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Cellular totipotency is critical for whole-organism generation, yet how totipotency is established remains poorly illustrated. Abundant transposable elements (TEs) are activated in totipotent cells, which is critical for embryonic totipotency. Here, we show that the histone chaperone RBBP4, but not its homolog RBBP7, is indispensable for maintaining the identity of mouse embryonic stem cells (mESCs). Auxin-induced degradation of RBBP4, but not RBBP7, reprograms mESCs to the totipotent 2C-like cells. Also, loss of RBBP4 enhances transition from mESCs to trophoblast cells. Mechanistically, RBBP4 binds to the endogenous retroviruses (ERVs) and functions as an upstream regulator by recruiting G9a to deposit H3K9me2 on ERVL elements, and recruiting KAP1 to deposit H3K9me3 on ERV1/ERVK elements, respectively. Moreover, RBBP4 facilitates the maintenance of nucleosome occupancy at the ERVK and ERVL sites within heterochromatin regions through the chromatin remodeler CHD4. RBBP4 depletion leads to the loss of the heterochromatin marks and activation of TEs and 2C genes. Together, our findings illustrate that RBBP4 is required for heterochromatin assembly and is a critical barrier for inducing cell fate transition from pluripotency to totipotency.

Although extended pluripotent stem cells (EPSCs) have the potential to form both embryonic and extraembryonic lineages, how their transcriptional regulatory mechanism differs from that of embryonic stem cells (ESCs) remains unclear. Here, we discovered that YY1 binds to specific open chromatin regions in EPSCs. Yy1 depletion in EPSCs leads to a gene expression pattern more similar to that of ESCs than control EPSCs. Moreover, Yy1 depletion triggers a series of epigenetic crosstalk activities, including changes in DNA methylation, histone modifications and high-order chromatin structures. Yy1 depletion in EPSCs disrupts the enhancer-promoter (EP) interactions of EPSC-specific genes, including Dnmt3l. Yy1 loss results in DNA hypomethylation and dramatically reduces the enrichment of H3K4me3 and H3K27ac on the promoters of EPSC-specific genes by upregulating the expression of Kdm5c and Hdac6 through facilitating the formation of CCCTC-binding factor (CTCF)-mediated EP interactions surrounding their loci. Furthermore, single-cell RNA sequencing (scRNA-seq) experiments revealed that YY1 is required for the derivation of extraembryonic endoderm (XEN)-like cells from EPSCs in vitro. Together, this study reveals that YY1 functions as a key regulator of multidimensional epigenetic crosstalk associated with extended pluripotency.

CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators by co-localization analysis with CTCF. We screened all factors that had ChIP-seq data in humans by co-localization analysis with human super conserved CTCF (hscCTCF) binding sites, and identified many new factors that overlapped with hscCTCF binding sites. Combined with CTCF loop information, we observed that clustered factors could promote CTCF loops. After in-depth mining of each factor, we found that many factors might have the potential to promote CTCF loops. Our data further demonstrated that BHLHE40 affected CTCF loops by regulating CTCF binding. Together, this study revealed that many factors have the potential to participate in or regulate CTCF loops, and discovered a new role for BHLHE40 in modulating CTCF loop formation.

In this study, a fully biobased benzoxazine monomer (E-s) was combined with SiO2 nanoparticles to construct superhydrophobic/superoleophilic coatings on polyethylene terephthalate fabrics by spray ...

CTCF plays key roles in gene regulation, chromatin insulation, imprinting, X chromosome inactivation and organizing the higher-order chromatin architecture of mammalian genomes. Previous studies have mainly focused on the roles of the canonical CTCF isoform. Here, we explore the functions of an alternatively spliced human CTCF isoform in which exons 3 and 4 are skipped, producing a shorter isoform (CTCF-s). Functionally, we find that CTCF-s competes with the genome binding of canonical CTCF and binds a similar DNA sequence. CTCF-s binding disrupts CTCF/cohesin binding, alters CTCF-mediated chromatin looping and promotes the activation of IFI6 that leads to apoptosis. This effect is caused by an abnormal long-range interaction at the IFI6 enhancer and promoter. Taken together, this study reveals a non-canonical function for CTCF-s that antagonizes the genomic binding of canonical CTCF and cohesin, and that modulates chromatin looping and causes apoptosis by stimulating IFI6 expression., CTCF plays key roles in gene regulation, chromatin insulation and organizing the higher-order chromatin architecture of mammalian genomes. Here the authors investigate the function an alternatively spliced shorter CTCF isoform, finding that this isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis.

