Bipartite structure of the inactive mouse X chromosome

Background

In mammals, one of the female X chromosomes and all imprinted genes are expressed exclusively from a single allele in somatic cells. To evaluate structural changes associated with allelic silencing, we have applied a recently developed Hi-C assay that uses DNase I for chromatin fragmentation to mouse F1 hybrid systems.

Results

We find radically different conformations for the two female mouse X chromosomes. The inactive X has two superdomains of frequent intrachromosomal contacts separated by a boundary region. Comparison with the recently reported two-superdomain structure of the human inactive X shows that the genomic content of the superdomains differs between species, but part of the boundary region is conserved and located near the Dxz4/DXZ4 locus. In mouse, the boundary region also contains a minisatellite, Ds-TR, and both Dxz4 and Ds-TR appear to be anchored to the nucleolus. Genes that escape X inactivation do not cluster but are located near the periphery of the 3D structure, as are regions enriched in CTCF or RNA polymerase. Fewer short-range intrachromosomal contacts are detected for the inactive alleles of genes subject to X inactivation compared with the active alleles and with genes that escape X inactivation. This pattern is also evident for imprinted genes, in which more chromatin contacts are detected for the expressed allele.

Conclusions

By applying a novel Hi-C method to map allelic chromatin contacts, we discover a specific bipartite organization of the mouse inactive X chromosome that probably plays an important role in maintenance of gene silencing.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0728-8) contains supplementary material, which is available to authorized users.

Role of p14ARF-HDM2-p53 axis in SOX6-mediated tumor suppression

Sex-determining region Y box 6 (SOX6) has been described as a tumor-suppressor gene in several cancers. Our previous work has suggested that SOX6 upregulated p21^Waf1/Cip1(p21) expression in a p53-dependent manner; however, the underlying mechanism has remained elusive. In this study, we confirmed that SOX6 can suppress cell proliferation in vitro and in vivo by stabilizing p53 protein and subsequently upregulating p21. Co-immunoprecipitation and immunocytofluorescence assays demonstrated that SOX6 can promote formation of the p14ARF-HDM2-p53 ternary complex by promoting translocation of p14ARF (p14 alternate reading frame tumor suppressor) to the nucleoplasm, thereby inhibiting HDM2-mediated p53 nuclear export and degradation. Chromatin immunoprecipitation combined with PCR assay proved that SOX6 can bind to a potential binding site in the regulatory region of the c-Myc gene. Furthermore, we confirmed that SOX6 can downregulate the expression of c-Myc, as well as its direct target gene nucleophosmin 1 (NPM1), and that the SOX6-induced downregulation of NPM1 is linked to translocation of p14ARF to the nucleoplasm. Finally, we showed that the highly conserved high-mobility group (HMG) domain of SOX6 is required for SOX6-mediated p53 stabilization and tumor inhibitory activity. Collectively, these results reveal a new mechanism of SOX6-mediated tumor suppression involving p21 upregulation via the p14ARF-HDM2-p53 axis in an HMG domain-dependent manner.

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

High-throughput methods based on chromosome conformation capture have greatly advanced our understanding of the three-dimensional (3D) organization of genomes but are limited in resolution by their reliance on restriction enzymes. Here we describe a method called DNase Hi-C for comprehensively mapping global chromatin contacts. DNase Hi-C uses DNase I for chromatin fragmentation, leading to greatly improved efficiency and resolution over that of Hi-C. Coupling this method with DNA-capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture. We applied targeted DNase Hi-C to characterize the 3D organization of 998 large intergenic noncoding RNA (lincRNA) promoters in two human cell lines. Our results revealed that expression of lincRNAs is tightly controlled by complex mechanisms involving both super-enhancers and the Polycomb repressive complex. Our results provide the first glimpse of the cell type-specific 3D organization of lincRNA genes.

