Mapping adipocyte interactome networks by HaloTag-enrichment-mass spectrometry.

Mapping protein interaction complexes in their natural state in vivo is arguably the Holy Grail of protein network analysis. Detection of protein interaction stoichiometry has been an important technical challenge, as few studies have focused on this. This may, however, be solved by artificial intelligence (AI) and proteomics. Here, we describe the development of HaloTag-based affinity purification mass spectrometry (HaloMS), a high-throughput HaloMS assay for protein interaction discovery. The approach enables the rapid capture of newly expressed proteins, eliminating tedious conventional one-by-one assays. As a proof-of-principle, we used HaloMS to evaluate the protein complex interactions of 17 regulatory proteins in human adipocytes. The adipocyte interactome network was validated using an in vitro pull-down assay and AI-based prediction tools. Applying HaloMS to probe adipocyte differentiation facilitated the identification of previously unknown transcription factor (TF)-protein complexes, revealing proteome-wide human adipocyte TF networks and shedding light on how different pathways are integrated.

PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment.

Polycomb group proteins (PcG), polycomb repressive complexes 1 and 2 (PRC1 and 2), repress lineage inappropriate genes during development to maintain proper cellular identities. It has been recognized that PRC1 localizes at the replication fork, however, the precise functions of PRC1 during DNA replication are elusive. Here, we reveal that a variant PRC1 containing PCGF1 (PCGF1-PRC1) prevents overloading of activators and chromatin remodeling factors on nascent DNA and thereby mediates proper deposition of nucleosomes and correct downstream chromatin configurations in hematopoietic stem and progenitor cells (HSPCs). This function of PCGF1-PRC1 in turn facilitates PRC2-mediated repression of target genes such as Hmga2 and restricts premature myeloid differentiation. PCGF1-PRC1, therefore, maintains the differentiation potential of HSPCs by linking proper nucleosome configuration at the replication fork with PcG-mediated gene silencing to ensure life-long hematopoiesis.

Tailoring Microstructure and Morphology via Sequential Fluorination to Enhance the Photovoltaic Performance of Low-Cost Polymer Donors for Organic Solar Cells.

For utilizing organic solar cells (OSCs) for commercial applications, reducing the overall cost of the photo absorbent materials is also very crucial. Herein, such a challenge is addressed by synergistically controlling the amount of fluorine (F)-substituents (n = 2, 4) on a low-cost wide-bandgap molecular design involving alternate fluorinated-thienyl benzodithiophene donor and 2,5-difluoro benzene (2FBn) or 2,3,5,6 tetrafluorobenzene (4FBn) to form two new polymer donors PBDT-2FBn and PBDT-4FBn, respectively. As expected, sequential fluorination causes a lowering of the frontier energy levels and planarization of polymer backbone via F···S and C-H···F noncovalent molecular locks, which results in more pronounced molecular packing and enhanced crystallinity from PBDT-2FBn to PBDT-4FBn. By mixing with IT-4F acceptor, PBDT-2FBn:IT-4F-based blend demonstrates favorable molecular orientation with shorter π-π stacking distance, higher carrier mobilities and desirable nanoscale morphology, hence delivering a higher power conversion efficiency (PCE) of 9.3% than PBDT-2FBn:IT-4F counterpart (8.6%). Furthermore, pairing PBDT-2FBn with BTP-BO-4Cl acceptor further improved absorption range and promoted privileged morphology for efficient exciton dissociation and charge transport, resulting in further improvement of PCE to 10.2% with remarkably low energy loss of 0.46 eV. Consequently, this study provides valuable guidelines for designing efficient and low-cost polymer donors for OSC applications.

Cooperative recruitment of RDR6 by SGS3 and SDE5 during small interfering RNA amplification in Arabidopsis.