Objectives Mammalian spermatogenesis is a biological process of male gamete formation. Gonocytes are the only precursors of spermatogonial stem cells (SSCs) which develop into mature spermatozoa. DDX5 is one of DEAD‐box RNA helicases and expresses in male germ cells, suggesting that Ddx5 plays important functions during spermatogenesis. Here, we explore the functions of Ddx5 in regulating the specification of gonocytes. Materials and Methods Germ cell‐specific Ddx5 knockout (Ddx5 ‐/‐) mice were generated. The morphology of testes and epididymides and fertility in both wild‐type and Ddx5 ‐/‐ mice were analysed. Single‐cell RNA sequencing (scRNA‐seq) was used to profile the transcriptome in testes from wild‐type and Ddx5 ‐/‐ mice at postnatal day (P) 2. Dysregulated genes were validated by single‐cell qRT‐PCR and immunofluorescent staining. Results In male mice, Ddx5 was expressed in germ cells at different stages of development. Germ cell‐specific Ddx5 knockout adult male mice were sterile due to completely devoid of germ cells. Male germ cells gradually disappeared in Ddx5 ‐/‐ mice from E18.5 to P6. Single‐cell transcriptome analysis showed that genes involved in cell cycle and glial cell line‐derived neurotrophic factor (GDNF) pathway were significantly decreased in Ddx5‐deficient gonocytes. Notably, Ddx5 ablation impeded the proliferation of gonocytes. Conclusions Our study reveals the critical roles of Ddx5 in fate determination of gonocytes, offering a novel insight into the pathogenesis of male sterility., Under normal physiologic conditions in the neonatal testes, exogenous growth factor GDNF stimulates intracellular signaling through binding to its receptor GFRα1 and RET in cell membranes of the gonocytes. Subsequently, spermatogenesis is believed to initiate shortly after gonocytes give rise to spermatogonia. Spermatogonia could proliferate via mitosis and differentiate to produce spermatocytes. Germ cell‐specific knockout of Ddx5 results in low expression level of GDNF signaling pathway‐related genes (such as receptor Gfra1 and Ret) in gonocytes. The disruption of spermatogenesis takes place before spermatogonia formation in the testes of Ddx5 konckout mice. Ddx5 deletion leads to a complete lack of germ cells and infertility in male adults.

R-loop dynamics occur before changes in gene expression and are required for somatic cell reprogramming., R-loops modulate genome stability and regulate gene expression, but the functions and the regulatory mechanisms of R-loops in stem cell biology are still unclear. Here, we profiled R-loops during somatic cell reprogramming and found that dynamic changes in R-loops are essential for reprogramming and occurred before changes in gene expression. Disrupting the homeostasis of R-loops by depleting RNaseH1 or catalytic inactivation of RNaseH1 at D209 (RNaseH1D209N) blocks reprogramming. Sox2, but not any other factor in the Yamanaka cocktail, overcomes the inhibitory effects of RNaseH1 activity loss on reprogramming. Sox2 interacts with the reprogramming barrier factor Ddx5 and inhibits the resolvase activity of Ddx5 on R-loops and thus facilitates reprogramming. Furthermore, reprogramming efficiency can be modulated by dCas9-mediated RNaseH1/RNaseH1D209N targeting the specific R-loop regions. Together, these results show that R-loops play important roles in reprogramming and shed light on the regulatory module of Sox2/Ddx5 on R-loops during reprogramming.

Transcriptional activation of p21 (cyclin-dependent kinase inhibitor 1A) due to DNA damage often alters the distribution of histone variant H2A.Z at the p21 gene. However, whether the human INO80 complex regulates changes in H2A.Z at the p21 promoter is unclear. We show here that activation of p21 expression by doxorubicin (Doxo) in U2OS cells is required for removal of H2A.Z by INO80 at the p53-binding site proximal region (-2.2 kb) of the p21 promoter. A purified INO80 complex, but not the INO80E653Q mutant-complex, which lost DNA-sliding activity, is mainly responsible for removing H2A.Z from reconstituted nucleosomes in vitro. This activity was enhanced with MOF-mediated histone acetylation, suggesting that INO80 more readily removes H2A.Z from loosened nucleosomes. Also, co-occupancy of INO80 and H2A.Z -2.2 kb upstream of the p21 transcriptional start site (TSS) was observed. H2A.Z at this region was removed in a short time after Doxo treatment and activated p21 expression. However, p21 induction was inhibited by INO80 knockdown by delaying H2A.Z removal, indicating the need for INO80. Moreover, shMOF-mediated histone acetylation reduced recruitment of INO80 -2.2 kb upstream of p21 TSS and inhibited the removal of H2A.Z in Doxo-treated cells. These data provide new insights into the transcriptional regulation of p21 by the INO80 complex.

