonic stem cells through modulating the formation of super-enhancers.

Hippo-YAP signaling pathway functions in early lineage differentiation of pluripotent stem cells, but the detailed mechanisms remain elusive. We found that knockout (KO) of Mst1 and Mst2, two key components of the Hippo signaling in mouse embryonic stem cells (ESCs), resulted in a disruption of differentiation into mesendoderm lineage. To further uncover the underlying regulatory mechanisms, we performed a series of ChIP-seq experiments with antibodies against YAP, ESC master transcription factors and some characterized histone modification markers as well as RNA-seq assays using wild type and Mst KO samples at ES and day 4 embryoid body stage respectively. We demonstrate that YAP is preferentially co-localized with super-enhancer (SE) markers such as Nanog, Sox2, Oct4 and H3K27ac in ESCs. The hyper-activation of nuclear YAP in Mst KO ESCs facilitates the binding of Nanog, Sox2 and Oct4 as well as H3K27ac modification at the loci where YAP binds. Moreover, Mst depletion results in novel SE formation and enhanced liquid-liquid phase-separated Med1 condensates on lineage associated genes, leading to the upregulation of these genes and the distortion of ESC differentiation. Our study reveals a novel mechanism on how Hippo-YAP signaling pathway dictates ESC lineage differentiation.

Evaluation of N2O sources after fertilizers application in vegetable soil by dual isotopocule plots approach.

Nitrogen (N) fertilizer is the major deriver of nitrous oxide (N2O) emissions in agricultural soil. In the vegetable fields in China both inorganic and organic fertilizers are largely applied as basic sources of nitrogen. Identifying the effects of fertilizer type on soil microbial activities involved in N2O emissions would be of great help for future development of N2O reduction strategies. N2O isotopocule deltas, including δ15Nbulk, δ18O and SP (the 15N site preference in N2O), have been used to analyze microbial pathways of N2O production under different treatments, including bio-organic fertilizer treatment, half bio-organic fertilizer and half urea (mixed fertilizer) treatment, urea treatment and no fertilizer treatment. We measured environmental factors, N2O fluxes and N2O isotopocule deltas to evaluate the dynamics of N2O emissions and constructed the dual isotopocule plots (δ15Nbulk vs. SP and δ18O vs. SP) of the main N2O emission phases to assess contribution of the involved microbial processes (bacterial nitrification, bacterial denitrification, nitrifier denitrification and fungal denitrification). According to the results of the main N2O emission phases, we found that bio-organic fertilizer and mix fertilizer treatments had significantly lower N2O emissions compared to urea treatment, with average N2O fluxes of 1477 ± 204, 1243 ± 187 and 1941 ± 164 µg m-3 h-1, respectively, but there were no significant effects on mineral N and cabbage yield. In addition, the urea treatment and the mixed fertilizer treatment had close and higher nitrogen use efficiency. Furthermore, the δ18O vs. SP plot was useful for providing insight into microbial processes, showing that fungal denitrification/bacterial nitrification was the dominant microbial pathway and bio-organic fertilizer and mix fertilizer treatments had higher denitrification and N2O reduction compared to urea treatment. Those findings demonstrated that the partial replacement of urea with bio-organic fertilizer was a better choice, by means of enhancing denitrification to reduce N2O emissions and also guaranteeing the nitrogen use efficiency and the cabbage yield.

NANOG-dependent function of TET1 and TET2 in establishment of pluripotency.

Molecular control of the pluripotent state is thought to reside in a core circuitry of master transcription factors including the homeodomain-containing protein NANOG, which has an essential role in establishing ground state pluripotency during somatic cell reprogramming. Whereas the genomic occupancy of NANOG has been extensively investigated, comparatively little is known about NANOG-associated proteins and their contribution to the NANOG-mediated reprogramming process. Using enhanced purification techniques and a stringent computational algorithm, we identify 27 high-confidence protein interaction partners of NANOG in mouse embryonic stem cells. These consist of 19 previously unknown partners of NANOG that have not been reported before, including the ten-eleven translocation (TET) family methylcytosine hydroxylase TET1. We confirm physical association of NANOG with TET1, and demonstrate that TET1, in synergy with NANOG, enhances the efficiency of reprogramming. We also find physical association and reprogramming synergy of TET2 with NANOG, and demonstrate that knockdown of TET2 abolishes the reprogramming synergy of NANOG with a catalytically deficient mutant of TET1. These results indicate that the physical interaction between NANOG and TET1/TET2 proteins facilitates reprogramming in a manner that is dependent on the catalytic activity of TET1/TET2. TET1 and NANOG co-occupy genomic loci of genes associated with both maintenance of pluripotency and lineage commitment in embryonic stem cells, and TET1 binding is reduced upon NANOG depletion. Co-expression of NANOG and TET1 increases 5-hydroxymethylcytosine levels at the top-ranked common target loci Esrrb and Oct4 (also called Pou5f1), resulting in priming of their expression before reprogramming to naive pluripotency. We propose that TET1 is recruited by NANOG to enhance the expression of a subset of key reprogramming target genes. These results provide an insight into the reprogramming mechanism of NANOG and uncover a new role for 5-methylcytosine hydroxylases in the establishment of naive pluripotency.

