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Wounds on Chinese yam (Dioscorea opposita) tubers can ocurr during harvest and handling, and rapid suberisation of the wound is required to prevent pathogenic infection and desiccation. However, little is known about the causal relationship among suberin deposition, relevant gene expressions and endogenous phytohormones levels in response to wounding. In this study, the effect of wounding on phytohormones levels and the expression profiles of specific genes involved in wound-induced suberisation were determined. Wounding rapidly increased the expression levels of genes, including PAL , C4H , 4CL , POD , KCSs , FARs , CYP86A1 , CYP86B1 , GPATs , ABCGs and GELPs , which likely involved in the biosynthesis, transport and polymerisation of suberin monomers, ultimately leading to suberin deposition. Wounding induced phenolics biosynthesis and being polymerised into suberin poly(phenolics) (SPP) in advance of suberin poly(aliphatics) (SPA) accumulation. Specifically, rapid expression of genes (e.g. PAL , C4H , 4CL , POD) associated with the biosynthesis and polymerisation of phenolics, in consistent with SPP accumulation 3 days after wounding, followed by the massive accumulation of SPA and relevant gene expressions (e.g. KCSs , FARs , CYP86A1 / B1 , GPATs , ABCGs , GELPs). Additionally, wound-induced abscisic acid (ABA) and jasmonic acid (JA) consistently correlated with suberin deposition and relevant gene expressions indicating that they might play a central role in regulating wound suberisation in yam tubers. Wounds on Chinese yam (Dioscorea opposita) tubers can ocurr during harvesting and handling, and rapid suberisation is required to prevent infection and desiccation. However, little is known about the causal relationship among suberin deposition, relevant gene expressions and endogenous phytohormones levels in response to wounding. Wound-induced abscisic acid and jasmonic acid are likely to regulate the biosynthesis, transport and polymerisation of suberin monomers by activating relevant gene expressions, which might be involved in suberisation of cells in wound area. [ABSTRACT FROM AUTHOR]

Summary: Circadian clocks are 24‐h endogenous oscillators in physiological and behavioral processes. Though recent transcriptomic studies have been successful in revealing the circadian rhythmicity in gene expression, the power calculation for omics circadian analysis have not been fully explored. In this paper, we develop a statistical method, namely CircaPower, to perform power calculation for circadian pattern detection. Our theoretical framework is determined by three key factors in circadian gene detection: sample size, intrinsic effect size and sampling design. Via simulations, we systematically investigate the impact of these key factors on circadian power calculation. We not only demonstrate that CircaPower is fast and accurate, but also show its underlying cosinor model is robust against variety of violations of model assumptions. In real applications, we demonstrate the performance of CircaPower using mouse pan‐tissue data and human post‐mortem brain data, and illustrate how to perform circadian power calculation using mouse skeleton muscle RNA‐Seq pilot as case study. Our method CircaPower has been implemented in an R package, which is made publicly available on GitHub (https://github.com/circaPower/circaPower). [ABSTRACT FROM AUTHOR]

Psychosis is a defining feature of schizophrenia and highly prevalent in bipolar disorder. Notably, individuals with these illnesses also have major disruptions in sleep and circadian rhythms, and disturbances of sleep and circadian rhythms can precipitate or exacerbate psychotic symptoms. Psychosis is associated with the striatum, though to our knowledge, no study to date has directly measured molecular rhythms and determined how they are altered in the striatum of subjects with psychosis. We performed RNA sequencing and both differential expression and rhythmicity analyses to investigate diurnal alterations in gene expression in human postmortem striatal subregions (nucleus accumbens, caudate, and putamen) in subjects with psychosis (n = 36) relative to unaffected comparison subjects (n = 36). Across regions, we found differential expression of immune-related transcripts and a substantial loss of rhythmicity in core circadian clock genes in subjects with psychosis. In the nucleus accumbens, mitochondrial-related transcripts had decreased expression in subjects with psychosis, but only in those who died at night. Additionally, we found a loss of rhythmicity in small nucleolar RNAs and a gain of rhythmicity in glutamatergic signaling in the nucleus accumbens of subjects with psychosis. Between-region comparisons indicated that rhythmicity in the caudate and putamen was far more similar in subjects with psychosis than in matched comparison subjects. Together, these findings reveal differential and rhythmic gene expression differences across the striatum that may contribute to striatal dysfunction and psychosis in psychotic disorders. [ABSTRACT FROM AUTHOR]