Polycomb repressive complex 1 (PRC1) is an important regulator of gene expression and development. PRC1 contains the E3 ligases RING1A/B, which monoubiquitinate lysine 119 at histone H2A (H2AK119ub1), and has been sub-classified into six major complexes based on the presence of a PCGF subunit. Here, we report that PCGF5, one of six PCGF paralogs, is an important requirement in the differentiation of mouse embryonic stem cells (mESCs) towards a neural cell fate. Although PCGF5 is not required for mESC self-renewal, its loss blocks mESC neural differentiation by activating the SMAD2/TGF-β signaling pathway. PCGF5 loss-of-function impairs the reduction of H2AK119ub1 and H3K27me3 around neural specific genes and keeps them repressed. Our results suggest that PCGF5 might function as both a repressor for SMAD2/TGF-β signaling pathway and a facilitator for neural differentiation. Together, our findings reveal a critical context-specific function for PCGF5 in directing PRC1 to control cell fate., Polycomb-group proteins are key regulators of transcriptional programs that maintain cell identity. Here the authors provide evidence that PCGF5, a subunit of Polycomb Repressor Complex 1, is important for the differentiation of mouse embryonic stem cells towards a neural cell fate.

Polycomb repressive complex 2 and the epigenetic mark that it deposits, H3K27me3, are evolutionarily conserved and play critical roles in development and cancer. However, their roles in cell fate decisions in early embryonic development remain poorly understood. Here we report that knockout of polycomb repressive complex 2 genes in human embryonic stem cells causes pluripotency loss and spontaneous differentiation toward a meso-endoderm fate, owing to de-repression of BMP signalling. Moreover, human embryonic stem cells with deletion of EZH1 or EZH2 fail to differentiate into ectoderm lineages. We further show that polycomb repressive complex 2-deficient mouse embryonic stem cells also release Bmp4 but retain their pluripotency. However, when converted into a primed state, they undergo spontaneous differentiation similar to that of hESCs. In contrast, polycomb repressive complex 2 is dispensable for pluripotency when human embryonic stem cells are converted into the naive state. Our studies reveal both lineage- and pluripotent state-specific roles of polycomb repressive complex 2 in cell fate decisions., Polycomb repressive complex 2 (PRC2) plays an essential role in development by modifying chromatin but what this means at a cellular level is unclear. Here, the authors show that ablation of PRC2 genes in human embryonic stem cells and in mice results in changes in pluripotency and the primed state of cells.

Super-enhancers (SEs) are cis-regulatory elements enriching lineage specific key transcription factors (TFs) to form hotspots. A paucity of identification and functional dissection promoted us to investigate SEs during myoblast differentiation. ChIP-seq analysis of histone marks leads to the uncovering of SEs which remodel progressively during the course of differentiation. Further analyses of TF ChIP-seq enable the definition of SE hotspots co-bound by the master TF, MyoD and other TFs, among which we perform in-depth dissection for MyoD/FoxO3 interaction in driving the hotspots formation and SE activation. Furthermore, using Myogenin as a model locus, we elucidate the hierarchical and complex interactions among hotspots during the differentiation, demonstrating SE function is propelled by the physical and functional cooperation among hotspots. Finally, we show MyoD and FoxO3 are key in orchestrating the Myogenin hotspots interaction and activation. Altogether our results identify muscle-specific SEs and provide mechanistic insights into the functionality of SE.

Two novel eugenol-based difunctional benzoxazine monomers, named E-pea and E-dda, were successfully synthesized with a solvent-less method from eugenol, paraformaldehyde, 4,7,10-trioxa-1,13-tridecanediamine and 1,12-dodecanediamine. Their molecular structures were verified with Fourier Transform Infrared (FTIR) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy. Their curing behaviors were studied using differential scanning colorimetry (DSC) and FTIR techniques and a possible polymerization mechanism was proposed. Thermogravimetric analysis (TGA) was adopted to study the thermal stability of two polybenzoxazines, revealing that the fully polymerized E-pea and E-dda (denoted as PE-pea and PE-da) were both fairly thermostable with a char yield of 46.0 wt% at 800 ℃. Finally, contact angle tests manifest that the surface free energy (SFE) of PE-dda film was as low as 16.88 mJ/m2 while that of PE-pea film was 28.56 mJ/m2. Such an obvious increase in PE-pea’s SFE value is mainly caused by the inherent hydrophilicity of ether bonds.

