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).

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.

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

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.

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.

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

For the commercialization of organic solar cells (OSCs), the fabrication of large-area modules a solution process is important. The fabrication of OSCs 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 a solution process, hybrid hole transport layers (h-HTLs) incorporating WO and MoO are developed.

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

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

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.

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.

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 (PCBM) and nonfullerene acceptors (ITIC and IDIC), by introducing asymmetric structural isomers of donor units.

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.

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.

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.

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.

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.

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.

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 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.

Effect of single pyrrole replacement with β-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.

MuB is an AAA+ ATPase that forms helical filaments to control target selection for DNA transposition.

MuB is an ATP-dependent nonspecific DNA-binding protein that regulates the activity of the MuA transposase and captures target DNA for transposition. Mechanistic understanding of MuB function has previously been hindered by MuB's poor solubility. Here we combine bioinformatic, mutagenic, biochemical, and electron microscopic analyses to unmask the structure and function of MuB.

ParA-mediated plasmid partition driven by protein pattern self-organization.

DNA segregation ensures the stable inheritance of genetic material prior to cell division. Many bacterial chromosomes and low-copy plasmids, such as the plasmids P1 and F, employ a three-component system to partition replicated genomes: a partition site on the DNA target, typically called parS, a partition site binding protein, typically called ParB, and a Walker-type ATPase, typically called ParA, which also binds non-specific DNA. In vivo, the ParA family of ATPases forms dynamic patterns over the nucleoid, but how ATP-driven patterning is involved in partition is unknown.

Binding of hairpin pyrrole and imidazole polyamides to DNA: relationship between torsion angle and association rate constants.

N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides are small organic molecules that bind to DNA with sequence specificity and can be used as synthetic DNA-binding ligands. In this study, five hairpin eight-ring Py-Im polyamides 1-5 with different number of Im rings were synthesized, and their binding behaviour was investigated with surface plasmon resonance assay. It was found that association rate (k(a)) of the Py-Im polyamides with their target DNA decreased with the number of Im in the Py-Im polyamides.

ATP control of dynamic P1 ParA-DNA interactions: a key role for the nucleoid in plasmid partition.

P1 ParA is a member of the Walker-type family of partition ATPases involved in the segregation of plasmids and bacterial chromosomes. ATPases of this class interact with DNA non-specifically in vitro and colocalize with the bacterial nucleoid to generate a variety of reported patterns in vivo. Here, we directly visualize ParA binding to DNA using total internal reflection fluorescence microscopy.

Phage Mu transposition immunity: protein pattern formation along DNA by a diffusion-ratchet mechanism.

DNA transposons integrate into host chromosomes with limited target sequence specificity. Without mechanisms to avoid insertion into themselves, transposons risk self-destruction. Phage Mu avoids this problem by transposition immunity, involving MuA-transposase and MuB ATP-dependent DNA-binding protein.