Histone acetylation has been shown to involve in stress responses. However, the detailed molecular mechanisms that how histone deacetylases and transcription factors function in drought stress response remain to be understood. In this research, we show that ENAP1 and ENAP2 are positive regulators of drought tolerance in plants, and the enap1enap2 double mutant is more sensitive to drought stress. Both ENAP1 and ENAP2 interact with MYB44, a transcription factor that interacts with histone deacetylase HDT4. Genetics data show that myb44 null mutation enhances the sensitivity of enap1enap2 to drought stress. Whereas, HDT4 negatively regulates plant drought response, the hdt4 mutant represses enap1enap2myb44 drought sensitive phenotype. In the normal condition, ENAP1/2 and MYB44 counteract the HDT4 function for the regulation of H3K27ac. Upon drought stress, the accumulation of MYB44 and reduction of HDT4 leads to the enrichment of H3K27ac and the activation of target gene expression. Overall, this research provides a novel molecular mechanism by which ENAP1, ENAP2 and MYB44 form a complex to restrict the function of HDT4 in the normal condition; under drought condition, accumulated MYB44 and reduced HDT4 lead to the elevation of H3K27ac and the expression of drought responsive genes, as a result, plants are drought tolerant. Author summary: Water deficiency has become one of the greatest concerns limiting sustainable crop production. Uncovering the molecular mechanisms of drought stress response has been one of hot research topics worldwide. Histone modification and transcription factors have been shown to function in the drought stress response collectively. Yet, the detailed molecular mechanisms are still remained to study. In this research, we found a novel molecular mechanism that the histone binding protein ENAP1 and ENAP2 form a complex with MYB44 to restrict the function of histone deacetylase HDT4 from regulating H3K27 acetylation in the target genes in a normal condition; Whereas, under drought condition, MYB44 proteins are accumulated, and the HDT4 proteins are reduced, leading to elevations of H3K27ac and the expression of drought responsive genes, as a result, plants are drought tolerant. This research provides a new insight of how histone deacetylase, histone binding protein and transcription factor coordinate to regulate drought stress response in plants. [ABSTRACT FROM AUTHOR]

Macrophages induce a number of inflammatory response genes in response to stimulation with microbial ligands. In response to endotoxin Lipid A, a gene-activation cascade of primary followed by secondary-response genes is induced. Epigenetic state is an important regulator of the kinetics, specificity, and mechanism of gene activation of these two classes. In particular, SWI/SNF chromactin-remodeling complexes are required for the induction of secondary-response genes, but not primary-response genes, which generally exhibit open chromatin. Here, we show that a recently discovered variant of the SWI/SNF complex, the noncanonical BAF complex (ncBAF), regulates secondary-response genes in the interferon (IFN) response pathway. Inhibition of bromodomaincontaining protein 9 (BRD9), a subunit of the ncBAF complex, with BRD9 bromodomain inhibitors (BRD9i) or a degrader (dBRD9) led to reduction in a number of interferon-stimulated genes (ISGs) following stimulation with endotoxin lipid A. BRD9-dependent genes overlapped highly with a subset of genes differentially regulated by BET protein inhibition with JQ1 following endotoxin stimulation. We find that the BET protein BRD4 is cobound with BRD9 in unstimulated macrophages and corecruited upon stimulation to ISG promoters along with STAT1, STAT2, and IRF9, components of the ISGF3 complex activated downstream of IFN-alpha receptor stimulation. In the presence of BRD9i or dBRD9, STAT1-, STAT2-, and IRF9-binding is reduced, in some cases with reduced binding of BRD4. These results demonstrate a specific role for BRD9 and the ncBAF complex in ISG activation and identify an activity for BRD9 inhibitors and degraders in dampening endotoxin- and IFN-dependent gene expression. [ABSTRACT FROM AUTHOR]

Summary: Thousands of differentially expressed genes (DEGs) have been identified in rice under drought stress conditions. However, the regulatory mechanism of these DEGs remains largely unclear. Here, we report an interplay between histone H3K4me3 modification and transcription factor OsbZIP23 in the regulation of a dehydrin gene cluster under drought stress conditions in rice. When the H3K4me3 modification level was increased, the dehydrin gene expression levels were increased, and the binding levels of OsbZIP23 to the promoter of the dehydrin genes were also enhanced. Conversely, the H3K4me3 modification and dehydrin gene expression levels were downregulated in the osbzip23 mutant under drought stress conditions. Our study uncovers a collaboration between transcription factor and H3K4me3 modification in the regulation of drought‐responsive genes, which will help us to further understand the gene regulation mechanism under stress conditions in plants. [ABSTRACT FROM AUTHOR]