In this work, eugenol/stearylamine-based benzoxazine (E-s) and pyrogallol/furfurylamine-based benzoxazine (PY-f) were synthesized from renewable raw materials and mixed to prepare a series of copolymers. The curing behavior of E-s/PY-f mixtures were characterized by differential scanning calorimetry (DSC). The result shows that the curing temperature decreased obviously with the increase of PY-f content. When the mass ratio of E-s to PY-f was 8:2, the exothermic peak temperature (Tp) of the sample (EP20) dropped to 194 ℃, which was 70 ℃ lower than that of E-s. Then, the representative copolymerization mechanism of E-s and PY-f was proposed. Furthermore, EP20 was adopted to prepare the copolymer coating (PEP) on mild steel (MS) for anti-corrosion application. The results of electrochemical impedance spectroscopy (EIS) indicated that PEP-coated MS well kept its corrosion resistance after being immersed in 3.5 wt% NaCl aqueous solution for 30 days. Hence, the copolymer of bio-based benzoxazines is promising for preparing superior anti-corrosion material with low curing temperature.

In this work, the effect of pyrogallol which served as a phenolic nucleophile on the ring-opening polymerization and curing kinetics of the eugenol/stearylamine-based benzoxazine (E-s) was examined with phenol as a contrast. The differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FTIR) results revealed that pyrogallol demonstrated higher ability to promote the ring-opening polymerization of E-s compared to phenol. The exothermal peak temperature of E-s was reduced from 254 °C to 168 °C with the addition of pyrogallol. Moreover, the curing kinetics of the E-s and pyrogallol mixture (E-s/py) were studied with Kissinger, Ozawa, Flynn-Wall-Ozawa and Friedman methods. The results indicated that the apparent activation energies (Ea) of E-s decreased with the addition of pyrogallol. In addition, the polymerization process of E-s/py followed the autocatalytic kinetic model based on Friedman method.

Abstract Induced pluripotent stem cells can be derived from somatic cells through ectopic expression of transcription factors or chemical cocktails. Chemical iPSCs (C-iPSCs) and OSKM-iPSCs (4F-iPSCs) have been suggested to have similar characteristics to mouse embryonic stem cells (mESCs). However, their epigenetic equivalence remains incompletely understood throughout the genome. In this study, we have generated mouse C-iPSCs and 4F-iPSCs, and further compared the genome-wide DNA methylomes of C-iPSCs, 4F-iPSCs, and mESCs that were maintained in 2i and LIF. Three pluripotent stem cells tend to be low methylated overall, however, DNA methylations in some specific regions (such as retrotransposons) are cell type-specific. Importantly, C-iPSCs are more hypomethylated than 4F-iPSCs. Bisulfite sequencing indicated that DNA methylation status in several known imprinted clusters, such as: Dlk1-Dio3 and Peg12-Ube3a, in C-iPSCs are closer to those of mESCs than 4F-iPSCs. Overall, our data demonstrate the reprogramming methods-dependent epigenetic differences of C-iPSCs and 4F-iPSCs and reveal that C-iPSCs are more hypomethylated than OSKM-integrated iPSCs.

RYBP (Ring1 and YY1 Binding Protein) is critical for pluripotency and differentiation of embryonic stem cells (ESCs). RYBP depletion disturbs both neural and myocardial differentiation of ESCs. Moreover, low level of RYBP is correlated with diseases such as glioblastoma. To study the biological function of RYBP in neural differentiation of ESCs, here we generated Rybp homozygous knockout murine ESC line based on Sox1-GFP reporter using CRISPR/Cas9 genome editing technology. The last two exons of Rybp gene in which contain 115 amino acids have been replaced with PGK-Pruo by homologous recombination.

It is imperative to develop efficient and durable separating materials to treat oily waste-water. In this work, Cardanol, which can be easily obtained from cashew nut shell, was employed to synthesize benzoxazine monomer (C-a), and superhydrophobic/superoleophilic PC-a/SiO2 films were further prepared on commercial polyester fabrics through a simple spray coating technique followed by a thermal curing method. The resultant PC-a/SiO2 fabrics had an excellent performance for several types of heavy oil/water separation driven solely by gravity, with oil fluxes of around 6500–9500 L·m−2·h−1, separation efficiencies of all over 90%, and an excellent recyclability. In addition, the PC-a/SiO2 fabrics achieved efficient collection of light oil from water. More importantly, PC-a/SiO2 fabrics possessed a self-cleaning property and a strong durability in harsh environments, such as acid/alkali immersion, UV irradiation and high temperature treatment. Hence, the bio-based PC-a/SiO2 modified fabric has a promising future in the field of oil/water separation.