HIV co-infection accelerates decay of humoral responses in spontaneous resolvers of HCV infection

Acute hepatitis C virus (HCV) infection is primarily followed by chronic infection, while spontaneous recovery of HCV infection (SR-HCV) occurs in a minority of those infected. Identification of SR-HCV clinically depends on two combined indicators, persistently undetectable peripheral HCV RNA and positivity for anti-HCV. However, the characteristics of dynamic variation in anti-HCV antibodies in SR-HCV, especially in those patients co-infected with HIV, are still undefined. In this study, a cohort of patients infected with HCV through commercial blood collection practices was studied. We found that the annual decreasing rate of anti-HCV presented a gradually accelerated process in HCV resolvers. However, the variation in the decline of anti-HCV presented a slowly accelerated process within the early decrease stage and a gradually decelerated process within the latter decrease stage. In addition, we deduced that it expended approximately 16 years from natural HCV recovery to undetectable peripheral anti-HCV in HCV resolvers co-infected with HIV, while this time was estimated to be 20 years in SR-HCV without HIV co-infection. Our data indicated that the decay of anti-HCV was accelerated by HIV-related impairment of immune function. The prevalence of HCV infection may be severely underestimated in this large-scale retrospective epidemiologic investigation in an HIV-infected population.

Regulation of transepithelial ion transport in the rat late distal colon by the sympathetic nervous system

The colorectum (late distal colon) is innervated by the sympathetic nervous system, and many colorectal diseases are related to disorders of the sympathetic nervous system. The sympathetic regulation of colorectal ion transport is rarely reported. The present study aims to investigate the effect of norepinephrine (NE) in the normal and catecholamine-depleted condition to clarify the regulation of the sympathetic adrenergic system in ion transport in the rat colorectum. NE-induced ion transport in the rats colorectum was measured by short-circuit current (I(sc)) recording; the expression of beta-adrenoceptors and NE transporter (NET) were quantified by real-time PCR, and western blotting. When the endogenous catecholamine was depleted by reserpine, the baseline I(sc) in the colorectum was increased significantly comparing to controls. NE evoked downward deltaI(sc) in colorectum of treated rats was 1.8-fold of controls. The expression of beta(2)-adrenoceptor protein in the colorectal mucosa was greater than the control, though the mRNA level was reduced. However, NET expression was significantly lower in catecholamine-depleted rats compared to the controls. In conclusion, the sympathetic nervous system plays an important role in regulating basal ion transport in the colorectum. Disorders of sympathetic neurotransmitters result in abnormal ion transport, beta-adrenoceptor and NET are involved in the process.

Peroxisome proliferator-activated receptor α activation attenuates the inflammatory response to protect the liver from acute failure by promoting the autophagy pathway

Peroxisome proliferator-activated receptor α (PPARα) has been reported to induce a potent anti-inflammatory response. Autophagy is a recently recognized rudimentary cellular response to inflammation and injury. The aim of the present study was to test the hypothesis that PPARα activation mediates autophagy to inhibit liver inflammation and protect against acute liver failure (ALF). PPARα expression during ALF and the impact of PPARα activation by Wy-14 643 on the hepatic immune response were studied in a D-galactosamine/lipopolysaccharide-induced mouse model. Autophagy was inhibited by 3-methyladenine or small interfering RNA (siRNA) against Atg7. In both the mouse model and human ALF subjects, PPARα was significantly downregulated in the injured liver. PPARα activation by pretreatment with Wy-14 643 protected against liver injury in mice. The protective effect of PPARα activation relied on the suppression of inflammatory mechanisms through the induction of autophagy. This hypothesis is supported by the following evidence: first, PPARα activation suppressed proinflammatory responses and inhibited phosphorylated NF-κBp65, phosphorylated JNK and phosphorylated ERK pathways in vivo. Second, protection by PPARα activation was due to the induction of autophagy because inhibition of autophagy by 3-methyladenine or Atg7 siRNA reversed liver protection and inflammation. Third, PPARα activation directly induced autophagy in primary macrophages in vitro, which protected cells from a lipopolysaccharide-induced proinflammatory response. Here, for the first time, we have demonstrated that PPARα-mediated induction of autophagy ameliorated liver injury in cases of ALF by attenuating inflammatory responses, indicating a potential therapeutic application for ALF treatment.

