AI is a viable alternative to high throughput screening: a 318-target study

High throughput screening (HTS) is routinely used to identify bioactive small molecules. This requires physical compounds, which limits coverage of accessible chemical space. Computational approaches combined with vast on-demand chemical libraries can access far greater chemical space, provided that the predictive accuracy is sufficient to identify useful molecules. Through the largest and most diverse virtual HTS campaign reported to date, comprising 318 individual projects, we demonstrate that our AtomNet® convolutional neural network successfully finds novel hits across every major therapeutic area and protein class. We address historical limitations of computational screening by demonstrating success for target proteins without known binders, high-quality X-ray crystal structures, or manual cherry-picking of compounds. We show that the molecules selected by the AtomNet® model are novel drug-like scaffolds rather than minor modifications to known bioactive compounds. Our empirical results suggest that computational methods can substantially replace HTS as the first step of small-molecule drug discovery.

Application of targeted liposomes-based salvianolic acid A for the treatment of ischemic stroke

Novel therapeutics for the treatment of ischemic stroke remains to be the unmet clinical needs. Previous studies have indicated that salvianolic acid A (SAA) is a promising candidate for the treatment of the brain diseases. However, SAA has poor absolute bioavailability and does not efficiently cross the intact blood-brain barrier (BBB), which limit its efficacy. To this end we developed a brain-targeted liposomes for transporting SAA via the BBB by incorporating the liposomes to a transport receptor, insulin-like growth factor-1 receptor (IGF1R). The liposomes were prepared by ammonium sulfate gradients loading method. The prepared SAA-loaded liposomes (Lipo/SAA) were modified with IGF1R monoclonal antibody to generate IGF1R antibody-conjugated Lipo/SAA (IGF1R-targeted Lipo/SAA). The penetration of IGF1R-targeted Lipo/SAA into the brain was confirmed by labeling with Texas Red, and their efficacy were evaluate using middle cerebral artery occlusion (MCAO) model. The results showed that IGF1R-targeted Lipo/SAA are capable of transporting SAA across the BBB into the brain, accumulation in brain tissue, and sustained releasing SAA for several hours. Administration o IGF1R-targeted Lipo/SAA notably reduced infarct size and neuronal damage, improved neurological function and inhibited cerebral inflammation, which had much higher efficiency than no-targeted SAA.

Minor protopanaxadiol type sapogenins from the alkali hydrolysate of stems-leaves of Panax notoginseng

Two new protopanaxadiol type sapogenins, (3β,12β)-3,12,20-trihydroxydammar-24-en-26-al (1) and (3β,12β)-3,12,20-trihydroxydammar-24-en-26-oic acid (2), were isolated from the alkali hydrolysate of stems-leaves of Panax notoginseng, along with seven known analogues (3-9). Their structures were elucidated by spectroscopic analyses and single-crystal X-ray diffraction. Compound 2 and the known sapogenins 5-8 displayed weak to moderate inhibition of NO production in LPS-induced RAW264.7 macrophages with IC50 values from 44.5 to 143.6 μM, respectively.

The CSB chromatin remodeler regulates PARP1- and PARP2-mediated single-strand break repair at actively transcribed DNA regions

Efficient repair of oxidized DNA is critical for genome-integrity maintenance. Cockayne syndrome protein B (CSB) is an ATP-dependent chromatin remodeler that collaborates with Poly(ADP-ribose) polymerase I (PARP1) in the repair of oxidative DNA lesions. How these proteins integrate during DNA repair remains largely unknown. Here, using chromatin co-fractionation studies, we demonstrate that PARP1 and PARP2 promote recruitment of CSB to oxidatively-damaged DNA. CSB, in turn, contributes to the recruitment of XRCC1, and histone PARylation factor 1 (HPF1), and promotes histone PARylation. Using alkaline comet assays to monitor DNA repair, we found that CSB regulates single-strand break repair (SSBR) mediated by PARP1 and PARP2. Strikingly, CSB's function in SSBR is largely bypassed when transcription is inhibited, suggesting CSB-mediated SSBR occurs primarily at actively transcribed DNA regions. While PARP1 repairs SSBs at sites regardless of the transcription status, we found that PARP2 predominantly functions in actively transcribed DNA regions. Therefore, our study raises the hypothesis that SSBR is executed by different mechanisms based on the transcription status.

Role of toll-like receptors in the pathogenesis of COVID-19: Current and future perspectives

The coronavirus disease 2019 (COVID-19) pandemic underlines a persistent threat of respiratory tract infectious diseases and warrants preparedness for a rapid response. At present, COVID-19 has had a serious social impact and imposed a heavy global burden on public health. The exact pathogenesis of COVID-19 has not been fully elucidated. Since the outbreak of COVID-19, a renewed attention has been brought to Toll-like receptors (TLRs). Available data and new findings have demonstrated that the interaction of human TLRs and SARS-CoV-2 is a vital mediator of COVID-19 immunopathogenesis. TLRs such as TLR2, 4, 7 and 8 are potentially important in viral combat and activation of immunity in patients with COVID-19. Therapeutics targeting TLRs are currently considered promising options against the pandemic. A number of TLR-targeting immunotherapeutics are now being investigated in preclinical studies and different phases of clinical trials. In addition, innovative vaccines based on TLRs under development could be a promising approach for building a new generation of vaccines to solve the current challenges. In this review, we summarize recent progress in the role of TLRs in COVID-19, focusing the new candidate drugs targeting TLRs, the current technology and potential paths forward for employing TLR agonists as vaccine adjuvants.

[Early death and causes of death of patients with autism spectrum disorders: A systematic review]

To study of premature/early death of autistic patients from the perspective of life course can help families, medical institutions and policy makers better deal with the adverse effects of autism. Several studies have shown that autistic patients have a high risk of death, however, the results are still inconsistent. To assess the risk of mortality among the autistic patients, we undertook a comprehensive search of MEDLINE, Web of Science and EMBASE databases. This paper reviewed the studies on the negative disease outcomes of autism spectrum disorders, including the risk of death, causes of death and several research hotspots in this field. Strict inclusion/exclusion criteria were used. Information was extracted from selected papers, tabulated and synthesized. In the study, 15 studies were included, with a total of 216 045 individuals. The main outcome was all-cause mortality in association with autism and the secondary outcome was cause-specific mortality. The results showed that all-cause mortality was higher for the autistic patients (RR=2.32, 95%CI: 1.98-2.72, I²=87.1%, P < 0.001). Risk ratio showed a greater inequality for female than male (male: RR=2.00, 95%CI: 1.57-2.55, I²=93.2%, P < 0.001; female: RR=4.66, 95%CI: 3.30-6.58, I²=92.0%, P < 0.001). Compared with the unnatural death, the risk of natural death was higher (RR=3.44, 95%CI: 1.27-9.26, I²=80.2%, P=0.025). As autism had many comorbidities, which would bring more health risks and natural deaths possibilities. There were some structural differences in unnatural death. Accidental injury death and suicide were two kinds of causes. Lacking social skills would weaken the ability to ask for help when encountering injuries. This paper put forward some suggestions for futures. First, to well study the comorbidity can reduce the risk of death from a medical point of view. Second, the scientists and policymakers should pay attention to the social environment and provide a safer environment for the autistic patients. Third, for women and for adolescents without cognitive impairment, due to their high risk of suicide, the society should provide them with more supportive social networks and improve their life satisfaction. Fourth, it is necessary to balance the rehabilitation resources in various regions in China and provide more high-quality lifelong rehabilitation monitoring and care services.

Piceatannol-3'-O-β-d-glucopyranoside alleviates nephropathy via regulation of High mobility group B-1 (HMGB1)/Toll-like receptor 4 (TLR4)/Nuclear factor kappa B (NF-κB) signalling pathway

OBJECTIVES

Nephrotic syndrome (NS) remains a therapeutic challenge for nephrologists. Piceatannol-3'-O-β-d-glucopyranoside (PG) is a major active ingredient in Quzha. The purpose of the study was to assess the renoprotection of PG.

METHODS

In vitro, the podocyte protection of PG was assessed in MPC-5. SD rats were injected with adriamycin to induce nephropathy in vivo. The determination of biochemical changes and inflammatory cytokines was performed, and pathological changes were examined by histopathological examination. Immunostaining and western blot analyses were used to analyse expression levels of proteins.

KEY FINDINGS

The results showed that PG improved adriamycin-induced podocyte injury, attenuated nephropathy, improved hypoalbuminemia and hyperlipidaemia, and lowered cytokine levels. The podocyte protection of PG was further verified by reduction of desmin and increasing synaptopodin expression. Furthermore, treatment with PG down-regulated the expression of HMGB1, TLR4 and NF-κB along with its upstream regulator, IKKβ and yet up-regulated IκBα expression by western blot analysis.

CONCLUSIONS

Overall, our data showed that PG has a favourable renoprotection in experimental nephrosis, apparently by amelioration of podocyte injury. PG might mediate these effects via modulation of the HMGB1/TLR4/NF-κB signalling pathway. The study first provides a promising leading compound for the treatment of NS.

Effectiveness and safety of acupuncture for insulin resistance in women with polycystic ovary syndrome: A systematic review and meta-analysis

Objective

To perform a systematic review and meta-analysis of randomized controlled trials (RCTs) to evaluate acupuncture's clinical effect on insulin resistance (IR) in women with polycystic ovary syndrome (PCOS).

Methods

PubMed, Cochrane Library, Embase databases, and Chinese databases, including China National Knowledge Infrastructure, Technology Journal Database, and Wanfang Database, were searched without language restrictions from inception to December 20, 2021. Only RCTs in which acupuncture had been examined as the sole or adjunctive PCOS-IR treatment were included. Our primary endpoint was the homeostasis model assessment of insulin resistance (HOMA-IR). The secondary outcomes were fasting blood glucose (FBG), fasting insulin (FINS), body mass index (BMI), and adverse events.