RNA-binding proteins (RBPs), in addition to their functions in cellular homeostasis, play important roles in lineage specification and maintaining cellular identity. Despite their diverse and essential functions, which touch on nearly all aspects of RNA metabolism, the roles of RBPs in somatic cell reprogramming are poorly understood. Here we show that the DEAD-box RBP DDX5 inhibits reprogramming by repressing the expression and function of the non-canonical polycomb complex 1 (PRC1) subunit RYBP. Disrupting Ddx5 expression improves the efficiency of iPSC generation and impedes processing of miR-125b, leading to Rybp upregulation and suppression of lineage-specific genes via RYBP-dependent ubiquitination of H2AK119. Furthermore, RYBP is required for PRC1-independent recruitment of OCT4 to the promoter of Kdm2b, a histone demethylase gene that promotes reprogramming by reactivating endogenous pluripotency genes. Together, these results reveal important functions of DDX5 in regulating reprogramming and highlight the importance of a Ddx5-miR125b-Rybp axis in controlling cell fate.

In this paper a post-crosslinked polymeric adsorbent PDHT-2 with high specific surface area was prepared by Friedel–Crafts reaction of the pendant vinyl groups without an externally added crosslinking agent. It was obvious that both the specific surface area and the pore volume of starting copolymer PDHT-1 increased significantly after post-crosslinking. Batch adsorption runs of phenol from aqueous solution onto adsorbent PDHT-1 and PDHT-2 were researched, and commercial macroporous resin XAD-4 was chosen for comparison purpose. Experimental results showed that the adsorption isotherms could be fitted by Langmuir model and Freundlich model and the adsorption capacity onto PDHT-2 was much larger than that onto PDHT-1 and XAD-4 with respect to phenol and phenolic compound, which possibly resulted from its larger specific surface area. The adsorption process for phenol onto the three adsorbents was proved to be exothermic and spontaneous in nature. The thermodynamic parameters such as Gibb’s free energy (Δ G ), change in enthalpy (Δ H ) and change in entropy (Δ S ) had been calculated. The adsorption kinetic curves obeyed the pseudo-second order model and the intraparticle diffusion process was the rate-controlling step.

Histone Arg methylation has been correlated with transcriptional activation of p53 target genes. However, whether this modification is reversed to repress the expression of p53 target genes is unclear. Here, we report that peptidylarginine deiminase 4, a histone citrullination enzyme, is involved in the repression of p53 target genes. Inhibition or depletion of PAD4 elevated the expression of a subset of p53 target genes, including p21/CIP1/WAF1, leading to cell cycle arrest and apoptosis. Moreover, the induction of p21, cell cycle arrest, and apoptosis by PAD4 depletion is p53 dependent. Protein-protein interaction studies showed an interaction between p53 and PAD4. Chromatin immunoprecipitation assays showed that PAD4 is recruited to the p21 promoter in a p53-dependent manner. RNA polymerase II (Pol II) activities and the association of PAD4 are dynamically regulated at the p21 promoter during UV irradiation. Paused RNA Pol II and high levels of PAD4 were detected before UV treatment. At early time points after UV treatment, an increase of histone Arg methylation and a decrease of citrullination were correlated with a transient activation of p21. At later times after UV irradiation, a loss of RNA Pol II and an increase of PAD4 were detected at the p21 promoter. The dynamics of RNA Pol II activities after UV treatment were further corroborated by permanganate footprinting. Together, these results suggest a role of PAD4 in the regulation of p53 target gene expression.

Brd4 is a bromodomain protein that binds to acetylated chromatin. It regulates cell growth, although the underlying mechanism has remained elusive. Brd4 has also been shown to control transcription of viral genes, whereas its role in transcription of cellular genes has not been fully elucidated. Here we addressed the role of Brd4 in cell growth and transcription using a small hairpin (sh) RNA approach. The Brd4 shRNA vector stably knocked down Brd4 protein expression by approximately 90% in NIH3T3 cells and mouse embryonic fibroblasts. Brd4 knockdown cells were growth impaired and grew more slowly than control cells. When synchronized by serum starvation and released, Brd4 knockdown cells were arrested at G(1), whereas control cells progressed to S phase. In microarray analysis, although numerous genes were up-regulated during G(1) in control cells, many of these G(1) genes were not up-regulated in Brd4 knockdown cells. Reintroduction of Brd4 rescued expression of these G(1) genes in Brd4 knockdown cells, allowing cells to progress toward S phase. Chromatin immunoprecipitation analysis showed that Brd4 was recruited to the promoters of these G(1) genes during G(0)-G(1) progression. Furthermore, Brd4 recruitment coincided with increased binding of Cdk9, a component of P-TEFb and RNA polymerase II to these genes. Brd4 recruitment was low to absent at genes not affected by Brd4 shRNA. The results indicate that Brd4 stimulates G(1) gene expression by binding to multiple G(1) gene promoters in a cell cycle-dependent manner.