Abstract Ethnopharmacological relevance Plants of Epilobium angustifolium are popular in China to treatment of traumatic injury, subduing inflammation and menstrual disorders. In European, the preparations or extracts containing E. angustifolium are popular to treat prostate diseases. Recent research suggested that E. angustifolium showed therapeutic effects in early stage of BPH, inflammation of urethra and prostate, as well as micturition problems. And the related researches were focus on aqueous extract and its main constituent of oenothein B. Aim of the study This study aims to evaluate the therapeutic effect against BPH of the ethyl acetate extracts (EAE) and n -butanol extracts (BUE) from E. angustifolium and to chemical investigation of the active constituents. Materials and methods The in vitro anti-BPH activity was assessed by determining the benign prostatic hyperplasia epithelial-1 (BPH-1) cell viability using MTT assay as well as suppressing of prostate specific antigen (PSA) secretion in prostate epithelial cancer hormone-dependent (LNCaP) cells measured by ELISA method. The in vivo anti-BPH was evaluated by testosterone propionate induced BPH SD rats. After oral administration of BUE at 100, 200 and 400 mg/kg B.W. for 28 days, the prostate weight and index, plasma androgen level, histopathological alteration, oxidative and inflammatory-related factors in prostate were assessed. Phytochemical investigation on active extracts was carried by chromatographic and spectroscopic techniques. Anti-BPH activities of the isolates were evaluated in vitro. Results BUE and EAE from E. angustifolium exhibited significant anti-BPH effect in vitro. Further in vivo study demonstrated that BUE exhibited therapeutic effects against TP-induced BPH in SD rats via down-regulating of the androgen level, suppressing the expression of NF-κB and eventually alleviating the inflammatory responses and oxidative stress. Phytochemical research on BUE and EAE extracts led to the isolation and identification of 50 compounds. In vitro anti-BPH screening revealed that 26 compounds exhibited anti-proliferation in BHP-1 cell and 36 compounds showed PSA inhibition in LNCap cell, in which 7 compounds exhibited very significant anti-BPH activities in both two cell lines (P < 0.01), 5 compounds with extremely significant activities in one of the cell lines (P < 0.001), and compound 25 exhibited the most potent anti-BPH activity (P < 0.001). Conclusions E. angustifolium exhibited the therapeutic potential against BPH, and its active compounds may be used as candidate for treatment of BPH. Graphical abstract fx1 [ABSTRACT FROM AUTHOR]

Somatic cells can be reprogrammed to induced pluripotent stem (iPS) cells by ectopic expression of specific sets of transcription factors. Oct4, Sox2, and Klf4, factors that share many target genes in embryonic stem (ES) cells, are critical components in various reprogramming protocols. Nevertheless, it remains unclear whether these factors function together or separately in reprogramming. Here we show that Klf4 interacts directly with Oct4 and Sox2 when expressed at levels sufficient to induce iPS cells. Endogenous Klf4 also interacts with Oct4 and Sox2 in iPS cells and in mouse ES cells. The Klf4 C terminus, which contains three tandem zinc fingers, is critical for this interaction and is required for activation of the target gene Nanog. In addition, Klf4 and Oct4 co-occupy the Nanog promoter. A dominant negative mutant of Klf4 can compete with wild-type Klf4 to form defective Oct4/Sox2/Klf4 complexes and strongly inhibit reprogramming. In the absence of Klf4 overexpression, interaction of endogenous Klf4 with Oct4/Sox2 is also required for reprogramming. This study supports the idea that direct interactions between Klf4, Oct4, and Sox2 are critical for somatic cell reprogramming. [ABSTRACT FROM AUTHOR]

Schizophrenia is associated with disrupted cognitive control and sleep-wake cycles. Here we identify diurnal rhythms in gene expression in the human dorsolateral prefrontal cortex (dlPFC), in schizophrenia and control subjects. We find significant diurnal (24 h) rhythms in control subjects, however, most of these transcripts are not rhythmic in subjects with schizophrenia. Instead, subjects with schizophrenia have a different set of rhythmic transcripts. The top pathways identified in transcripts rhythmic only in subjects with schizophrenia are associated with mitochondrial function. Importantly, these rhythms drive differential expression patterns of these and several other genes that have long been implicated in schizophrenia (including BDNF and GABAergic-related transcripts). Indeed, differential expression of these transcripts is only seen in subjects that died during the night, with no change in subjects that died during the day. These data provide insights into a potential mechanism that underlies changes in gene expression in the dlPFC with schizophrenia. Sleep disturbance is common in psychiatric disease, and this may contribute to altered circadian rhythm in gene expression. Here the authors show that rhythms in gene expression in the dorsolateral prefrontal cortex in schizophrenia are different to that seen in healthy controls. [ABSTRACT FROM AUTHOR]