Results

Our analysis included 17 eligible RCTs (N = 1511 participants). Compared with other treatments, acupuncture therapy yielded a greater mean reduction in HOMA-IR (MD = -0.15; 95% CI, -0.27 to -0.03; P = 0.01) and BMI (MD = -1.47; 95% CI, -2.46 to -0.47; P = 0.004). Besides acupuncture was associated with a lower risk of adverse events than other treatments (RR, 0.15; 95% CI, 0.10 to 0.22; P < 0.01). Additionally, the combination treatment of acupuncture and medicine is more effective in improving HOMA-IR (MD = -0.91; 95% CI, -1.11 to -0.71; P < 0.01), FBG (MD = -0.30; 95% CI, -0.56 to -0.04; P = 0.02), FINS (MD = -2.33; 95% CI, -2.60 to -2.06; P < 0.01) and BMI (MD = -1.63; 95% CI, -1.94 to -1.33; P < 0.01) than medicine alone.

Conclusions

Acupuncture is relatively effective in improving HOMA-IR and BMI in PCOS-IR. Besides, it's safer than other treatments and could be an adjuvant strategy for improving PCOS-IR. Further large-scale, long-term RCTs with strict methodological standards are justified.

[Changes of brain network characteristics in patients with depression before and after precise repetitive transcranial magnetic stimulation]

Objective: To investigate the changes of brain network characteristics in patients with depression before and after precise repetitive transcranial magnetic stimulation (rTMS) treatment. Methods: Patients with depression in the Second Affiliated Hospital of Xinxiang Medical University and healthy volunteers in the community of Xinxiang city from February 2018 to March 2019 were simultaneously recruited. The left dorsolateral prefrontal cortex was precisely selected as the stimulation target through the latest Human Brainnetome Atlas, and the near infrared navigation was used to achieve accurate brain stimulation treatment in combination with the structural magnetic resonance data. Moreover, functional connectivity was analyzed before and after rTMS treatment in significantly altered brain areas of patients with depression. Results: Nineteen patients (11 males and 8 females) with depression were included, aged (34±11) years. Meanwhile, 22 healthy controls (9 males and 13 females), aged (30±9) years, were also enrolled. Functional connectivity of insular cortex was decreased in depression patients when the insula was analyzed as the target area (P<0.05). The functional connection from insula to middle frontal lobe and superior parietal lobe in patients with depression decreased before rTMS treatment (P<0.05), but increased after rTMS treatment (P<0.05). The functional connection between dIg_L of the insula and the right middle prefrontal lobe was correlated with Beck Anxiety Index (BAI) before rTMS treatment and Beck Depression Index (BDI) after rTMS treatment (r=0.737, P=0.003; r=0.696, P=0.005). Conclusions: Abnormal functional connectivity of insula may be the brain imaging mechanism of rTMS treatment. Precise brain region selection based on Human Brainnetome Atlas provides a new technical method for clinical rTMS precision treatment.

Non-clinical safety evaluation of salvianolic acid A: acute, 4-week intravenous toxicities and genotoxicity evaluations

BACKGROUND

Toxicological problem associated with herbal medicine is a significant public health problem. Hence, it is necessary to elaborate on the safety of herbal medicine. Salvianolic acid A (SAA) is a major active compound isolated from Danshen, a popular herbal drug and medicinal food plant in China. The aim of the present study was to explore the toxicological profile of SAA.

METHODS

The acute toxicity studies were performed in mice and Beagle dogs with single administration with SAA. A 4-week subchronic toxicity was test in dogs. SAA was intravenously administered at doses of 20, 80 and 300 mg/kg. Clinical observation, laboratory testing and necropsy and histopathological examination were performed. The genotoxic potential of SAA was evaluated by 2 types of genotoxicity tests: a reverse mutation test in bacteria and bone marrow micronucleus test in mice.

RESULTS

In acute toxicities, the LD50 of SAA is 1161.2 mg/kg in mice. The minimum lethal dose (MLD) and maximal non-lethal dose (MNLD) of SAA were 682 mg/kg and 455 mg/kg in dogs, respectively. The approximate lethal dose range was 455-682 mg/kg. In the study of 4-week repeated-dose toxicity in dogs, focal necrosis in liver and renal tubular epithelial cell, the decrease in relative thymus weight, as well as abnormal changes in biochemical parameters, were observed in SAA 80 or 300 mg/kg group. The no observed adverse effect level (NOAEL) of SAA was 20 mg/kg. Thymus, liver and kidneys were the toxic targets. These toxic effects were transient and reversible. These results indicated that it should note examination of liver and kidney function during the administration of SAA in clinic. Furthermore, SAA had no mutagenic effect at any tested doses.

CONCLUSION

These results provide new toxicological information of SAA for its clinical application and functional food consumption.

Analyzing the Interaction of RBPJ with Mitotic Chromatin and Its Impact on Transcription Reactivation upon Mitotic Exit

The sequence-specific transcription factor RBPJ, also known as CSL (CBF1, Su(H), Lag1), is an evolutionarily conserved protein that mediates Notch signaling to guide cell fates. When cells enter mitosis, DNA is condensed and most transcription factors dissociate from chromatin; however, a few, select transcription factors, termed bookmarking factors, remain associated. These mitotic chromatin-bound factors are believed to play important roles in maintaining cell fates through cell division. RBPJ is one such factor that remains mitotic chromatin associated and therefore could function as a bookmarking factor. Here, we describe how to obtain highly purified mitotic cells from the mouse embryonal carcinoma cell line F9, perform chromatin immunoprecipitation with mitotic cells, and measure the first run of RNA synthesis upon mitotic exit. These methods serve as basis to understand the roles of mitotic bookmarking by RBPJ in propagating Notch signals through cell division.

Salvianolic acid A attenuates steroid resistant nephrotic syndrome through suPAR/uPAR-αvβ3 signaling Inhibition

ETHNOPHARMACOLOGICAL RELEVANCE

Salvianolic acid A (SAA) is extracted from traditional Chinese medicine Salvia miltiorrhiza and is the main water-soluble and the biologically active ingredient. SAA possesses a variety of pharmacological activities and has an excellent protective effect on kidney disease, especially steroid resistant nephrotic syndrome (SRNS), and has advantages in improving the efficacy of glucocorticoids, but its mechanism needs to be further explored.

PURPOSE

The study was designed to explore the effect of suPAR and uPAR in SRNS patients and evaluate the potential effect of SAA in improving podocyte steroid resistance and explore its mechanism.

METHODS AND MATERIALS

The ELISA kits were used to detect the levels of suPAR in the blood and urine of subjects. The levels of uPAR, GRα, and GRβ expression in renal tissues of SRNS patients was detected by immunohistochemistry and analyzed using the Pearson method. In vitro studies, steroid resistance model was induced by the TNF-α and IFN-γ. The protein and mRNA expression of Nephrin, GR, GRα and GRβ were analyzed using western blot and qRT-PCR. The activity of GR-DNA binding was detected by using TransAM™ GR kits. Adriamycin further induced steroid resistance podocyte. Flow cytometry was used to detect the effect of SAA on podocyte apoptosis. ELISA assay was used to detect the suPAR expression in the podocyte supernatant. Western blot and qRT-PCR were used to detect the protein and mRNA expression of uPAR and Nephrin in podocytes.

RESULTS

The serum and urine levels of suPAR were conspicuously higher in SRNS patients than healthy volunteers and SSNS patients, and the expression of uPAR in renal tissue of SRNS patients is negatively correlated with GRα, but positively correlated with GRβ. The combination of TNF-α and IFN-γ could conspicuously increase the GRβ expression and reduce GRα/GRβ, and induce steroid resistance in podocytes. Moreover, we found that SAA could reduce the apoptosis of podocytes and suppress the expression of suPAR/uPAR, and increase the expression of Nephrin.

CONCLUSION

The level of suPAR and uPAR expression may have important value in predicting glucocorticoids resistance in patients with idiopathic nephrotic syndrome (INS). The combination of TNF-α and IFN-γ induce podocytes can establish steroid resistance model in vitro. SAA could improve glucocorticoids resistance of podocyte which can be attributed in part to regulate the suPAR/uPAR-αvβ3 signaling pathway.

A Novel Flow Cytometric Assay to Identify Inhibitors of RBPJ-DNA Interactions

Notch signaling is often involved in cancer cell initiation and proliferation. Aberrant Notch activation underlies more than 50% of T-cell acute lymphoblastic leukemia (T-ALL); accordingly, chemicals disrupting Notch signaling are of potential to treat Notch-dependent cancer. Here, we developed a flow cytometry-based high-throughput assay to identify compounds that disrupt the interactions of DNA and RBPJ, the major downstream effector of Notch signaling. From 1492 compounds, we identified 18 compounds that disrupt RBPJ-DNA interactions in a dose-dependent manner. Cell-based assays further revealed that auranofin downregulates Notch-dependent transcription and decreases RBPJ-chromatin interactions in cells. Most strikingly, T-ALL cells that depend on Notch signaling for proliferation are more sensitive to auranofin treatment, supporting the notion that auranofin downregulates Notch signaling by disrupting RBPJ-DNA interaction. These results validate the feasibility of our assay scheme to screen for additional Notch inhibitors and provide a rationale to further test the use of auranofin in treating Notch-dependent cancer.

Curcumin, as a pleiotropic agent, improves doxorubicin-induced nephrotic syndrome in rats

ETHNOPHARMACOLOGICAL RELEVANCE

Curcumin, a phenolic compound extracted from the rhizome of turmeric (Curcuma longa L.), has been reported to have broad biological functions including potent antioxidant and renoprotective effects. It has been reported that Curcumin has a certain protective effect on the kidney. However, its mechanism of action needs further study.