Small interfering RNAs (siRNAs) are often amplified from transcripts cleaved by RNA-induced silencing complexes (RISCs) containing a small RNA (sRNA) and an Argonaute protein. Amplified siRNAs, termed secondary siRNAs, are important for reinforcement of target repression. In plants, target cleavage by RISCs containing 22-nucleotide (nt) sRNA and Argonaute 1 (AGO1) triggers siRNA amplification. In this pathway, the cleavage fragment is converted into double-stranded RNA (dsRNA) by RNA-dependent RNA polymerase 6 (RDR6), and the dsRNA is processed into siRNAs by Dicer-like proteins. Because nonspecific RDR6 recruitment causes nontarget siRNA production, it is critical that RDR6 is specifically recruited to the target RNA that serves as a template for dsRNA formation. Previous studies showed that Suppressor of Gene Silencing 3 (SGS3) binds and stabilizes 22-nt sRNA-containing AGO1 RISCs associated with cleaved target, but how RDR6 is recruited to targets cleaved by 22-nt sRNA-containing AGO1 RISCs remains unknown. Here, using cell-free extracts prepared from suspension-cultured Arabidopsis thaliana cells, we established an in vitro system for secondary siRNA production in which 22-nt siRNA-containing AGO1-RISCs but not 21-nt siRNA-containing AGO1-RISCs induce secondary siRNA production. In this system, addition of recombinant Silencing Defective 5 (SDE5) protein remarkably enhances secondary siRNA production. We show that RDR6 is recruited to a cleavage fragment by 22-nt siRNA-containing AGO1-RISCs in coordination with SGS3 and SDE5. The SGS3-SDE5-RDR6 multicomponent recognition system and the poly(A) tail inhibition may contribute to securing specificity of siRNA amplification.

Homology length dictates the requirement for Rad51 and Rad52 in gene targeting in the Basidiomycota yeast Naganishia liquefaciens.

Here, we report the development of methodologies that enable genetic modification of a Basidiomycota yeast, Naganishia liquifaciens. The gene targeting method employs electroporation with PCR products flanked by an 80 bp sequence homologous to the target. The method, combined with a newly devised CRISPR-Cas9 system, routinely achieves 80% gene targeting efficiency. We further explored the genetic requirement for this homologous recombination (HR)-mediated gene targeting. The absence of Ku70, a major component of the non-homologous end joining (NHEJ) pathway of DNA double-strand break repair, almost completely eliminated inaccurate integration of the marker. Gene targeting with short homology (80 bp) was almost exclusively dependent on Rad52, an essential component of HR in the Ascomycota yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. By contrast, the RecA homolog Rad51, which performs homology search and strand exchange in HR, plays a relatively minor role in gene targeting, regardless of the homology length (80 bp or 1 kb). The absence of both Rad51 and Rad52, however, completely eliminated gene targeting. Unlike Ascomycota yeasts, the absence of Rad52 in N. liquefaciens conferred only mild sensitivity to ionizing radiation. These traits associated with the absence of Rad52 are reminiscent of findings in mice.

Printable and Semitransparent Nonfullerene Organic Solar Modules over 30 cm2 Introducing an Energy-Level Controllable Hole Transport Layer.

For the commercialization of organic solar cells (OSCs), the fabrication of large-area modules via a solution process is important. The fabrication of OSCs via a solution process using a nonfullerene acceptor (NFA)-based photoactive layer is limited by the energetic mismatch and carrier recombination, reducing built-in potential and effective carriers. Herein, for the fabrication of high-performance NFA-based large-area OSCs and modules via a solution process, hybrid hole transport layers (h-HTLs) incorporating WO3 and MoO3 are developed. The high bond energies and electronegativities of W and Mo atoms afford changes in the electronic properties of the h-HTLs, which can allow easy control of the energy levels. The h-HTLs show matching energy levels that are suitable for both deep and low-lying highest occupied molecular orbital energy level systems with a stoichiometrically small amount of oxygen vacancies (forming W6+ and Mo6+ from the W5+ and Mo5+), affording high conductivity and good film forming properties. With the NFA-based photoactive layer, a large-area module fabricated via the all-printing process with an active area over 30 cm2 and a high power conversion efficiency (PCE) of 8.1% is obtained. Furthermore, with the h-HTL, the fabricated semitransparent module exhibits 7.2% of PCE and 22.3% of average visible transmittance with high transparency, indicating applicable various industrial potentials.

Draft Genome Sequence of Naganishia liquefaciens Strain N6, Isolated from the Japan Trench.

The draft genome sequence of the deep-sea yeast Naganishia liquefaciens strain N6, isolated from the Japan Trench, is reported here. This strain was previously classified into a Cryptococcus clade. Phylogenetic analysis using the presented sequence suggests that strain N6 is in the clade of the genus Naganishia.