A snoRNA modulates mRNA 3' end processing and regulates the expression of a subset of mRNAs.

mRNA 3' end processing is an essential step in gene expression. It is well established that canonical eukaryotic pre-mRNA 3' processing is carried out within a macromolecular machinery consisting of dozens of trans-acting proteins. However, it is unknown whether RNAs play any role in this process. Unexpectedly, we found that a subset of small nucleolar RNAs (snoRNAs) are associated with the mammalian mRNA 3' processing complex. These snoRNAs primarily interact with Fip1, a component of cleavage and polyadenylation specificity factor (CPSF). We have functionally characterized one of these snoRNAs and our results demonstrated that the U/A-rich SNORD50A inhibits mRNA 3' processing by blocking the Fip1-poly(A) site (PAS) interaction. Consistently, SNORD50A depletion altered the Fip1-RNA interaction landscape and changed the alternative polyadenylation (APA) profiles and/or transcript levels of a subset of genes. Taken together, our data revealed a novel function for snoRNAs and provided the first evidence that non-coding RNAs may play an important role in regulating mRNA 3' processing.

Microbial responses to inorganic nutrient amendment overridden by warming: Consequences on soil carbon stability.

Eutrophication and climate warming, induced by anthropogenic activities, are simultaneously occurring worldwide and jointly affecting soil carbon stability. Therefore, it is of great interest to examine whether and how they interactively affect soil microbial community, a major soil carbon driver. Here, we showed that climate warming, simulated by southward transferring Mollisol soil in agricultural ecosystems from the cold temperate climate zone (N) to warm temperate climate (C) and subtropical climate zone (S), decreased soil organic matter (SOM) by 6%-12%. In contrast, amendment with nitrogen, phosphorus and potassium enhanced plant biomass by 97% and SOM by 6% at the N site, thus stimulating copiotrophic taxa but reducing oligotrophic taxa in relative abundance. However, microbial responses to nutrient amendment were overridden by soil transfer in that nutrient amendment had little effect at the C site but increased recalcitrant carbon-degrading fungal Agaricomycetes and Microbotryomycetes taxa derived from Basidiomycota by 4-17 folds and recalcitrant carbon-degrading genes by 23%-40% at the S site, implying a possible priming effect. Consequently, SOM at the S site was not increased by nutrient amendment despite increased plant biomass by 108%. Collectively, we demonstrate that soil transfer to warmer regions overrides microbial responses to nutrient amendment and weakens soil carbon sequestration.

Land scale biogeography of arsenic biotransformation genes in estuarine wetland.

As an analogue of phosphorus, arsenic (As) has a biogeochemical cycle coupled closely with other key elements on the Earth, such as iron, sulfate and phosphate. It has been documented that microbial genes associated with As biotransformation are widely present in As-rich environments. Nonetheless, their presence in natural environment with low As levels remains unclear. To address this issue, we investigated the abundance levels and diversities of aioA, arrA, arsC and arsM genes in estuarine sediments at low As levels across Southeastern China to uncover biogeographic patterns at a large spatial scale. Unexpectedly, genes involved in As biotransformation were characterized by high abundance and diversity. The functional microbial communities showed a significant decrease in similarity along the geographic distance, with higher turnover rates than taxonomic microbial communities based on the similarities of 16S rRNA genes. Further investigation with niche-based models showed that deterministic processes played primary roles in shaping both functional and taxonomic microbial communities. Temperature, pH, total nitrogen concentration, carbon/nitrogen ratio and ferric iron concentration rather than As content in these sediments were significantly linked to functional microbial communities, while sediment temperature and pH were linked to taxonomic microbial communities. We proposed several possible mechanisms to explain these results.