AIM OF THE STUDY

The present research aims at investigating the therapeutic effects and its underlying mechanism of curcumin on NS.

MATERIALS AND METHODS

The conditionally immortalized mouse podocyte cell line was utilized to evaluate the podocyte-protective effect of curcumin and its effects on NF-κB pathway and Nrf2/ARE pathway in podocyte in vitro. Furthermore, the DOX-induced NS rats were utilized to investigate the therapeutic effects and its underlying mechanism of curcumin against NS in vivo.

RESULTS

The consequences of this study revealed that curcumin activated Nrf2, inhibited NF-κB pathway and up-regulated podocin in DOX-induced podocyte. Further research results showed that curcumin can considerably alleviate proteinuria and improve hypoalbuminemia in NS rats, and lower blood lipid levels to alleviate hyperlipidemia in NS rats, indicating that curcumin has significant therapeutic effects on rat NS. Further observation by electron microscopy and detection showed that curcumin can improve renal function and podocyte injury, which may be related to the repairment of mRNA expression and podocin protein. Interestingly, the results of the blood rheology test showed that curcumin can effectively reduce whole blood viscosity (WBV) and plasma viscosity (PV), and reduce hematocrit (Hct). In addition, the oxidative stress state of kidney in NS rats was considerably reversed by curcumin, which may be achieved by activating Nrf2 and increasing the expression of antioxidant enzymes HO-1, NQO-1. We also found that NF-κB pathway is activated in the kidney of NS rats, and curcumin can inhibit the activation of NF-κB by down-regulating the expression of NF-κB p65, reducing the level of p-IκBα and up-regulating the expression of IκBα.

CONCLUSION

These findings suggest that curcumin, as a multifunctional agent, exerts a protective effect on DOX-induced nephrotic syndrome in rats, which provides a pharmacological basis for the further development of curcumin and also provides a basis for the advantages of multi-targeted drugs in the processing of NS.

Working Memory of Patients with Mild Cognitive Impairment due to Brain Trauma Based on fNIRS

ABSTRACT

Objective To discuss the activation characteristics of the prefrontal cortex of people with mild cognitive impairment （MCI） due to brain trauma during working memory tasks. Methods The psychological experiment design software E-prime was used and N-back paradigm was adopted as working memory task. Functional near-infrared spectroscopy （fNIRS） was used to detect changes in cortical oxygenated hemoglobin concentrations of 22 channels within the prefrontal lobe of 24 people with MCI due to brain trauma （study group） and 27 healthy volunteers （control group） with matching gender and age. Behavioral data, such as the number of keystroke errors and reaction time, were recorded simultaneously. Independent samples t test and non-parametric test were used to compare the mean value of oxygenated hemoglobin concentration change, the number of key errors and the mean value of reaction time of the two groups in each task. Results （1） The differences in the number of errors and reaction time between the two groups in 1-back and 2-back tasks had statistical significance （P<0.05）.The main effects of task load and group were both significant （task F=14.11, P=0.001 1; group F=10.39, P=0.001 5）. （2） During the 1-back task, the differences in oxygenated hemoglobin concentration changes of the 22 channels between the two groups had no statistical significance （P>0.05）. During the 2-back task, the differences in oxygenated hemoglobin concentration changes of the two groups in channel 2, 3, 7, 9, 10, 11, 14, 15, 18, 19, 21 and 22 had statistical significance （P<0.05）. （3） In the 1-back task, the left frontal pole and dorsolateral prefrontal area in both groups were activated. In the 2-back task, the activation areas of the control group were the left frontal pole area and the left dorsolateral prefrontal area, while that of the study group almost covered most of the left and right frontal pole areas, which were scattered and the right area was activated, too. Conclusion Patients with MCI due to brain trauma have obvious working memory impairment, and during the 2-back working memory task, the activation of the prefrontal lobe decreased, but the activation range was wider.

Application of Mismatch Negative in Evaluation of Severity of Mental Disorders due to Traumatic Brain Injury

Objective To explore the applied value of mismatch negative （MMN） in evaluation of severity of mental disorders due to traumatic brain injury. Methods Thirty-five patients（case group） that conform to the diagnostic criteria of organic （traumatic brain injury） mental disorder in ICD-10 Classification of Mental and Behavioural Disorders criteria were selected. Twenty-four healthy subjects （normal control group） that matched the case group in terms of gender, age composition ratio and educational level were selected. All subjects were evaluated by Activity of Daily Living Scale （ADL） and Social Disability Screening Schedule （SDSS） and then examined by Event-Related Potential （ERP）. A statistical analysis of the data was made by SPSS 22.0 software. Results The 32 patients and 24 normal control subjects completed the study. The scores of ADL and SDSS were significantly higher in the case group than in the normal control group （P<0.05）. The latency of Fz, FCz, Cz and Pz in the case group was significantly longer than that in the normal control group （P<0.05）. In the case group, the latency of Fz, FCz, Cz and Pz was positively correlated with the scores of ADL and SDSS （P<0.05）. The equation can be well fitted with the scores of ADL and SDSS. The latency and amplitude of Fz, FCz, Cz and Pz were used as concomitant variables and whether or not the subjects had mental disorders due to traumatic brain injury as dependent variables. Conclusion The latency of MMN can be used as an indicator in potential evaluation of the severity of mental disorders due to traumatic brain injury, which means that the longer the latency of MMN is, the more severe mental disorders due to traumatic brain injury may be. The combined application of ADL, SDSS and MMN can be an objective indicator in preliminary judgment of mental disorders due to traumatic brain injury.

HDAC1 negatively regulates selective mitotic chromatin binding of the Notch effector RBPJ in a KDM5A-dependent manner

Faithful propagation of transcription programs through cell division underlies cell-identity maintenance. Transcriptional regulators selectively bound on mitotic chromatin are emerging critical elements for mitotic transcriptional memory; however, mechanisms governing their site-selective binding remain elusive. By studying how protein-protein interactions impact mitotic chromatin binding of RBPJ, the major downstream effector of the Notch signaling pathway, we found that histone modifying enzymes HDAC1 and KDM5A play critical, regulatory roles in this process. We found that HDAC1 knockdown or inactivation leads to increased RBPJ occupancy on mitotic chromatin in a site-specific manner, with a concomitant increase of KDM5A occupancy at these sites. Strikingly, the presence of KDM5A is essential for increased RBPJ occupancy. Our results uncover a regulatory mechanism in which HDAC1 negatively regulates RBPJ binding on mitotic chromatin in a KDM5A-dependent manner. We propose that relative chromatin affinity of a minimal regulatory complex, reflecting a specific transcription program, renders selective RBPJ binding on mitotic chromatin.

Mechanistic insights into the regulation of transcription and transcription-coupled DNA repair by Cockayne syndrome protein B

Cockayne syndrome protein B (CSB) is a member of the SNF2/SWI2 ATPase family and is essential for transcription-coupled nucleotide excision DNA repair (TC-NER). CSB also plays critical roles in transcription regulation. CSB can hydrolyze ATP in a DNA-dependent manner, alter protein-DNA contacts and anneal DNA strands. How the different biochemical activities of CSB are utilized in these cellular processes have only begun to become clear in recent years. Mutations in the gene encoding CSB account for majority of the Cockayne syndrome cases, which result in extreme sun sensitivity, premature aging features and/or abnormalities in neurology and development. Here, we summarize and integrate recent biochemical, structural, single-molecule and somatic cell genetic studies that have advanced our understanding of CSB. First, we review studies on the mechanisms that regulate the different biochemical activities of CSB. Next, we summarize how CSB is targeted to regulate transcription under different growth conditions. We then discuss recent advances in our understanding of how CSB regulates transcription mechanistically. Lastly, we summarize the various roles that CSB plays in the different steps of TC-NER, integrating the results of different studies and proposing a model as to how CSB facilitates TC-NER.

Poly(ADP-ribose) polymerase 1 (PARP1) promotes oxidative stress-induced association of Cockayne syndrome group B protein with chromatin

Cockayne syndrome protein B (CSB) is an ATP-dependent chromatin remodeler that relieves oxidative stress by regulating DNA repair and transcription. CSB is proposed to participate in base-excision repair (BER), the primary pathway for repairing oxidative DNA damage, but exactly how CSB participates in this process is unknown. It is also unclear whether CSB contributes to other repair pathways during oxidative stress. Here, using a patient-derived CS1AN-sv cell line, we examined how CSB is targeted to chromatin in response to menadione-induced oxidative stress, both globally and locus-specifically. We found that menadione-induced, global CSB-chromatin association does not require CSB's ATPase activity and is, therefore, mechanistically distinct from UV-induced CSB-chromatin association. Importantly, poly(ADP-ribose) polymerase 1 (PARP1) enhanced the kinetics of global menadione-induced CSB-chromatin association. We found that the major BER enzymes, 8-oxoguanine DNA glycosylase (OGG1) and apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1), do not influence this association. Additionally, the level of γ-H2A histone family member X (γ-H2AX), a marker for dsDNA breaks, was not increased in menadione-treated cells. Therefore, our results support a model whereby PARP1 localizes to ssDNA breaks and recruits CSB to participate in DNA repair. Furthermore, this global CSB-chromatin association occurred independently of RNA polymerase II-mediated transcription elongation. However, unlike global CSB-chromatin association, both PARP1 knockdown and inhibition of transcription elongation interfered with menadione-induced CSB recruitment to specific genomic regions. This observation supports the hypothesis that CSB is also targeted to specific genomic loci to participate in transcriptional regulation in response to oxidative stress.