miRNAs affect the development of hepatocellular carcinoma via dysregulation of their biogenesis and expression

The pathogenesis of hepatocellular carcinoma (HCC) is not fully understood, which has affected the early diagnosis and treatment of HCC and the survival time of patients. MicroRNAs (miRNAs) are a class of evolutionarily conserved small, non-coding RNAs, which regulate the expression of various genes post-transcriptionally. Emerging evidence indicates that the key enzymes involved in the miRNA biosynthesis pathway and some tumor-specific miRNAs are widely deregulated or upregulated in HCC and closely associated with the occurrence and development of various cancers, including HCC. Early studies have shown that miRNAs have critical roles in HCC progression by targeting many critical protein-coding genes, thereby contributing to the promotion of cell proliferation; the avoidance of apoptosis, inducing via angiogenesis; and the activation of invasion and metastasis pathways. Experimental data indicate that discovery of increasing numbers of aberrantly expressed miRNAs has opened up a new field for investigating the molecular mechanism of HCC progression. In this review, we describe the current knowledge about the roles and validated targets of miRNAs in the above pathways that are known to be hallmarks of HCC, and we also describe the influence of genetic variations in miRNA biosynthesis and genes.

Asymmetrical cortical vessel sign on susceptibility-weighted imaging: a novel imaging marker for early neurological deterioration and unfavorable prognosis

BACKGROUND AND PURPOSE

Susceptibility-weighted imaging (SWI) is a high spatial resolution technique that can indirectly demonstrate increased cerebral oxygen extraction. Our aim was to assess whether asymmetric cortical vessel sign (ACVS) on SWI could be associated with early neurological deterioration (END) as well as 90-day unfavorable outcome in patients with acute ischaemic stroke.

MATERIALS AND METHODS

Consecutive patients with acute middle cerebral artery (MCA) territory infarction were prospectively enrolled. ACVS was defined as more and/or larger vessels with greater signal loss than those in the opposite hemisphere on minimum intensity projection of SWI. The neurofunctional fluctuation during acute phase as well as 90-day outcomes were assessed. A National Institutes of Health Stroke Scale increment ≥2 points and ≥4 points despite standard treatment in the first 72 h after admission was defined as END2 and END4, respectively.

RESULTS

In all, 572 patients were finally enrolled. ACVS on SWI was present in 39 (6.8%) subjects. Multivariate analysis indicated that ACVS is an independent predictor for END2 [odds ratio (OR) 4.47, 95% confidence interval (CI) 1.99-10.05) and END4 (OR 4.24, 95% CI 1.94-9.23). Furthermore, ACVS also correlates with 90-day unfavorable outcome defined as a modified Rankin Scale score >1 point (OR 2.93, 95% CI 1.15-7.48). Both positive and negative predictive values of ACVS for END2, END4 and 90-day prognosis were reasonable and both could be slightly enhanced as long as patients with contralateral artery stenosis or occlusion were excluded.

CONCLUSION

In patients with MCA territory acute ischaemic stroke, especially in those without contralateral internal carotid artery/MCA stenosis or occlusion, ACVS might be considered as a neuroimaging predictor for END and unfavorable prognosis.

A polymorphism in melanoma differentiation-associated gene 5 may be a risk factor for enterovirus 71 infection

Enterovirus 71 (EV71) infection has a wide variety of clinical manifestations, from no symptoms to fatal disease. Host immune response may be a determinant of disease severity. We investigated the association of polymorphisms in three pattern recognition receptor (PRR) genes-toll-like receptor 3 (TLR3) (rs3775291), retinoic acid-inducible gene I (RIG-I) (rs10813831) and melanoma differentiation-associated gene 5 (MDA5) (rs1990760)-with the severity of EV71 infection. Polymorphisms of candidate genes in 87 EV71-infected patients and 57 asymptomatic controls were detected. Binary logistic regression analysis revealed statistically significant differences in polymorphism of MDA5 (rs1990760) between patients with severe EV71 infection and asymptomatic controls in an additive model (OR 0.424, 95% CI 0.213-0.845, p 0.015) and a dominant model (OR 0.256, 95% CI 0.103-0.635, p 0.003). Polymorphism of MDA5 (rs1990760) (OR 0.399, 95% CI 0.199-0.798, p 0.009) was found to be associated with the severity of EV71 infection with the analysis of ordinal logistic regression. These results indicated the association between MDA5 (rs1990760) polymorphism and an increased risk of a severe EV71 infection in Chinese children, which offers potential for investigating the innate immune mechanism of EV71 infection and identifying at-risk infants, for whom a preventive strategy may reduce the severity of EV71 infection.