Nucleosome positioning and histone modification play a critical role in gene regulation, but their role during reprogramming has not been fully elucidated. Here, we determined the genome-wide nucleosome coverage and histone methylation occupancy in mouse embryonic fibroblasts (MEFs), induced pluripotent stem cells (iPSCs) and pre-iPSCs. We found that nucleosome occupancy increases in promoter regions and decreases in intergenic regions in pre-iPSCs, then recovers to an intermediate level in iPSCs. We also found that nucleosomes in pre-iPSCs are much more phased than those in MEFs and iPSCs. During reprogramming, nucleosome reorganization and histone methylation around transcription start sites (TSSs) are highly coordinated with distinctively transcriptional activities. Bivalent promoters gradually increase, while repressive promoters gradually decrease. High CpG (HCG) promoters of active genes are characterized by nucleosome depletion at TSSs, while low CpG (LCG) promoters exhibit the opposite characteristics. In addition, we show that vitamin C (VC) promotes reorganizations of canonical, H3K4me3- and H3K27me3-modified nucleosomes on specific genes during transition from pre-iPSCs to iPSCs. These data demonstrate that pre-iPSCs have a more open and phased chromatin architecture than that of MEFs and iPSCs. Finally, this study reveals the dynamics and critical roles of nucleosome positioning and chromatin organization in gene regulation during reprogramming.

Pre-harvest treatments with 2 mM salicylic acid (SA) and 0.2 mM methyl jasmonate (MeJA) significantly reduced lesion diameters on sweet cherry fruit caused by Monilinia fructicola compared with control post-harvest treatments. Pre-harvest treatment of sweet cherry with SA or MeJA induced β-1,3-glucanase, phenylalanine ammonia-lyase (PAL) and peroxidase (POD) activities during the early storage time. The efficacy of inducing resistance in sweet cherry fruit pre-harvest-treated with SA or MeJA to M. fructicola was better than that for fruit with post-harvest treatments, especially, at 25 °C. Activities of β-1,3-glucanase and PAL in SA- or MeJA-treated cherry fruit stored at 25 °C for both pre- and post-harvest treatments were significantly higher than those in fruit stored at 0 °C. SA with a concentration of 2 mM showed direct fungitoxicity on M. fructicola and significantly inhibited mycelial growth and spore germination of the pathogen in vitro. MeJA at 0.2 mM had little inhibitory effect on mycelial growth and spore germination of M. fructicola. The fruit treated with MeJA pre-harvest expressed higher activity of β-1,3-glucanase and PAL than fruit treated with SA and the control during the early storage time.

Peach fruit ( Amygdalus persica cv. Okubao) were inoculated with either antagonist Cryptococcus laurentii or pathogen Penicillium expansum and stored at 20 and 0 °C to investigate the effect of antagonist and pathogen on some pro- and anti-oxidant enzymes in non-infected flesh of fruit during storage. Both C. laurentii and P. expansum markedly induced activities of polyphenol oxidase (PPO), peroxidase (POD) and superoxide dismutase (SOD) in peach fruit at 20 °C, whereas only P. expansum had a significant effect on the inducing of malondialdehyde (MDA) content of the fruit. C. laurentii showed more efficiency in the promotion of PPO, POD and SOD activities of peach fruit than P. expansum . At 0 °C the inducing effect on the pro- and anti-oxidant enzymes by the yeast and pathogen was complex. The results indicated that both C. laurentii and P. expansum could induce anti-oxidant enzyme synthesis at 20 and 0 °C, but the rate of induction depended on storage temperature, inoculation time and treatment. PPO might play a key role in the defence system at both temperatures.

The addition of 2% (w/v) sodium bicarbonate (SBC) in the suspensions of antagonistic yeast Cryptococcus laurentii or Trichosporon pullulans significantly limited spore germination and germ tube elongation of Penicillium expansum and Alternaria alternata in potato dextrose broth (PDB) medium. Biocontrol activity of C. laurentii or T. pullulans against postharvest decay caused by P. expansum and A. alternata in pear fruits was significantly increased when C. laurentii or T. pullulans combined with SBC. Combining C. laurentii or T. pullulans with SBC provided a more effective control on P. expansum and A. alternata than applying the antagonistic yeast or SBC alone. Effects of C. laurentii with and without SBC on controlling P. expansum and A. alternata were better than those of T. pullulans. C. laurentii in combination with SBC showed the best control of disease caused by A. alternata in pear fruits.