Expression and Purification of Recombinant Proteins Using the Baculovirus System

This article describes how to analyze protein expression in cells infected with recombinant baculovirus on a small scale for optimizing protein production, how to maximize and scale up recombinant protein production, and how to purify recombinant proteins. © 2018 by John Wiley & Sons, Inc.

Glucohexaose-induced protein phosphatase 2C regulates cell redox status of cucumber seedling

Protein Phosphatase 2C (PP2C) is an important phosphatase-like protein in eukaryotic organisms that can negatively regulate protein kinase cascade abscisic acid (ABA) signal system through phosphorylation and carry out vital roles in various cell processes. The previous study indicated that the accumulation of reactive oxygen species (ROS) is a part of mechanism of glucohexaose-induced resistance in cucumber cotyledons, and CsPP2C80s might play a crucial role in processes related to ROS produce and signal transduction. To identify the mechanism of CsPP2C80s involved in glucohexaose and ABA signaling regulating cell redox status, the effects of glucohexaose and ROS inhibitor pretreatment on endogenous ABA content and ABA signaling genes expression levels of cucumber seedlings were analysed. These results suggest that cucumber CsPP2C80s are involved in ROS accumulation and ABA signal transduction pathway induced by glucohexaose, CsPP2C80s play a positive regulatory role in process of ABA combined with ABA receptors (PYLs) to activate SNF1-related protein kinases 2 (SnRK2s) and regulate NADPH oxidase to produce extracellular hydrogen peroxide (H2O2), providing unequivocal molecular evidence of PP2C-mediated ABA response mechanisms functioning in cell redox status induced by glucohexaose.

[Applied Value of Electroencephalogram in Assessment of Mild Psychiatry Impairment]

OBJECTIVES

To explore the applied value of electroencephalogram （EEG） in assessment of psychiatric impairment among patients with mental disorders due to traumatic brain injury.

METHODS

According to the ICD-10, a total of 271 subjects were enrolled and assessed with the criterion of mental disorders due to traumatic brain injury. Activity of Daily Living Scale （ADL）, Functional Activities Questionnaire （FAQ） and Social Disability Screening Schedule （SDSS） were used to evaluate the severity of patients. All the participants were tested by Wechsler Adult Intelligence Scale （WAIS） and examined by EEG.

RESULTS

Totally 215 patients accomplished the study. The results of Glasgow Coma Scale （GCS）, the severity of craniocerebral injury and the scores of FAQ, SDSS and ADL showed significant difference among the patients with different severity of EEG （P<0.05）. The grades of psychiatric impairment showed significant difference among the patients with different abnormal EEG （P<0.05）.

CONCLUSIONS

EEG can reflect the severity of craniocerebral injury, assist evaluate the social function and activity of daily living of patients with mental disorders due to traumatic brain injury, and distinguish the mild psychiatric impairment grades, which suggest that EEG has a certain reference value in the assessment of psychiatric impairment.

NAP1L1 accelerates activation and decreases pausing to enhance nucleosome remodeling by CSB

Cockayne syndrome protein B (CSB) belongs to the SWI2/SNF2 ATP-dependent chromatin remodeler family, and CSB is the only ATP-dependent chromatin remodeler essential for transcription-coupled nucleotide excision DNA repair. CSB alone remodels nucleosomes ∼10-fold slower than the ACF remodeling complex. Strikingly, NAP1-like histone chaperones interact with CSB and greatly enhance CSB-mediated chromatin remodeling. While chromatin remodeling by CSB and NAP1-like proteins is crucial for efficient transcription-coupled DNA repair, the mechanism by which NAP1-like proteins enhance chromatin remodeling by CSB remains unknown. Here we studied CSB's DNA-binding and nucleosome-remodeling activities at the single molecule level in real time. We also determined how the NAP1L1 chaperone modulates these activities. We found that CSB interacts with DNA in two principle ways: by simple binding and a more complex association that involves gross DNA distortion. Remarkably, NAP1L1 suppresses both these interactions. Additionally, we demonstrate that nucleosome remodeling by CSB consists of three distinct phases: activation, translocation and pausing, similar to ACF. Importantly, we found that NAP1L1 promotes CSB-mediated remodeling by accelerating both activation and translocation. Additionally, NAP1L1 increases CSB processivity by decreasing the pausing probability during translocation. Our study, therefore, uncovers the different steps of CSB-mediated chromatin remodeling that can be regulated by NAP1L1.

[Changes and the impact on immune function of opioid-dependent subjects by Jitai tabelets during the withdrawal stage]

Objective: To detect the changes in the immune function of opioid-dependent subjects during the withdrawal stage through the administration of Jitai tablet. Methods: Subjects were treated as Jitai tablet alone, Jitai tablet plus buprenorphine and placebo, in a randomized,double-blind, placebo-controlled trial. Before and after the 14(th) day of withdrawal, levels of immunoglobulin (IgM, IgA, IgG), T cell subsets (CD(3)(+), CD(4)(+), CD(8)(+), CD(4)(+)/CD(8)(+)) and cytokines (IL-2, IFN-γ, IL-4, IFN-γ/IL-4) were detected. Results: Compared with healthy people, immunity function before withdrawal among the opioid abusers showed higher levels of IgM, IL-2, IFN-γ, IL-4 and lower level of CD(3)(+)T, as (1.67±0.87) g/L, (14.44±13.50)%, (20.23±15.10)%, (1.97±1.59)%, (47.01±13.62)%, respectively, with difference statistically significant (P<0.05). There was no big difference of other immunity indicators between the two groups (P>0.05). At the 14(th) day of withdrawal in placebo group, levels of IL-4 returned to normal while IFN-γ/IL-4 ratio increased by 3.43 times (P<0.05). Levels of IgA, IgG, CD(4)(+) and CD(4)(+)/CD(8)(+) ratio fluctuated within normal range. There were no significant changes in other immunity indicators (P>0.05). Compared with placebo group, fluctuation of IgG and IgM decreased in Jitai group during withdrawal period, together with a normal level of IgM at the 14(th) day. Level of IL-4 abnormally rose up by 0.54 times in Jitai tablet plus buprenorphine group, while IFN-γ/IL-4 ratio been switched back at the 14(th) day of withdrawal. Other immune indicators were not affected by medical interventions. Conclusion: We noticed that certain impairment of the immune function might be restored by Jitai tablet during the withdrawal period.

Anti-inflammatory and Anti-oxidative Activities of Paeonol and Its Metabolites Through Blocking MAPK/ERK/p38 Signaling Pathway

The possible protective and curative effects of paeonol on carrageenan-induced acute hind paw edema in rats and dextran sulfate sodium (DSS)-induced colitis in mice have been evaluated. After oral administration, paeonol (20 and 40 mg/kg) reduced the edema increase in paw volumes and also the development of DSS-induced murine colitis. Furthermore, anti-inflammatory and anti-oxidant activities of paeonol (1) together with its 10 metabolites (M2~M11) were investigated by using in vitro anti-inflammatory and anti-oxidant assays. M3 and M11 exhibited significant 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities (with EC50 values of 93.44 and 23.24 μM, respectively). All the metabolites except M8 showed hydroxyl radical scavenging activities, and M3 and M11 were the most potent agents (with EC50 values of 336.02 and 124.05 μM, respectively). Inhibitory effects of paeonol, M2~M11 on the overproduction of nitric oxide (NO), and the release of TNF-α were also tested. M3 and M11 potently inhibited lipopolysaccharide (LPS)-induced overproduction of NO in macrophage RAW 264.7. Western blot results demonstrated that paeonol, M3, and M11 downregulated the high expression of inducible nitric oxide synthase (iNOS) and COX-2 proteins, and the effects of M3 and M11 were more potent when compared with paeonol. These findings indicated that paeonol may play anti-inflammatory and anti-oxidant roles by changing to its active metabolites after absorption. In addition, further investigations on the mechanism showed that paeonol, M3, and M11 blocked the phosphorylation of MAPK/ERK 1/2 and p38, whereas they showed no effect on the phosphorylation of JNK. The above results suggested that pre-treatment with paeonol might be an effective therapeutic intervention against inflammatory diseases including colitis.

Complete mitochondrial genome sequence and gene organization of Chinese indigenous chickens with phylogenetic considerations

In this study, we sequenced the complete mitochondrial DNA of Chinese indigenous Jinhu Black-bone and Rugao chickens. The two chicken mitochondrial genomes were deposited in GenBank under accession Nos. KP742951 and KR347464, respectively. The complete mitochondrial genomes of Jinhu Black-bone and Rugao chickens were sequenced and found to span 16,785 and 16,786 bp, respectively, and consisted of 22 tRNA genes, two rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and one control region (D-loop). The majority of genes were positioned on the H-strand, and the ND6 and eight tRNA genes were found to be encoded on the L-strand. The mitogenomes showed a similar gene order to that of the published Gallus gallus genome, as neither included a control region. The overall base composition of the genome of the two chickens was A = 30.22/30.28%, G = 13.57/13.49%, T = 23.74/23.76%, and C = 32.48/32.48%. Nucleotide skewness of the coding strands of the two chicken genomes (AT-skew = 0.12, GC-skew = -0.41) was biased towards T and G. Phylogenetic analysis revealed 29 subspecies, and the molecular genetic relationship among the 29 subspecies was identical to that of traditional taxonomy.