Correlation between the embolism area and pulmonary arterial systolic pressure as an indicator of pulmonary arterial hypertension in patients with acute pulmonary thromboembolism

OBJECTIVE

We tested whether correlation between embolism area and pulmonary arterial pressure may serve as an indicator of pulmonary arterial hypertension in patients with acute pulmonary thromboembolism.

PATIENTS AND METHODS

In total, 204 patients who underwent spiral computed tomography (CT) pulmonary angiography and ultrasonic cardiogram were enrolled. The patients were stratified according to their pulmonary arterial systolic pressure into those with normal values, or those with mild, moderate, or severe pulmonary arterial hypertension. The embolism area was quantified using Qanadli score.

RESULTS

We found that embolism area correlated positively with pulmonary arterial systolic pressure (r = 0.514). Specifically, embolism areas of four study groups were, respectively, 17.72 ± 13.61%, 18.25 ± 13.78%, 33.39 ± 10.99%, 40.46 ± 15.75%, obviously increasing along with progression of the disease. Pulmonary arterial systolic pressure was above 41 mm Hg when the embolism area was >33%, and above 70 mm Hg with the embolism area of > 40%.

CONCLUSIONS

Assessment of the embolism area is useful in the clinical evaluation of pulmonary arterial systolic pressure, but appears to be more applicable to moderate and severe pulmonary arterial hypertension.

Role of mitogen-activated protein kinase cascades in 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced apoptosis in neuronal pheochromocytoma cells

Mitogen-activated protein kinases (MAPKs) are involved in neuronal death caused by many cytotoxins. Conventional MAPKs consist of three family members: extracellular signal-regulated kinase-1/2 (ERK1/2), c-Jun N-terminal kinase (JNK) and p38. It has been originally shown that ERK1/2 is important for cell survival, whereas JNK and p38 are deemed stress responsive and thus involved in apoptosis. However, information describing the role of MAPKs in 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-induced neurotoxicity is insufficient. The aim of this study was to identify the role of MAPK cascades in TCDD-induced neurotoxicity using differentiated pheochromocytoma (PC12) cells as a model for neuronal cells. Cell viability assay, terminal deoxynucleotidyl transferase dUTP nick-end labeling assay and flow cytometry analysis showed that TCDD attenuated cell viability with a dose- and time-dependent manner and significantly induced apoptosis in primary cortical neurons and PC12 cells. Western blot analysis indicated that TCDD markedly activated the expression of ERK1/2, JNK and p38 in TCDD-treated PC12 cells. Furthermore, PD98059 (ERK1/2 inhibitor), SP600125 (JNK inhibitor) and SB202190 (p38 inhibitor) notably blocked the effect of TCDD on cell apoptosis. Based on the findings above, it is concluded that the activation of MAPK signaling pathways may be associated with TCDD-mediated neuronal apoptosis.