High-Performance Nonfullerene Organic Photovoltaics Applicable for Both Outdoor and Indoor Environments through Directional Photon Energy Transfer.

With the advent of the smart factory and the Internet of Things (IoT) sensors, organic photovoltaics (OPVs) gained attention because of their ability to provide indoor power generation as an off-grid power supply. To satisfy these applications, OPVs must be capable of power generation in both outdoor and indoor at the same time for developing environmentally independent devices. For high performances in indoor irradiation, a strategy that maximizes photon utilization is essential. In this study, graphene quantum dots (GQDs), which have unique emitting properties, are introduced into a ZnO layer for efficient photon utilization of nonfullerene-based OPVs under indoor irradiation. GQDs exhibit high absorption properties in the 350-550 nm region and strong emission properties in the visible region due to down-conversion from lattice vibration. Using these properties, GQDs provide directional photon energy transfer to the bulk-heterojunction (BHJ) layer because the optical properties overlap. Additionally, the GQD-doped ZnO layer enhances shunt resistance (RSh) and forms good interfacial contact with the BHJ layer that results in increased carrier dissociation and transportation. Consequently, the fabricated device based on P(Cl-Cl)(BDD = 0.2) and IT-4F introduces GQDs exhibiting a maximum power conversion efficiency (PCE) of 14.0% with a superior enhanced short circuit current density (JSC) and fill factor (FF). Furthermore, the fabricated device exhibited high PCEs of 19.6 and 17.2% under 1000 and 200 lux indoor irradiation of light emitting diode (LED) lamps, respectively.

13.9%-Efficiency and Eco-Friendly Nonfullerene Polymer Solar Cells Obtained by Balancing Molecular Weight and Solubility in Chlorinated Thiophene-Based Polymer Backbones.

To industrialize nonfullerene polymer solar cells (NFPSCs), the molecular design of the donor polymers must feature low-cost materials and a high overall yield. Two chlorinated thiophene-based polymers, P(F-Cl) and P(Cl-Cl), are synthesized by introducing halogen effects like fluorine (F) and chlorine (Cl) to the previously reported P(Cl), which exhibits low complexity. However, the molecular weights of these polymers are insufficient owing to their low solubility, which in turn is caused by introducing rigid halogen atoms during the polymerization. Thus, they show relatively low power conversion efficiencies (PCEs) of 11.8% and 10.3%, respectively. To overcome these shortcomings, two new terpolymers are designed and synthesized by introducing a small amount of 1,3-bis(5-bromothiophen-2-yl)-5,7-bis(2-ethylhexyl)benzo[1,2-c:4,5-c']dithiophene-4,8-dione (BDD) unit into each backbone, namely, P(F-Cl)(BDD = 0.2) and P(Cl-Cl)(BDD = 0.2). As a result, both polymers remain inexpensive and show a better molecular weight-solubility balance, achieving high PCEs of 12.7% and 13.9%, respectively, in NFPSCs processed using eco-friendly solvents.

Drastic Changes in Properties of Donor-Acceptor Polymers Induced by Asymmetric Structural Isomers for Application to Polymer Solar Cells.

Appropriate design of donor-acceptor (D-A) conjugated polymers is important for enhancing their physical, optical, and electrochemical properties. The rapid development of D-A conjugated polymers based on fullerene and nonfullerene derivatives in the past decade has led to an improvement in the performance of polymer solar cells (PSCs). In this study, we designed and synthesized two donor polymers based on the DTffBT acceptor unit, with matching optical absorption range and energy levels with fullerene (PC71BM) and nonfullerene acceptors (ITIC and IDIC), by introducing asymmetric structural isomers of donor units. We demonstrated that materials design by structural modification dramatically affects the physical, optical, and electrochemical properties as well as the crystallinity and photovoltaic performance of the polymers. The results provide valuable insights into materials design for efficient PSCs.

A 3-Fluoro-4-hexylthiophene-Based Wide Bandgap Donor Polymer for 10.9% Efficiency Eco-Friendly Nonfullerene Organic Solar Cells.