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons

HnRNP L is a ubiquitous splicing-regulatory protein that is critical for the development and function of mammalian T cells. Previous work has identified a few targets of hnRNP L-dependent alternative splicing in T cells and has described transcriptome-wide association of hnRNP L with RNA. However, a comprehensive analysis of the impact of hnRNP L on mRNA expression remains lacking. Here we use next-generation sequencing to identify transcriptome changes upon depletion of hnRNP L in a model T-cell line. We demonstrate that hnRNP L primarily regulates cassette-type alternative splicing, with minimal impact of hnRNP L depletion on transcript abundance, intron retention, or other modes of alternative splicing. Strikingly, we find that binding of hnRNP L within or flanking an exon largely correlates with exon repression by hnRNP L. In contrast, exons that are enhanced by hnRNP L generally lack proximal hnRNP L binding. Notably, these hnRNP L-enhanced exons share sequence and context features that correlate with poor nucleosome positioning, suggesting that hnRNP may enhance inclusion of a subset of exons via a cotranscriptional or epigenetic mechanism. Our data demonstrate that hnRNP L controls inclusion of a broad spectrum of alternative cassette exons in T cells and suggest both direct RNA regulation as well as indirect mechanisms sensitive to the epigenetic landscape.

Genetic Variants That Predispose to DNA Double-Strand Breaks in Lymphocytes From a Subset of Patients With Familial Colorectal Carcinomas

BACKGROUND & AIMS

DNA structural lesions are prevalent in sporadic colorectal cancer. Therefore, we proposed that gene variants that predispose to DNA double-strand breaks (DSBs) would be found in patients with familial colorectal carcinomas of an undefined genetic basis (UFCRC).

METHODS

We collected primary T cells from 25 patients with UFCRC and matched patients without colorectal cancer (controls) and assayed for DSBs. We performed exome sequence analyses of germline DNA from 20 patients with UFCRC and 5 undiagnosed patients with polyposis. The prevalence of identified variants in genes linked to DNA integrity was compared with that of individuals without a family history of cancer. The effects of representative variants found to be associated with UFCRC was confirmed in functional assays with HCT116 cells.

RESULTS

Primary T cells from most patients with UFCRC had increased levels of the DSB marker γ(phosphorylated)histone2AX (γH2AX) after treatment with DNA damaging agents, compared with T cells from controls (P < .001). Exome sequence analysis identified a mean 1.4 rare variants per patient that were predicted to disrupt functions of genes relevant to DSBs. Controls (from public databases) had a much lower frequency of variants in the same genes (P < .001). Knockdown of representative variant genes in HCT116 CRC cells increased γH2AX. A detailed analysis of immortalized patient-derived B cells that contained variants in the Werner syndrome, RecQ helicase-like gene (WRN, encoding T705I), and excision repair cross-complementation group 6 (ERCC6, encoding N180Y) showed reduced levels of these proteins and increased DSBs, compared with B cells from controls. This phenotype was rescued by exogenous expression of WRN or ERCC6. Direct analysis of the recombinant variant proteins confirmed defective enzymatic activities.

CONCLUSIONS

These results provide evidence that defects in suppression of DSBs underlie some cases of UFCRC; these can be identified by assays of circulating lymphocytes. We specifically associated UFCRC with variants in WRN and ERCC6 that reduce the capacity for repair of DNA DSBs. These observations could lead to a simple screening strategy for UFCRC, and provide insight into the pathogenic mechanisms of colorectal carcinogenesis.

The CSB chromatin remodeler and CTCF architectural protein cooperate in response to oxidative stress

Cockayne syndrome is a premature aging disease associated with numerous developmental and neurological abnormalities, and elevated levels of reactive oxygen species have been found in cells derived from Cockayne syndrome patients. The majority of Cockayne syndrome cases contain mutations in the ATP-dependent chromatin remodeler CSB; however, how CSB protects cells from oxidative stress remains largely unclear. Here, we demonstrate that oxidative stress alters the genomic occupancy of the CSB protein and increases CSB occupancy at promoters. Additionally, we found that the long-range chromatin-structure regulator CTCF plays a pivotal role in regulating sites of genomic CSB occupancy upon oxidative stress. We show that CSB directly interacts with CTCF in vitro and that oxidative stress enhances the CSB-CTCF interaction in cells. Reciprocally, we demonstrate that CSB facilitates CTCF-DNA interactions in vitro and regulates CTCF-chromatin interactions in oxidatively stressed cells. Together, our results indicate that CSB and CTCF can regulate each other's chromatin association, thereby modulating chromatin structure and coordinating gene expression in response to oxidative stress.

Abstract 4739: Genetic predisposition to DNA double strand break repair defect defines a new class of familial colon cancer

Colorectal cancer (CRC) is the second most common fatal cancer in the U.S., with ∼ 30% cases familial (FCRC). Genetic predispositions have only been defined for 25% of FCRC (including Lynch syndrome, Familial Adenomatous Polyposis (FAP), and MutYH polyposis). For the genetically undefined group (uFCRC), understanding of disease pathogenesis is limited, and the absence of defined defects in relevant pathways that could support molecular diagnosis results in under- and over-screening. We hypothesized that uFCRC would arise distinctly from moderately penetrant germline defects in repair of DNA double-strand breaks (DSBs). Such defects in DSB repair would lead to a moderate level of constitutional genomic instability (CGI) that could be assayed from patient peripheral blood lymphocytes (PBLs). We further hypothesized that such DNA lesions would often be heterozygous, associated with haploinsufficiency or dominant-negative effects, and would impair protein interactions important for DNA repair.

We combined exome sequencing with biological assays to screen a rich resource of uFCRC clinical samples from the Fox Chase Cancer Center Risk Assessment Program. Exome sequencing of PBLs from patients (N = 25) identified a mean of 1.4 rare variants/patient that were 1) strongly predicted to damage protein function using multiple functional predictors (SIFT, Polyphen-2, Provean, and MutationAssessor), 2) involved in pathways that suppress DSBs, and 3) have not been previously implicated in CRC. Further, many of the variant genes were commonly mutated in CRCs and other cancers in TCGA database. Comparison of PBLs from patients and age- and sex- matched controls revealed increased DSB levels (basal and with DNA damaging agents) in 18/25 patients vs. 1/25 normal controls (P = 0.001, AUC = 0.85). Next, knockdown of variant genes in HCT116 CRC cells increased DSB formation with or without damaging agents.

As a proof-of-concept, we studied one patient in detail who had candidate disease-causing variants in 2 DNA repair genes, ERCC6 and WRN. Both variants were dysfunctional in biochemical tests. We established patient-derived EBV-lines and observed, at baseline and with several DNA damaging agents, elevated levels of γH2AX foci and larger nuclear comets, indicative of DSBs. This phenotype could be rescued by expression of wild type WRN or ERCC6 and conversely induced by knockdown in CRC cells. Further, the patient derived lines exhibited reduced expression of WRN and ERCC6, implicating haploinsufficiency of these genes in the phenotype observed.

Our data support the hypothesis that defects in DSB repair genes cause moderate-level CGI that commonly presents as uFCRC. Our studies identify novel genetic subsets of FCRC, and could potentially predict familial risk and improve screening and diagnosis.

Citation Format: sanjeevani arora, Hong Yan, Iltaeg Cho, Hua-Ying Fan, Biao Luo, xiaowu gai, dale bodian, joe vockley, yan zhou, elizabeth handorf, mark andrake, emmanuelle nicolas, Ilya Serebriiskii, tim yen, michael hall, greg enders, erica golemis. Genetic predisposition to DNA double strand break repair defect defines a new class of familial colon cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4739. doi:10.1158/1538-7445.AM2015-4739

Rhein prevents endotoxin-induced acute kidney injury by inhibiting NF-κB activities

This study aimed to explore the effect and mechanisms of rhein on sepsis-induced acute kidney injury by injecting lipopolysaccharide (LPS) and cecal ligation and puncture (CLP) in vivo, and on LPS-induced HK-2 cells in vitro. For histopathological analysis, rhein effectively attenuated the severity of renal injury. Rhein could significantly decrease concentration of BUN and SCr and level of TNF-α and IL-1β in two different mouse models of experimental sepsis. Moreover, rhein could markedly attenuate circulating leukocyte infiltration and enhance phagocytic activity of macrophages partly impaired at 12 h after CLP. Rhein could enhance cell viability and suppresse the release of MCP-1 and IL-8 in LPS-stimulated HK-2 cells Furthermore, rhein down regulated the expression of phosphorylated NF-κB p65, IκBα and IKKβ stimulated by LPS both in vivo and in vitro. All these results suggest that rhein has protective effects on endotoxin-induced kidney injury. The underlying mechanism of rhein on anti-endotoxin kidney injury may be closely related with its anti-inflammatory and immunomodulatory properties by decreasing NF-κB activation through restraining the expression and phosphorylation of the relevant proteins in NF-κB signal pathway, hindering transcription of NF-κB p65.These evidence suggest that rhein has a potential application to treat endotoxemia-associated acute kidney injury.

Single nucleotide polymorphisms in the mitochondrial displacement loop and age-at-onset of non-small cell lung cancer

The associations between single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) of mitochondrial DNA (mtDNA) and cancer risk and disease outcome have been extensively analyzed. We investigated the association between age-at-onset and SNPs in the mitochondrial D-loop using a population-based series of non-small cell lung cancer (NSCLC) patients. The D-loop region of mtDNA from NSCLC patients was amplified and sequenced. The age-at-onset curve of NSCLC patients was calculated using the Kaplan-Meier method at each SNP site and values were compared using the log-rank test. The SNP sites of nucleotides 200G/A and 16362T/C were identified to determine their association with age-at-onset of NSCLC using the log-rank test. The nucleotide 207G/A was identified for its association with age-at-onset at a borderline significance level (P = 0.060). We found that genetic polymorphisms in the D-loop were predictive markers for age-at-onset in NSCLC patients. Accordingly, the analysis of genetic polymorphisms in the mitochondrial D-loop can be used to identify NSCLC patient subgroups at high risk of early onset.

Therapeutic effect of a hydroxynaphthoquinone fraction on dextran sulfate sodium-induced ulcerative colitis

AIM: To evaluate the therapeutic effect of hydroxynaphthoquinone mixture (HM) on dextran sulfate sodium (DSS)-induced colitis and explore the underlying mechanisms.