Activation of mGluR4 promotes proliferation of rat neural progenitor cells while mediating activation of ERK1/2 signaling pathway

Metabotropic glutamate receptors (mGluRs) influence the proliferation and differentiation of neural progenitor cells (NPCs) in the brain. They may play a major role in neurogenesis during embryonic development and in the adult brain. In this study, we investigated the expression of mGluR4 in NPCs and its possible role in the proliferation of rat embryonic NPCs in vitro, the expression of cyclin D1 and the activation of signaling pathways of mitogen—activated protein kinases (MAPKs). The results showed that mGluR4 protein was expressed in NPCs in vitro. mGluR4 selective agonist VU0155041 promoted the proliferation of NPCs by increasing cell activity, diameter of neurospheres and cell division. In addition, mGluR4 siRNA decreased the proliferation of NPCs. The protein expression of cyclin D1 increased with VU0155041 treatment and decreased after siRNA treatment. We also demonstrated that activation of ERK1/2 signaling pathways was involved in the proliferation of NPCs. VU0155041 increased phosphorylation of p—ERK1/2 levels, and mGluR4 siRNA decreased p—ERK1/2 levels. Furthermore, p—p38 expression was decreased by VU0155041 but was increased by mGluR4 siRNA. ERK1/2 inhibitor U0126 attenuated the increase of proliferation and cyclin D1 induced by VU0155041. These findings indicate that mGluR4 promotes the proliferation of rat NPCs and cyclin D1 expression through activation of ERK1/2 signaling pathways in vitro, suggesting that mGluR4 may play an important role in brain development. This study will help to develop a new potential therapeutic agent for brain injury and for the prevention of neurodegenerative disorders.

Sleep duration and incidence of colorectal cancer in postmenopausal women

Background:

Sleep duration is dependent on circadian rhythm that controls a variety of key cellular functions. Circadian disruption has been implicated in colorectal tumorigenesis in experimental studies. We prospectively examined the association between sleep duration and risk of colorectal cancer (CRC).

Methods:

In the Women’s Health Initiative Observational Study, 75 828 postmenopausal women reported habitual sleep duration at baseline 1993–1998. We used Cox proportional hazards regression model to estimate the hazard ratio (HR) of CRC and its associated 95% confidence interval (CI).

Results:

We ascertained 851 incident cases of CRC through 2010, with an average 11.3 years of follow-up. Compared with 7 h of sleep, the HRs were 1.36 (95% CI 1.06–1.74) and 1.47 (95% CI 1.10–1.96) for short (⩽5 h) and long (⩾9 h) sleep duration, respectively, after adjusting for age, ethnicity, fatigue, hormone replacement therapy (HRT), physical activity, and waist to hip ratio. The association was modified by the use of HRT (P-interaction=0.03).

Conclusion:

Both extreme short and long sleep durations were associated with a moderate increase in the risk of CRC in postmenopausal women. Sleep duration may be a novel, independent, and potentially modifiable risk factor for CRC.

The genome in space and time: does form always follow function? How does the spatial and temporal organization of a eukaryotic genome reflect and influence its functions?

Recent systematic studies using newly developed genomic approaches have revealed common mechanisms and principles that underpin the spatial organization of eukaryotic genomes and allow them to respond and adapt to diverse functional demands. Genomes harbor, interpret, and propagate genetic and epigenetic information, and the three-dimensional (3D) organization of genomes in the nucleus should be intrinsically linked to their biological functions. However, our understanding of the mechanisms underlying both the topological organization of genomes and the various nuclear processes is still largely incomplete. In this essay, we focus on the functional relevance as well as the biophysical properties of common organizational themes in genomes (e.g. looping, clustering, compartmentalization, and dynamics), and examine the interconnection between genome structure and function from this angle. Present evidence supports the idea that, in general, genome architecture reflects and influences genome function, and is relatively stable. However, the answer as to whether genome architecture is a hallmark of cell identity remains elusive.

A genome-wide 3C-method for characterizing the three-dimensional architectures of genomes

Accumulating evidence demonstrates that the three-dimensional (3D) organization of chromosomes within the eukaryotic nucleus reflects and influences genomic activities, including transcription, DNA replication, recombination and DNA repair. In order to uncover structure-function relationships, it is necessary first to understand the principles underlying the folding and the 3D arrangement of chromosomes. Chromosome conformation capture (3C) provides a powerful tool for detecting interactions within and between chromosomes. A high throughput derivative of 3C, chromosome conformation capture on chip (4C), executes a genome-wide interrogation of interaction partners for a given locus. We recently developed a new method, a derivative of 3C and 4C, which, similar to Hi-C, is capable of comprehensively identifying long-range chromosome interactions throughout a genome in an unbiased fashion. Hence, our method can be applied to decipher the 3D architectures of genomes. Here, we provide a detailed protocol for this method.