Nonfullerene organic solar cells (NFOSCs) are attracting increasing academic and industrial interest due to their potential uses for flexible and lightweight products using low-cost roll-to-roll technology. In this work, two wide bandgap (WBG) polymers, namely P(fTh-BDT)-C6 and P(fTh-2DBDT)-C6, are designed and synthesized using benzodithiophene (BDT) derivatives. Good oxidation stability and high solubility are achieved by simultaneously introducing fluorine and alkyl chains to a single thiophene (Th) unit. Solid P(fTh-2DBDT)-C6 films present WBG optical absorption, suitable frontier orbital levels, and strong π-π stacking effects. In addition, P(fTh-2DBDT)-C6 exhibits good solubility in both halogenated and nonhalogenated solvents, suggesting its suitability as donor polymer for NFOSCs. The P(fTh-2DBDT)-C6:3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone))-5,5,11,11-tetrakis(5-hexylthienyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']dithiophene (ITIC-Th) based device processed using chlorobenzene/1,8-diiodooctane (CB/DIO) exhibits a remarkably high power conversion efficiency (PCE) of 11.1%. Moreover, P(fTh-2DBDT)-C6:ITIC-Th reaches a high PCE of 10.9% when processed using eco-friendly solvents, such as o-xylene/diphenyl ether (DPE). The cell processed using CB/DIO maintains 100% efficiency after 1272 h, while that processed using o-xylene/DPE presents a 101% increase in efficiency after 768 h and excellent long-term stability. The results of this study demonstrate that simultaneous fluorination and alkylation are effective methods for designing donor polymers appropriate for high-performance NFOSCs.

Effect on Electrode Work Function by Changing Molecular Geometry of Conjugated Polymer Electrolytes and Application for Hole-Transporting Layer of Organic Optoelectronic Devices.

In this study, we synthesized three conjugated polymer electrolytes (CPEs) with different conjugation lengths to control their dipole moments by varying spacers. P-type CPEs (PFT-D, PFtT-D, and PFbT-D) were generated by the facile oxidation of n-type CPEs (PFT, PFtT, and PFbT) and introduced as the hole-transporting layers (HTLs) of organic solar cells (OSCs) and polymer light-emitting diodes (PLEDs). To identify the effect on electrode work function tunability by changing the molecular conformation and arrangement, we simulated density functional theory calculations of these molecules and performed ultraviolet photoelectron spectroscopy analysis for films of indium tin oxide/CPEs. Additionally, we fabricated OSCs and PLEDs using the CPEs as the HTLs. The stability and performance were enhanced in the optimized devices with PFtT-D CPE HTLs compared to those of PEDOT:PSS HTL-based devices.

Preferential 5-Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein.

Tet (ten-eleven translocation) family proteins oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG-methylated 382 bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region.

The application of fluorescence-conjugated pyrrole/imidazole polyamides in the characterization of protein-DNA complex formation.

N-Methylpyrrole (Py)-N-methylimidazole-(Im) polyamides are sequence-specific DNA-binding modules that are widely used for gene regulation, as synthetic transcriptional factors and as sequence-specific DNA alkylating agents. Recently, Py-Im polyamides have been conjugated with fluorophores, resulting in conjugates that are useful for the detection of specific DNA sequences. A Förster resonance energy transfer has been observed between Cy3- and Cy5-conjugated Py-Im polyamides on the nucleosome, indicating that fluorescence-conjugated Py-Im polyamides could possibly be used to characterise protein-DNA complexes. In this minireview, we discuss recent reports regarding fluorescence-conjugated Py-Im polyamides and their future application in the characterization of protein-DNA complex formation.

Synergistic effect of ATP for RuvA-RuvB-Holliday junction DNA complex formation.

The Escherichia coli RuvB hexameric ring motor proteins, together with RuvAs, promote branch migration of Holliday junction DNA. Zero mode waveguides (ZMWs) constitute of nanosized holes and enable the visualization of a single fluorescent molecule under micromolar order of the molecules, which is applicable to characterize the formation of RuvA-RuvB-Holliday junction DNA complex. In this study, we used ZMWs and counted the number of RuvBs binding to RuvA-Holliday junction DNA complex. Our data demonstrated that different nucleotide analogs increased the amount of Cy5-RuvBs binding to RuvA-Holliday junction DNA complex in the following order: no nucleotide, ADP, ATPγS, and mixture of ADP and ATPγS. These results suggest that not only ATP binding to RuvB but also ATP hydrolysis by RuvB facilitates a stable RuvA-RuvB-Holliday junction DNA complex formation.

ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues.

Elucidating the dynamic organization of nuclear RNA foci is important for understanding and manipulating these functional sites of gene expression in both physiological and pathological states. However, such studies have been difficult to establish in vivo as a result of the absence of suitable RNA imaging methods. Here, we describe a high-resolution fluorescence RNA imaging method, ECHO-liveFISH, to label endogenous nuclear RNA in living mice and chicks. Upon in vivo electroporation, exciton-controlled sequence-specific oligonucleotide probes revealed focally concentrated endogenous 28S rRNA and U3 snoRNA at nucleoli and poly(A) RNA at nuclear speckles. Time-lapse imaging reveals steady-state stability of these RNA foci and dynamic dissipation of 28S rRNA concentrations upon polymerase I inhibition in native brain tissue. Confirming the validity of this technique in a physiological context, the in vivo RNA labeling did not interfere with the function of target RNA nor cause noticeable cytotoxicity or perturbation of cellular behavior.

Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole-imidazole polyamides binding to DNA in the nucleosome.

Sequence-specific DNA-binding modules, N-methylpyrrole (Py)-N-methylimidazole-(Im) polyamides have been recently conjugated with fluorophores, and some of these conjugates could be used for the detection of specific DNA sequences. In this study, we synthesized two Py-Im polyamides 1 and 2, which interact with the 145-bp nucleosome positioning sequence 601. We conjugated the cyanine dye Cy3 or Cy5 with 1 or 2. In the absence of target DNA, the fluorescent conjugate of a Py-Im polyamide had lower fluorescence intensity compared with Cy3 or Cy5 alone. In the presence of either the target DNA or the nucleosome, the fluorescence intensity of the conjugates increased. Furthermore, we observed a Förster resonance energy transfer between the Cy3-Py-Im polyamide and the Cy5-Py-Im polyamide on the nucleosome. These results open up the possibilities that fluorescent conjugates of Py-Im polyamides can be used for characterization of the dynamic interactions within protein-DNA complexes.

Effect of single pyrrole replacement with ß-alanine on DNA binding affinity and sequence specificity of hairpin pyrrole/imidazole polyamides targeting 5'-GCGC-3'.

N-Methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that can recognize predetermined DNA sequences with high sequence specificity. As many eukaryotic promoter regions contain highly GC-rich sequences, it is valuable to synthesize and characterize Py-Im polyamides that recognize GC-rich motifs. In this study, we synthesized four hairpin Py-Im polyamides 1-4, which recognize 5'-GCGC-3' and investigated their binding behavior with surface plasmon resonance assay. Py-Im polyamides 2-4 contain two, one, and one ß-alanine units, replacing the Py units of 1, respectively. The binding affinities of 2-4 to the target DNA increased 430, 390, and 610-fold, respectively, over that of 1. The association and dissociation rates of 2 to the target DNA were improved by 11 and 37-fold, respectively, compared with those of 1. Interestingly, the association and dissociation rates of 3 and 4 were higher than those of 2, even though the binding affinities of 2, 3, and 4 to the target DNA were comparable to each other. The binding affinity of 2 to DNA with a 2bp mismatch was reduced by 29-fold, compared with that to the matched DNA. Moreover, the binding affinities of 3 and 4 to the same mismatched DNA were reduced by 270 and 110-fold, respectively, indicating that 3 and 4 have greater specificities than 2 and are suitable as DNA-binding modules for engineered epigenetic regulation.

In vivo fluorescent adenosine 5'-triphosphate (ATP) imaging of Drosophila melanogaster and Caenorhabditis elegans by using a genetically encoded fluorescent ATP biosensor optimized for low temperatures.

Adenosine 5'-triphosphate (ATP) is the major energy currency of all living organisms. Despite its important functions, the spatiotemporal dynamics of ATP levels inside living multicellular organisms is unclear. In this study, we modified the genetically encoded Förster resonance energy transfer (FRET)-based ATP biosensor ATeam to optimize its affinity at low temperatures. This new biosensor, AT1.03NL, detected ATP changes inside Drosophila S2 cells more sensitively than the original biosensor did, at 25 °C. By expressing AT1.03NL in Drosophila melanogaster and Caenorhabditis elegans, we succeeded in imaging the in vivo ATP dynamics of these model animals at single-cell resolution.