METHODS: BALB/c mice received 3.5% DSS for 6 d to induce ulcerative colitis. Groups of mice were orally administered HM 3.5, 7 and 14 mg/kg and mesalazine 200 mg/kg per day for 7 d. During the experiment, clinical signs and body weight, stool consistency and visible fecal blood were monitored and recorded daily. A disease activity index score was calculated for each animal. At the conclusion of the experiment, the colonic histopathological lesions were evaluated. Myeloperoxidase (MPO) activity and tumor necrosis factor-α (TNF-α) levels were determined. Protein expression levels of TNF-α, nuclear factor-κB (NF-κB) p65, inhibitor of κB (IκB) and phosphorylation of IκB (p-IκB) were analyzed by Western blot analysis.

RESULTS: Administration of 3.5% DSS for 6 d successfully induced acute colitis associated with soft stool, diarrhea, rectal bleeding, and colon shortening, as well as a loss of body weight. Administration of HM effectively attenuated the severity of colonic mucosa injury. For histopathological analysis, HM treatment improved histological alterations and lowered pathological scores compared with the DSS only group. This manifested as a reduction in the extent of colon injury and inflammatory cell infiltration, as well as the degree of mucosal destruction. In addition, HM at doses of 7 and 14 mg/kg significantly decreased MPO activity in colonic tissue (0.98 ± 0.22 U/g vs 1.32 ± 0.24 U/g, 0.89 ± 0.37 U/g vs 1.32 ± 0.24 U/g tissue, P < 0.05) and serum TNF-α levels (68.78 ± 7.34 ng/L vs 88.98 ± 17.79 ng/L, 64.13 ± 14.13 ng/L vs 88.98 ± 17.79 ng/L, P < 0.05). Furthermore, HM down-regulated the expression of TNF-α, NF-κB p65 and p-IκBα in colonic tissue while up-regulating IκBα protein expression. These results suggest that the significant anti-inflammatory effect of HM may be attributable to its inhibition of TNF-α production and NF-κB activation.

CONCLUSION: HM had a favorable therapeutic effect on DSS-induced ulcerative colitis, supporting its further development and clinical application in inflammatory bowel disease.

Effects of danshensu on platelet aggregation and thrombosis: in vivo arteriovenous shunt and venous thrombosis models in rats

Danshensu, a type of dihydroxyphenyl lactic acid, is one of the most abundant active phenolic acids in the dried root of Salvia miltiorrhizae (Lamiaceae)--widely used traditional Chinese medicine. The effects of danshensu on platelet aggregation and thrombus formation in rats were examined using various methods. It was found that danshensu significantly reduced thrombus weight in 2 experimental thrombosis models; dose-dependent inhibition of adenosine diphosphate (ADP) and arachidonic acid (AA)-induced platelet aggregation occurred in normal and blood stasis-induced rats; Danshensu also significantly mitigated blood viscosity, plasma viscosity and hematocrit levels. Moreover, danshensu significantly inhibited venous thrombosis-induced expression of cyclooxygenases-2 (COX-2) rather than cyclooxygenases-1(COX-1) in the venous walls, down regulated thromboxane B2 (TXB2) and up regulated 6-keto prostaglandin F1α (6-keto-PGF1α), normalizing the TXB2/6-keto-PGF1α ratio. In addition, danshensu did not induce gastric lesions and even had protective effects on aspirin-induced ulcer formation at doses as high as 60 mg/kg. These findings suggest that the antithrombotic and antiplatelet aggregation effects of danshensu are attributed to its highly selective inhibition of COX-2 and ability to normalize the thromboxane A2(TXA2)/prostacyclin(PGI2) balance. These findings suggest that danshensu have great prospects in antithrombotic and antiplatelet therapy.

The sequence-specific transcription factor c-Jun targets Cockayne syndrome protein B to regulate transcription and chromatin structure

Cockayne syndrome is an inherited premature aging disease associated with numerous developmental and neurological defects, and mutations in the gene encoding the CSB protein account for the majority of Cockayne syndrome cases. Accumulating evidence suggests that CSB functions in transcription regulation, in addition to its roles in DNA repair, and those defects in this transcriptional activity might contribute to the clinical features of Cockayne syndrome. Transcription profiling studies have so far uncovered CSB-dependent effects on gene expression; however, the direct targets of CSB's transcriptional activity remain largely unknown. In this paper, we report the first comprehensive analysis of CSB genomic occupancy during replicative cell growth. We found that CSB occupancy sites display a high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, we found that CSB occupancy is enriched at sites containing the TPA-response element. Consistent with this binding site preference, we show that CSB and the transcription factor c-Jun can be found in the same protein-DNA complex, suggesting that c-Jun can target CSB to specific genomic regions. In support of this notion, we observed decreased CSB occupancy of TPA-response elements when c-Jun levels were diminished. By modulating CSB abundance, we found that CSB can influence the expression of nearby genes and impact nucleosome positioning in the vicinity of its binding site. These results indicate that CSB can be targeted to specific genomic loci by sequence-specific transcription factors to regulate transcription and local chromatin structure. Additionally, comparison of CSB occupancy sites with the MSigDB Pathways database suggests that CSB might function in peroxisome proliferation, EGF receptor transactivation, G protein signaling and NF-κB activation, shedding new light on the possible causes and mechanisms of Cockayne syndrome.

Cockayne syndrome is a devastating inherited disease, in which patients appear to age prematurely, have sun sensitivity and suffer from profound neurological and developmental defects. Mutations in the CSB gene account for the majority of Cockayne syndrome cases. CSB is an ATP-dependent chromatin remodeler, and these proteins can use energy from ATP-hydrolysis to alter contacts between DNA and histones of a nucleosome, the basic units of chromatin structure. CSB functions in DNA repair, but accumulating evidence reveals that CSB also functions in transcription regulation. Here, we determined the genomic localization of CSB to identify its gene targets and found that CSB occupancy displays high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, CSB is enriched at genomic regions containing the binding site for the c-Jun transcription factor, and we found that these two proteins interact, uncovering a new targeting mechanism for CSB. We also demonstrate that CSB can influence gene expression in the vicinity of its binding sites and alter local chromatin structure. Together, this study supports the hypothesis that defects in the regulation of gene expression and chromatin structure by CSB might contribute to the diverse clinical features of Cockayne syndrome.

RBPJ, the major transcriptional effector of Notch signaling, remains associated with chromatin throughout mitosis, suggesting a role in mitotic bookmarking

Mechanisms that maintain transcriptional memory through cell division are important to maintain cell identity, and sequence-specific transcription factors that remain associated with mitotic chromatin are emerging as key players in transcriptional memory propagation. Here, we show that the major transcriptional effector of Notch signaling, RBPJ, is retained on mitotic chromatin, and that this mitotic chromatin association is mediated through the direct association of RBPJ with DNA. We further demonstrate that RBPJ binds directly to nucleosomal DNA in vitro, with a preference for sites close to the entry/exit position of the nucleosomal DNA. Genome-wide analysis in the murine embryonal-carcinoma cell line F9 revealed that roughly 60% of the sites occupied by RBPJ in asynchronous cells were also occupied in mitotic cells. Among them, we found that a fraction of RBPJ occupancy sites shifted between interphase and mitosis, suggesting that RBPJ can be retained on mitotic chromatin by sliding on DNA rather than disengaging from chromatin during mitotic chromatin condensation. We propose that RBPJ can function as a mitotic bookmark, marking genes for efficient transcriptional activation or repression upon mitotic exit. Strikingly, we found that sites of RBPJ occupancy were enriched for CTCF-binding motifs in addition to RBPJ-binding motifs, and that RBPJ and CTCF interact. Given that CTCF regulates transcription and bridges long-range chromatin interactions, our results raise the intriguing hypothesis that by collaborating with CTCF, RBPJ may participate in establishing chromatin domains and/or long-range chromatin interactions that could be propagated through cell division to maintain gene expression programs.

How does a cell remember what it should be after cell division? One mechanism that is beginning to emerge is the retention of a few key regulatory proteins on the highly condensed mitotic chromatin during cell division. These proteins are called mitotic bookmarks, as they are believed to offer critical information as to how genetic information should be read immediately after mitosis. We have found that a protein called RBPJ, which plays pivotal roles in regulating cell-fate choices, is retained on mitotic chromatin. RBPJ transmits to DNA signals elicited by the Notch pathway: a pathway that conveys information resulting from the communication between two adjacent cells. Unlike many other factors, we found that RBPJ can bind to nucleosomes, which are the basic unit of packaged DNA consisting of DNA wrapped around eight histone proteins. We also found that RBPJ interacts with and binds to DNA sites regulated by the CTCF protein, which plays important roles in regulating long-range DNA interactions. Together, our results suggest that RBPJ can function as a mitotic bookmarking factor, to help maintain genetic programs, higher-order structural information and consequently the memory of cell identity through cell division.

Effectiveness of a hydroxynaphthoquinone fraction from Arnebia euchroma in rats with experimental colitis

AIM: To evaluate the potential effectiveness of hydroxynaphthoquinone mixture (HM) in rats with 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis.

METHODS: Colitis was induced by intracolonic administration of TNBS (80 mg/kg, dissolved in 50% ethanol). Rats were treated daily for 7 d with HM (2.5, 5, 10 mg/kg) and mesalazine 100 mg/kg 24 h after TNBS instillation. Disease progression was monitored daily by observation of clinical signs and body weight change. At the end of the experiment, macroscopic and histopathologic lesions of rats were scored, and myeloperoxidase (MPO) activity was determined. We also determined inflammatory cytokine tumor necrosis factor (TNF)-α level by ELISA, Western blotting and immunochemistry to explore the potential mechanisms of HM.