Oncogenic transcription factors are known to mediate the conversion of somatic cells to tumour or induced pluripotent stem cells (iPSCs). Here we report c-Jun as a barrier for iPSC formation. c-Jun is expressed by and required for the proliferation of mouse embryonic fibroblasts (MEFs), but not mouse embryonic stem cells (mESCs). Consistently, c-Jun is induced during mESC differentiation, drives mESCs towards the endoderm lineage and completely blocks the generation of iPSCs from MEFs. Mechanistically, c-Jun activates mesenchymal-related genes, broadly suppresses the pluripotent ones, and derails the obligatory mesenchymal to epithelial transition during reprogramming. Furthermore, inhibition of c-Jun by shRNA, dominant-negative c-Jun or Jdp2 enhances reprogramming and replaces Oct4 among the Yamanaka factors. Finally, Jdp2 anchors 5 non-Yamanaka factors (Id1, Jhdm1b, Lrh1, Sall4 and Glis1) to reprogram MEFs into iPSCs. Our studies reveal c-Jun as a guardian of somatic cell fate and its suppression opens the gate to pluripotency.

SummaryReactivation of the pluripotency network during somatic cell reprogramming by exogenous transcription factors involves chromatin remodeling and the recruitment of RNA polymerase II (Pol II) to target loci. Here, we report that Pol II is engaged at pluripotency promoters in reprogramming but remains paused and inefficiently released. We also show that bromodomain-containing protein 4 (BRD4) stimulates productive transcriptional elongation of pluripotency genes by dissociating the pause release factor P-TEFb from an inactive complex containing HEXIM1. Consequently, BRD4 overexpression enhances reprogramming efficiency and HEXIM1 suppresses it, whereas Brd4 and Hexim1 knockdown do the opposite. We further demonstrate that the reprogramming factor KLF4 helps recruit P-TEFb to pluripotency promoters. Our work thus provides a mechanism for explaining the reactivation of pluripotency genes in reprogramming and unveils an unanticipated role for KLF4 in transcriptional pause release.

CCCTC-binding factor (CTCF) is a ubiquitously expressed "master weaver" and plays multiple functions in the genome, including transcriptional activation/repression, chromatin insulation, imprinting, X chromosome inactivation, and high-order chromatin organization. It has been shown that CTCF facilitates the recruitment of the upstream binding factor onto ribosomal DNA (rDNA) and regulates the local epigenetic state of rDNA repeats. However, the mechanism by which CTCF modulates rRNA gene transcription has not been well understood. Here we found that wild-type CTCF augments the pre-rRNA level, cell size, and cell growth in cervical cancer cells. In contrast, RNA interference-mediated knockdown of CTCF reduced pre-rRNA transcription. CTCF positively regulates rRNA gene transcription in a RNA polymerase I-dependent manner. We identified an RRGR motif as a putative nucleolar localization sequence in the C-terminal region of CTCF that is required for activating rRNA gene transcription. Using mass spectrometry, we identified SMC2 and SMC4, two subunits of condensin complexes that interact with CTCF. Condensin negatively regulates CTCF-mediated rRNA gene transcription. Knockdown of SMC2 expression significantly facilitates the loading of CTCF and the upstream binding factor onto the rDNA locus and increases histone acetylation across the rDNA locus. Taken together, our study suggests that condensin competes with CTCF in binding to a specific rDNA locus and negatively regulates CTCF-mediated rRNA gene transcription.

Vitamin C, a micronutrient known for its anti-scurvy activity in humans, promotes the generation of induced pluripotent stem cells (iPSCs) through the activity of histone demethylating dioxygenases. TET hydroxylases are also dioxygenases implicated in active DNA demethylation. Here we report that TET1 either positively or negatively regulates somatic cell reprogramming depending on the absence or presence of vitamin C. TET1 deficiency enhances reprogramming, and its overexpression impairs reprogramming in the context of vitamin C by modulating the obligatory mesenchymal-to-epithelial transition (MET). In the absence of vitamin C, TET1 promotes somatic cell reprogramming independent of MET. Consistently, TET1 regulates 5-hydroxymethylcytosine (5hmC) formation at loci critical for MET in a vitamin C-dependent fashion. Our findings suggest that vitamin C has a vital role in determining the biological outcome of TET1 function at the cellular level. Given its benefit to human health, vitamin C should be investigated further for its role in epigenetic regulation.

Reprogramming of somatic cells to a pluripotent state holds huge potentials for regenerative medicine. However, a debate over which method is better, somatic cell nuclear transfer (SCNT) or induced pluripotent stem (iPS) cells, still persists. Both approaches have the potential to generate patient-specific pluripotent stem cells for replacement therapy. Yet, although SCNT has been successfully applied in various vertebrates, no human pluripotent stem cells have been generated by SCNT due to technical, legal and ethical difficulties. On the other hand, human iPS cell lines have been reported from both healthy and diseased individuals. A recent study reported the generation of triploid human pluripotent stem cells by transferring somatic nuclei into oocytes, a variant form of SCNT. In this essay, we discuss this progress and the potentials of these two reprogramming approaches for regenerative medicine.