Selective hierarchical patterning of silicon nanostructures via soft nanostencil lithography.

It is challenging to hierarchically pattern high-aspect-ratio nanostructures on microstructures using conventional lithographic techniques, where photoresist (PR) film is not able to uniformly cover on the microstructures as the aspect ratio increases. Such non-uniformity causes poor definition of nanopatterns over the microstructures. Nanostencil lithography can provide an alternative means to hierarchically construct nanostructures on microstructures via direct deposition or plasma etching through a free-standing nanoporous membrane. In this work, we demonstrate the multiscale hierarchical fabrication of high-aspect-ratio nanostructures on microstructures of silicon using a free-standing nanostencil, which is a nanoporous membrane consisting of metal (Cr), PR, and anti-reflective coating. The nanostencil membrane is used as a deposition mask to define Cr nanodot patterns on the predefined silicon microstructures. Then, deep reactive ion etching is used to hierarchically create nanostructures on the microstructures using the Cr nanodots as an etch mask. With simple modification of the main fabrication processes, high-aspect-ratio nanopillars are selectively defined only on top of the microstructures, on bottom, or on both top and bottom.

Sub-10 nm patterning with DNA nanostructures: a short perspective.

DNA is the hereditary material that contains our unique genetic code. Since the first demonstration of two-dimensional (2D) nanopatterns by using designed DNA origami ∼10 years ago, DNA has evolved into a novel technique for 2D and 3D nanopatterning. It is now being used as a template for the creation of sub-10 nm structures via either 'top-down' or 'bottom-up' approaches for various applications spanning from nanoelectronics, plasmonic sensing, and nanophotonics. This perspective starts with an histroric overview and discusses the current state-of-the-art in DNA nanolithography. Emphasis is put on the challenges and prospects of DNA nanolithography as the next generation nanomanufacturing technique.

Graphene-vertically aligned carbon nanotube hybrid on PDMS as stretchable electrodes.

Stretchable electrodes are a critical component for flexible electronics such as displays, energy devices, and wearable sensors. Carbon nanotubes (CNTs) and graphene have been considered for flexible electrode applications, due to their mechanical strength, high carrier mobility, and excellent thermal conductivity. Vertically aligned carbon nanotubes (VACNTs) provide the possibility to serve as interconnects to graphene sheets as stretchable electrodes that could maintain high electrical conductivity under large tensile strain. In this work, a graphene oxide (GO)-VACNT hybrid on a PDMS substrate was demonstrated. Here, 50 µm long VACNTs were grown on a Si/SiO2 wafer substrate via atmospheric pressure chemical vapor deposition. VACNTs were directly transferred by delamination from the Si/SiO2 to a semi-cured PDMS substrate, ensuring strong adhesion between VACNTs and PDMS upon full curing of the PDMS. GO ink was then printed on the surface of the VACNT carpet and thermally reduced to reduced graphene oxide (rGO). The sheet resistance of the rGO-VACNT hybrid was measured under uniaxial tensile strains up to 300% applied to the substrate. Under applied strain, the rGO-VACNT hybrid maintained a sheet resistant of 386 ± 55 Ω/sq. Cyclic stretching of the rGO-VACNT hybrid was performed with up to 50 cycles at 100% maximum tensile strain, showing no increase in sheet resistance. These results demonstrate promising performance of the rGO-VACNT hybrid for flexible electronics applications.

Controlling the Formation of Nanocavities in Kirkendall Nanoobjects through Sequential Thermal Ex Situ Oxidation and In Situ Reduction Reactions.

Controlling the porosity, the shape, and the morphology of Kirkendall hollow nanostructures is the key factor to tune the properties of these tailor-made nanomaterials which allow in turn broadening their applications. It is shown that by applying a continuous oxidation to copper nanowires following a temperature ramp protocol, one can synthesize cuprous oxide nanotubes containing periodic copper nanoparticles. A further oxidation of such nanoobjects allows obtaining cupric oxide nanotubes with a bamboo-like structure. On the other hand, by applying a sequential oxidation and reduction reactions to copper nanowires, one can synthesize hollow nanoobjects with complex shapes and morphologies that cannot be obtained using the Kirkendall effect alone, such as necklace-like cuprous oxide nanotubes, periodic solid copper nanoparticles or hollow cuprous oxide nanospheres interconnected with single crystal cuprous oxide nanorods, and aligned and periodic hollow nanospheres embedded in a cuprous oxide nanotube. The strategy demonstrated in this study opens new avenues for the engineering of hollow nanostructures with potential applications in gas sensing, catalysis, and energy storage.