RESULTS: After intracolonic instillation of TNBS, animals developed colitis associated with soft stool, diarrhea and marked colonic destruction. Administration of HM significantly attenuated clinical and histopathologic severity of TNBS-induced colitis in a dose-dependent manner. It abrogated body weight loss, diarrhea and inflammation, decreased macroscopic damage score, and improved histological signs, with a significant reduction of inflammatory infiltration, ulcer size and the severity of goblet cell depletion (all P < 0.05 vs TNBS alone group). HM could reduce MPO activity. In addition, it also decreased serum TNF-α level and down-regulated TNF-α expression in colonic tissue. This reduction was statistically significant when the dose of HM was 10 mg/kg (P < 0.05 vs TNBS alone group), and the effect was comparable to that of mesalazine and showed no apparent adverse effect. The underlying mechanism may be associated with TNF-α inhibition.

CONCLUSION: These findings suggest that HM possesses favourable therapeutic action in TNBS-induced colitis, which provides direct pharmacological evidence for its clinical application.

Trichosanthes kirilowii: A New Host of Cucurbit mild mosaic virus in China

Chinese cucumber (Trichosanthes kirilowii Maxim.) is a type of perennial liana plant of the Cucurbitaceae family that is mainly distributed in East Asia and northern Australia. It is an important medicinal plant and commonly used in Chinese herbalism, where it is considered to be one of the 50 fundamental herbs (2). During the summer and autumn of 2012, T. kirilowii plants showing symptoms of mild mosaic on the upper leaves and bright yellow color on the lower leaves were observed in the Haidian district of Beijing, China. Recently similar symptoms induced by Cucurbit mild mosaic virus (CuMMV) on squash have been reported. CuMMV is a new member of the genus Fabavirus in the Comovirinae subfamily, discovered in China in 2006 (1). Total RNA was extracted from five leaf samples of independent plants and used for reverse transcription with an oligo (dT)₁₈ primer, followed by PCR with a pair of CuMMV virus-specific primers FaR₁3012F (5'-CGAGTGCGAGTTAGAAATTGGGATG-3') and FaR₁5783R (5'-TCACTTTGAGGTGATAAAACAATCC-3') to amplify a 2,772-bp fragment including RNA-dependent RNA polymerase (RdRp) coding region. The expected target fragment was obtained in all symptomatic plant samples but not from an asymptomatic plant. Nucleotide sequence comparison analysis showed that the virus isolated from T. kirilowii (GenBank Accession No. KC959843) had 95.33% nucleotide identity and 99.15% amino acid identity in the RdRp sequence with a CuMMV isolate from squash (GenBank Accession No. FJ194941) (1). In addition, symptomatic samples tested positive for CuMMV by Western blot using CuMMV small coat protein (SCP) specific polyclonal antibody (1). To our knowledge, this is the first report of T. kirilowii as natural host of CuMMV in China. The impact of CuMMV on T. kirilowii production remains to be determined; however, the extended host range for this virus suggests a potential threat of CuMMV to cucurbit crops in China. References: (1) S. W. Dong et al. Arch. Virol.157:597, 2012. (2) J. H. Hong et al. China Pharmacist 7:561, 2004.

Cell wall degradation and the dynamic changes of Ca2+ and related enzymes in the developing aerenchyma of wheat (Triticum aestivum L.) under waterlogging

This research was aimed to study the cell wall degradation and the dynamic changes of Ca2+ and related enzymes in developing aerenchyma of wheat root under waterlogging. An examination of morphological development by light and electron microscope revealed that the structure of cell wall in middle cortical cells remained intact after 12 h of waterlogging and turned thinner after waterlogging for 24 h. At 48 h, the aerenchyma has been formed. The cellulase activity gradually increased in middle cortical cells within 24 h of waterlogging, and decreased with the formation of aerenchyma. Fluorescence detection and subcellular localization of Ca2+ showed the dynamic changing of Ca2+ at the cellular and subcellular levels during the development of aerenchyma. The activity of Ca2+-ATPase enhanced markedly in intercellular space, plasma membrane and tonoplast of some middle cortical cells after 8 h of waterlogging and remained high after 24 h, but it decreased after 48 h of waterlogging. All these suggests that cellulase, Ca2+ and Ca2+-ATPase show a dynamic distribution during the aerenchyma development which associated with the cell wall degradation of middle cortical cells. Moreover, there is a feedback regulation between Ca2+ and Ca2+-ATPase.

ATP-dependent chromatin remodeling by Cockayne syndrome protein B and NAP1-like histone chaperones is required for efficient transcription-coupled DNA repair

The Cockayne syndrome complementation group B (CSB) protein is essential for transcription-coupled DNA repair, and mutations in CSB are associated with Cockayne syndrome—a devastating disease with complex clinical features, including the appearance of premature aging, sun sensitivity, and numerous neurological and developmental defects. CSB belongs to the SWI2/SNF2 ATP–dependent chromatin remodeler family, but the extent to which CSB remodels chromatin and whether this activity is utilized in DNA repair is unknown. Here, we show that CSB repositions nucleosomes in an ATP–dependent manner in vitro and that this activity is greatly enhanced by the NAP1-like histone chaperones, which we identify as new CSB–binding partners. By mapping functional domains and analyzing CSB derivatives, we demonstrate that chromatin remodeling by the combined activities of CSB and the NAP1-like chaperones is required for efficient transcription-coupled DNA repair. Moreover, we show that chromatin remodeling and repair protein recruitment mediated by CSB are separable activities. The collaboration that we observed between CSB and the NAP1-like histone chaperones adds a new dimension to our understanding of the ways in which ATP–dependent chromatin remodelers and histone chaperones can regulate chromatin structure. Taken together, the results of this study offer new insights into the functions of chromatin remodeling by CSB in transcription-coupled DNA repair as well as the underlying mechanisms of Cockayne syndrome.

Cockayne syndrome is a devastating inherited disease; the average life span of those afflicted is 12 years. Cockayne syndrome patients have features of premature aging, are highly sensitive to sunlight, and suffer from numerous developmental and neurological disorders. The majority of Cockayne syndrome patients have mutations in the CSB protein; however, how these mutations can lead to Cockayne syndrome is largely unknown. CSB is essential for transcription-coupled DNA repair—a process that preferentially removes bulky DNA lesions that stall transcription, such as those created by ultraviolet light. In eukaryotes, DNA is packaged into nucleosomes, which consists of DNA wrapped around a set of core histone proteins, and nucleosomes can create barriers to the DNA repair process. In this study, we found that CSB can slide histones along DNA. We also found that histone chaperones, proteins that accept and donate histones, greatly facilitate this process. Importantly, we show that CSB derivatives that are unable to move nucleosomes or collaborate with histone chaperones cannot repair UV-induced DNA lesions. Our study reveals that nucleosome remodeling by CSB is important for transcription-coupled DNA repair and suggests that an inability to efficiently mobilize nucleosomes might contribute to the underlying mechanism of Cockayne syndrome.

Structure, function and regulation of CSB: a multi-talented gymnast

The Cockayne syndrome complementation group B protein, CSB, plays pivotal roles in transcription regulation and DNA repair. CSB belongs to the SNF2/SWI2 ATP-dependent chromatin remodeling protein family, and studies from many laboratories have revealed that CSB has multiple activities and modes of regulation. To understand the underlying mechanisms of Cockayne syndrome, it is necessary to understand how the biochemical activities of CSB are used to carry out its biological functions. In this review, we summarize our current knowledge of the structure, function and regulation of CSB, and discuss how these properties can impact the biological functions of this chromatin remodeler.

First Report of Leaf Spot Disease Caused by Exserohilum rostratum on Pineapple in Hainan Province, China

Pineapple (Ananas comosus (L.) Merr.) is an important perennial monocotyledonous plant that serves as an important fruit crop globally and is also produced in the Hainan Province of China where production in 2009 was 296,600 t. In July 2009, atypical symptoms of a leaf spot disease were observed on mature pineapple leaves in Chengmai County; approximately 15% of plants propagated from suckers became symptomatic after 150 to 300 days, eventually causing a 3 to 10% yield loss. In the initial infection stage, grayish white-to-yellowish white spots emerged on the leaf surfaces that ranged from 1.0 to 2.4 × 0.3 to 0.7 cm; black specks were not always present in the spots. Leaf spots also had distinctive light brown-to-reddish brown banding pattern on the edges. Several spots would often merge to form large lesions, 6.5 to 15.4 × 2.5 to 5.6 cm, covering more than 67% of the leaf surface, which can lead to death of the plant. Infected pineapple leaves collected from an orchard of Chengmai County were surface sterilized (75% ethanol for 30 s, 0.1% HgCl₂ for 2 min, and rinsed three times in sterile distilled water). Leaf pieces were placed on potato dextrose agar medium and then incubated at 25°C. The emerging fungal colonies were grayish white to brown. Similar strains were obtained from Qionghai City and Wanning City subsequently. Two isolates, ITF0706-1 and ITF0706-2, were used in confirmation of the identity of the pathogen and in pathogenicity tests. Colonies were fast growing (more than 15 mm per day at 25 to 30°C) with dense aerial mycelia. Conidia were fusiform, pyriform to oval or cylindrical, olive brown to dark brown, 3 to 10 septate (typically 5 to 8), 33.2 to 102.5 × 9.0 to 21.3 μm, with a strongly protruding hilum bulged from the basal cell, which were similar to the Type A conidia described by Lin et al. (3). The strains were subjected to PCR amplification of the internal transcribed spacer (ITS)1-5.8S-ITS2 regions with universal primer pair ITS1/ITS4. The ITS sequence comparisons (GenBank Accession Nos. JN711431 and JN711432) shared between 99.60 and 99.83% identity with the isolate CATAS-ER01 (GenBank Accession No. GQ169762). According to morphological and molecular analysis, the two strains were identified as Exserohilum rostratum (Drechs.) Leonard & Suggs. Pathogenicity experiments were conducted five times and carried out by spraying a conidial suspension (10⁵ CFU/ml) on newly matured leaves of healthy pineapple plants; plants sprayed with sterile water served as the negative control. Plants were incubated in the growth chamber at 20 to 25°C. Symptoms of leaf spot developed on test plants 7 days after inoculation while the control plants remained asymptomatic. Koch's postulates were fulfilled with the reisolation of the two fungal strains. Currently, E. rostratum is one of the most common pathogens on Bromeliads in Florida (2) and has been reported on Zea mays (4), Musa paradisiacal (3), and Calathea picturata (1) in China, but to our knowledge, this is the first report of leaf spot disease caused by E. rostratum on pineapple in Hainan Province of P.R. China. References: (1) L. L. Chern et al. Plant Dis. 95:1033, 2011. (2) R. M. Leahy. Plant Pathol. Circ. No. 393. Florida Department of Agriculture and Consumer Services Division of Plant Industry, 1999. (3) S. H. Lin et al. Australas. Plant Pathol. 40:246, 2011. (4) J. N. Tsai et al. Plant Pathol. Bull. 10:181, 2001.