Virologic factors associated with failure to passive-active immunoprophylaxis in infants born to HBsAg-positive mothers

In infants born to hepatitis B surface antigen (HBsAg)-positive mothers, failure after passive-active immunization still occurs. The role of maternal hepatitis B DNA level and other risk factors in this setting remains unclear. This study retrospectively evaluated virologic and other risk factors associated with immunoprophylaxis failure in infants born to HBsAg-positive mothers. Between January 2007 and March 2010, we reviewed the clinical and virologic tests in 869 mother-infant pairs. All infants received the identical passive-active immunization schedule after birth. The failure infants (HBsAg positive at 7-12 months of age) were compared to infants who were HBsAg negative when tested during this time period. Among 869 infants, 27 (3.1%) infants were immunoprophylaxis failures and the other 842 (96.9%) infants remained HBsAg negative. When mothers' pre-delivery HBV DNA levels were stratified to <6, 6-6.99, 7-7.99 and ≥ 8 log(10) copies/mL, the corresponding rates of immunoprophylaxis failure were 0%, 3.2% (3/95), 6.7% (19/282) and 7.6% (5/66), respectively (P < 0.001 for the trend). All failure infants were born to hepatitis B e antigen (HBeAg)-positive mothers. Multivariate logistic regression analysis identified maternal HBV DNA levels [odds ratio (OR) = 1.88, 95% confidence interval (CI): 1.07-3.30] and detectable HBV DNA in the cord blood (OR = 39.67, 95% CI: 14.22-110.64) as independent risk factors for immunoprophylaxis failure. All failure infants were born to HBeAg-positive mothers with HBV DNA levels ≥ 6 log(10) copies/mL. The presence of HBV DNA in cord blood predicted failure to passive-active immunization.

A case of occult bowel perforation after a cycle of chemotherapy for advanced epithelial ovarian carcinoma

Occult bowel perforation is a rare complication in chemotherapy of advanced epithelial ovarian cancer (EOC). The authors present a case of a 75-year-old woman who had appendectomy due to suppurative appendicitis five years prior, that experienced an occult bowel perforation resulting in continuous decline of electrolytes after a single cycle of nedaplatin (NDP) and paclitaxel during neoadjuvant treatment of advanced EOC. To the authors' knowledge, this is the first reported case of an occult bowel perforation after neoadjuvant chemotherapy (NAC) for ovarian cancer. The complication was highly suggestive of a cell lysis mechanism for the perforation.

miR-135a contributes to paclitaxel resistance in tumor cells both in vitro and in vivo

Cancer cell resistance to paclitaxel continues to be a major clinical problem. In this study, we utilized microRNA (miRNA) arrays to screen for differentially expressed miRNAs in paclitaxel-resistant cell lines established in vitro. We observed concordant upregulation of miR-135a in paclitaxel-resistant cell lines representing three human malignancies. Subsequently, the role of miRNA-135a was evaluated in an in vivo model of paclitaxel resistance. In this model, mice were inoculated subcutaneously with a non-small cell lung carcinoma cell line and treated with paclitaxel for a prolonged period. In paclitaxel-resistant cell lines, established either in vitro or in vivo, blockage of miR-135a sensitized resistant cell lines to paclitaxel-induced cell death. We further demonstrated a correlation between paclitaxel response and miR-135a expression in paclitaxel-resistant subclones that were established in vivo. The paclitaxel-resistant phenotype of these subclones was maintained upon retransplantation in new mice, as shown by decreased tumor response upon paclitaxel treatment compared with controls. Upregulation of miR-135a was associated with reduced expression of the adenomatous polyposis coli gene (APC). APC knockdown increased paclitaxel resistance in parental cell lines. Our results indicate that paclitaxel resistance is associated with upregulation of miR-135a, both in vitro and in vivo, and is in part determined by miR-135a-mediated downregulation of APC.