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests.

As two major forest types in the subtropics, broadleaved evergreen and broadleaved deciduous forests have long interested ecologists. However, little is known about their belowground ecosystems despite their ecological importance in driving biogeochemical cycling. Here, we used Illumina MiSeq sequencing targeting 16S rRNA gene and a microarray named GeoChip targeting functional genes to analyse microbial communities in broadleaved evergreen and deciduous forest soils of Shennongjia Mountain of Central China, a region known as 'The Oriental Botanic Garden' for its extraordinarily rich biodiversity. We observed higher plant diversity and relatively richer nutrients in the broadleaved evergreen forest than the deciduous forest. In odds to our expectation that plant communities shaped soil microbial communities, we found that soil organic matter quantity and quality, but not plant community parameters, were the best predictors of microbial communities. Actinobacteria, a copiotrophic phylum, was more abundant in the broadleaved evergreen forest, while Verrucomicrobia, an oligotrophic phylum, was more abundant in the broadleaved deciduous forest. The density of the correlation network of microbial OTUs was higher in the broadleaved deciduous forest but its modularity was smaller, reflecting lower resistance to environment changes. In addition, keystone OTUs of the broadleaved deciduous forest were mainly oligotrophic. Microbial functional genes associated with recalcitrant carbon degradation were also more abundant in the broadleaved deciduous forests, resulting in low accumulation of organic matters. Collectively, these findings revealed the important role of soil organic matter in shaping microbial taxonomic and functional traits.

Zfp281 mediates Nanog autorepression through recruitment of the NuRD complex and inhibits somatic cell reprogramming.

The homeodomain transcription factor Nanog plays an important role in embryonic stem cell (ESC) self-renewal and is essential for acquiring ground-state pluripotency during reprogramming. Understanding how Nanog is transcriptionally regulated is important for further dissecting mechanisms of ESC pluripotency and somatic cell reprogramming. Here, we report that Nanog is subjected to a negative autoregulatory mechanism, i.e., autorepression, in ESCs, and that such autorepression requires the coordinated action of the Nanog partner and transcriptional repressor Zfp281. Mechanistically, Zfp281 recruits the NuRD repressor complex onto the Nanog locus and maintains its integrity to mediate Nanog autorepression and, functionally, Zfp281-mediated Nanog autorepression presents a roadblock to efficient somatic cell reprogramming. Our results identify a unique transcriptional regulatory mode of Nanog gene expression and shed light into the mechanistic understanding of Nanog function in pluripotency and reprogramming.

Xiaoyao Pills, a Chinese patent medicine, treats mild and moderate depression: A randomized clinical trial combined with DNA methylation analysis.

BACKGROUND: Xiaoyao pills (XYP) is a commercial Chinese patent medicine used in the treatment of depression. However, the mechanisms underlying its therapeutic effects, as well as the patients who can benefit from XYP, have not been evaluated so far. OBJECTIVES: To this end, we conducted a double-blinded, random, and placebo-controlled clinical trial of orally administered XYP in patients with depression. METHODS: The 17-item Hamilton Depression Rating Scale (HAMD-17) scores were recorded at baseline, and every 2 weeks after the start of treatment. To further elucidate the epigenetic mechanism of XYP, we performed mRNA sequencing and genome-wide DNA methylation sequencing using peripheral blood leukocytes of patients and healthy. RESULTS: XYP effectively alleviated the symptoms in patients with mild or moderate depressive disorders, particularly that of psychomotor retardation. XYP restored aberrant gene expression and DNA methylation patterns associated with depression, and the normalization of DNA methylation correlated with downregulation of several genes. In addition, altered DNA methylation levels in the XYP-treated samples were attributed to increased expression of the DNA methyltransferase DNMT1. CONCLUSIONS: Our study provides new insights into the epigenetic mechanism underlying depression and the therapeutic effects of XYP, along with an experimental basis for using XYP in the treatment of depression. TRIAL REGISTRATION INFORMATION: The name of the registry and number: U.S. CLINICAL TRIALS REGISTRY: The link to the registration: ClinicalTrials.gov ISRCTN12746343 (https://www.isrctn.com/ISRCTN12746343). The name of the trial register is "Efficacy and safety of the Xiaoyao pill for improving the clinical symptoms of stagnation of liver qi (chi) and spleen deficiency". The clinical trial registration number is ISRCTN12746343.

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.