Reciprocally regulated chromatin association of Cockayne syndrome protein B and p53 protein

The Cockayne syndrome complementation group B (CSB) protein is an ATP-dependent chromatin remodeler with an essential function in transcription-coupled DNA repair, and mutations in the CSB gene are associated with Cockayne syndrome. The p53 tumor suppressor has been known to interact with CSB, and both proteins have been implicated in overlapping biological processes, such as DNA repair and aging. The significance of the interaction between CSB and p53 has remained unclear, however. Here, we show that the chromatin association of CSB and p53 is inversely related. Using in vitro binding and chromatin immunoprecipitation approaches, we demonstrate that CSB facilitates the sequence-independent association of p53 with chromatin when p53 concentrations are low and that this is achieved by the interaction of CSB with the C-terminal region of p53. Remarkably, p53 prevents CSB from binding to nucleosomes when p53 concentrations are elevated. Examining the enzymatic properties of CSB revealed that p53 excludes CSB from nucleosomes by occluding a nucleosome interaction surface on CSB. Together, our results suggest that the reciprocal regulation of chromatin access by CSB and p53 could be part of a mechanism by which these two proteins coordinate their activities to regulate DNA repair, cell survival, and aging.

Molecular structure and dimeric organization of the Notch extracellular domain as revealed by electron microscopy

Background

The Notch receptor links cell fate decisions of one cell to that of the immediate cellular neighbor. In humans, malfunction of Notch signaling results in diseases and congenital disorders. Structural information is essential for gaining insight into the mechanism of the receptor as well as for potentially interfering with its function for therapeutic purposes.

Methodology/Principal Findings

We used the Affinity Grid approach to prepare specimens of the Notch extracellular domain (NECD) of the Drosophila Notch and human Notch1 receptors suitable for analysis by electron microscopy and three-dimensional (3D) image reconstruction. The resulting 3D density maps reveal that the NECD structure is conserved across species. We show that the NECD forms a dimer and adopts different yet defined conformations, and we identify the membrane-proximal region of the receptor and its ligand-binding site.

Conclusions/Significance

Our results provide direct and unambiguous evidence that the NECD forms a dimer. Our studies further show that the NECD adopts at least three distinct conformations that are likely related to different functional states of the receptor. These findings open the way to now correlate mutations in the NECD with its oligomeric state and conformation.

Antiplatelet and antithrombotic activities of salvianolic acid A

INTRODUCTION

Salvianolic acid A (SAA), the water-soluble phenolic acids in Salvia miltiorrhiza, has shown the most potent bioactivities, including protection against cerebral lesion, defense from oxidative damage and improvement of remembrance. In the present study, we studied the antiplatelet and antithrombotic effects of a newly synthesized SAA with different methods both in vitro and in vivo.

MATERIALS AND METHODS

We tested the effect of antithrombotic activity of SAA in arterio-venous shunt model. The effects of SAA on adenosine diphosphate (ADP)-, Thrombin-, Arachidonic acid- induced rat platelets aggregation were tested both in vivo and in vitro. The activity of SAA on washed human platelet aggregation was determined by ADP stimulation. We also evaluated its property of modulation of hemorheology, assessed its bleeding side effect by measuring coagulation parameters after intravenous administration for 5 days and investigated the potential mechanisms underlying such activities.

RESULTS AND CONCLUSIONS

In vivo, SAA significantly reduced thrombus weight in the model of arterio-venous shunt. Meanwhile, SAA increased plasma cAMP level determined by radioimmunoassay in the same model. Intravenously administrated SAA (2.5-10 mg/kg) inhibited platelet aggregation induced by ADP in a dose-dependent manner. Notably, SAA did not affect coagulation parameters in rats after intravenous administration SAA for successive 5 days. In vitro, pretreatment with SAA on washed rat and human platelets significantly inhibited various agonists stimulated platelet aggregation and caused an increase in cAMP level in platelets activated by ADP. These findings support our hypothesis that SAA possesses antithrombotic activities. The antithrombotic effect might be related to its antiplatelet action and ability to modulate hemorheology without affecting coagulation system. The mechanisms underlying such activities may involve the induction of cAMP.

UV-induced association of the CSB remodeling protein with chromatin requires ATP-dependent relief of N-terminal autorepression

The ATP-dependent chromatin remodeler CSB is essential for transcription-coupled DNA repair, and mutations in CSB lead to Cockayne syndrome. Here, we examined the recruitment of CSB to chromatin after ultraviolet (UV) irradiation and uncovered a regulatory mechanism that ensures the specific association of this remodeler with chromatin. We demonstrate that ATP hydrolysis by CSB is essential for stable CSB-chromatin association after UV irradiation and that defects in this association underlie some forms of Cockayne syndrome. We also show that the N-terminal region of CSB negatively regulates chromatin association during normal cell growth. Of interest, in the absence of the negative regulatory region, ATP hydrolysis becomes dispensable for chromatin association, indicating that CSB uses energy from ATP hydrolysis to overcome the inhibitory effect imposed by its N-terminal region. Together, our results suggest that the recruitment of CSB to lesion-stalled transcription is an ATP-dependent process and involves a gross conformational change of CSB.

Interaction of HP1 and Brg1/Brm with the globular domain of histone H3 is required for HP1-mediated repression

The heterochromatin-enriched HP1 proteins play a critical role in regulation of transcription. These proteins contain two related domains known as the chromo- and the chromoshadow-domain. The chromo-domain binds histone H3 tails methylated on lysine 9. However, in vivo and in vitro experiments have shown that the affinity of HP1 proteins to native methylated chromatin is relatively poor and that the opening of chromatin occurring during DNA replication facilitates their binding to nucleosomes. These observations prompted us to investigate whether HP1 proteins have additional histone binding activities, envisioning also affinity for regions potentially occluded by the nucleosome structure. We find that the chromoshadow-domain interacts with histone H3 in a region located partially inside the nucleosomal barrel at the entry/exit point of the nucleosome. Interestingly, this region is also contacted by the catalytic subunits of the human SWI/SNF complex. In vitro, efficient SWI/SNF remodeling requires this contact and is inhibited in the presence of HP1 proteins. The antagonism between SWI/SNF and HP1 proteins is also observed in vivo on a series of interferon-regulated genes. Finally, we show that SWI/SNF activity favors loading of HP1 proteins to chromatin both in vivo and in vitro. Altogether, our data suggest that HP1 chromoshadow-domains can benefit from the opening of nucleosomal structures to bind chromatin and that HP1 proteins use this property to detect and arrest unwanted chromatin remodeling.

HP1 proteins are transcriptional regulators frequently associated with gene silencing, a phenomenon involving masking of promoter DNA by dense chromatin. Owing to their chromo-domain, these proteins can read and bind an epigenetic mark that on many non-expressed genes is present on histone H3 at the surface of the nucleosome (the fundamental packing unit of chromatin). However, the binding to this mark does not explain the repressing activity of HP1 proteins. Here, we show that these proteins can establish a second contact with histone H3, independently of the epigenetic mark. This second contact site is located inside the nucleosome, in a position likely to be inaccessible. Interestingly, this site is also contacted by a subunit of the SWI/SNF complex and this contact is required for the ATP-dependent chromatin remodeling catalyzed by SWI/SNF. We provide evidence suggesting that HP1 proteins use the SWI/SNF chromatin remodeling to gain access to the contact site inside the nucleosome and to prevent further remodeling by competing with SWI/SNF for binding at this position. These observations lead us to suggest that HP1 proteins function as gatekeepers on promoters, detecting and stopping unwanted exposure of internal nucleosomal sites.

Diverse regulation of SNF2h chromatin remodeling by noncatalytic subunits

SNF2h-based ATP-dependent chromatin remodeling complexes diverge in composition, nuclear localization, and biological function. Such differences have led to the hypothesis that SNF2h complexes differ mechanistically. One proposal is that the complexes have different functional interactions with the naked DNA adjacent to the nucleosome. We have used a series of templates with defined nucleosomal position and differing amounts and placement of adjacent DNA to compare the relative activities of SNF2h and SNF2h complexes. The complexes hACF, CHRAC, WICH, and RSF all displayed differences in functional interactions with these templates, which we attribute to the differences in the noncatalytic subunit. We suggest that the ability to sense adjacent DNA is a general property of the binding partners of SNF2h and that each partner provides distinct regulation that contributes to distinct cellular function.