The DNA sequence elements called insulators have two basic kinds of properties. Barrier elements block the propagation of heterochromatic structures into adjacent euchromatin. Enhancer blocking elements interfere with interaction between an enhancer and promoter when placed between them. We have dissected a compound insulator element found at the 5' end of the chicken β-globin locus, which possesses both activities. Barrier insulation is mediated by two kinds of DNA binding proteins: USF1/USF2, a heterodimer which recruits multiple enzyme complexes capable of marking histone on adjacent nucleosomes with 'activating' marks, and Vezf1, which protects against DNA methylation. We have found that the heterochromatic region upstream of the insulator element is maintained in its silent state by a dicer-dependent mechanism, suggesting a mechanism for Vezf1 function in the insulator. Enhancer blocking function in the β-globin insulator element is conferred by a binding site for CTCF. Consistent with this property, CTCF binding was found some years ago to be essential for imprinted expression at the Igf2/H19 locus. Work in many laboratories has since demonstrated that CTCF helps stabilize long-range interactions in the nucleus. We have recently shown that in the case of the human insulin locus such an interaction, over a distance of ~300kb, can result in stimulation of a target gene which itself is important for insulin secretion. This article is part of a Special Issue entitled: Chromatin in time and space.

Protein Arg methyltransferases function as coactivators of the tumor suppressor p53 to regulate gene expression. Peptidylarginine deiminase 4 (PAD4/PADI4) counteracts the functions of protein Arg methyltransferases in gene regulation by deimination and demethylimination. Here we show that the expression of a tumor suppressor gene, OKL38, is activated by the inhibition of PAD4 or the activation of p53 following DNA damage. Chromatin immunoprecipitation assays showed a dynamic change of p53 and PAD4 occupancy and histone Arg modifications at the OKL38 promoter during DNA damage, suggesting a direct role of PAD4 and p53 in the expression of OKL38. Furthermore, we found that OKL38 induces apoptosis through localization to mitochondria and induction of cytochrome c release. Together, our studies identify OKL38 as a novel p53 target gene that is regulated by PAD4 and plays a role in apoptosis.

Nat. Cell Biol. 17, 856–867 (2015); published online 22 June 2015; corrected after print 10 August 2015 In the version of this Article originally published, panels from Fig. 8e were mistakenly reproduced as Fig. 6g. The correct panels for Fig. 6g (KS/Jdp2-iPSC) are shown here and have been amended in all online versions of the Article.

H.J. YAO AND S.P. TIAN. 2005. Aims: To investigate effects of application of 200 lmol l )1 methyl jasmonate [MeJA (200)] and Cryptococcus laurentii alone or in combination against postharvest diseases (Monilinia fructicola and Penicillium expansum) in peach fruit stored at 25 and 0� C, and to evaluate the possible mechanisms involved. Methods and Results: The efficacy of controlling postharvest diseases by resistance induced in peach fruit treated with MeJA (200) and C. laurentii alone or in combination and the relationship between activities of defence-related enzymes in peach fruit and lesions caused by M. fructicola and P. expansum were examined. At the same time, the effects of MeJA (200) on the population of C. laurentii in the peach wounds and on the mycelial growth of M. fructicola and P. expansum in vitro were investigated. The results indicated that treatment of peach fruit with C. laurentii at 1 · 10 8 CFU ml )1 alone, or combining C. laurentii at 5 · 10 7 CFU ml )1 with MeJA (200) all resulted in a lower lesion diameter of brown rot and blue mould caused by M. fructicola and P. expansum compared with the controls in peach fruit. MeJA (200) enhanced the population of C. laurentii, and inhibited mycelial growth of P. expansum. However, it had a little effect on M. fructicola in vitro. MeJA and C. laurentii alone or in combination induced higher activities of Chitinase, b-1,3-glucanase, phenylalanine ammonia-lyase and peroxidase (POD) than applying the yeast alone at both 25 and 0� C. Conclusions: MeJA (200) not only directly inhibited mycelial spread of postharvest pathogens, but also increased population of C. laurentii, which induced stronger disease resistance in fruit than MeJA or yeast alone, and resulted in a lower lesion diameter of brown rot and blue mould caused by M. fructicola and P. expansum. Significance and Impact of the Study: MeJA (200) in combination with C. laurentii was beneficial for controlling brown rot and blue mould caused by M. fructicola and P. expansum in peach fruit. The inhibitory mechanism was mainly because of resistance induced in peach fruit by MeJA and C. laurentii. In addition, direct inhibition of MeJA on P. expansum also played a role in controlling blue mould.