Generation of induced pluripotent stem cells (iPSCs) by defined factors is an extremely inefficient process, because there is a strong epigenetic block preventing cells from achieving pluripotency. Here we report that virally expressed factors bound to the promoters of their target genes to the same extent in both iPSCs and unreprogrammed cells (URCs). However, expression of endogenous pluripotentcy genes was observed only in iPSCs. Comparison of local chromatin structure of the OCT4 locus revealed that there was a cohesin-complex-mediated intrachromosomal loop that juxtaposes a downstream enhancer to the gene's promoter, enabling activation of endogenous stemness genes. None of these long-range interactions were observed in URCs. Knockdown of the cohesin-complex gene SMC1 by RNAi abolished the intrachromosomal interaction and affected pluripotency. These findings highlight the importance of the SMC1-orchestrated intrachromosomal loop as a critical epigenetic barrier to the induction of pluripotency.

A long noncoding RNA directly builds an intrachromosomal interaction complex to establish allele-specific transcriptional gene silencing over a large chromosomal domain.

BackgroundElderly patients are reportedly at higher risk of postoperative cognitive dysfunction (POCD) after inhalational anesthesia with sevoflurane. We hypothesized that the incidence of POCD would be higher in elderly patients undergoing major surgery under inhalational rather than intravenous anesthesia. We also measured plasma S-100β protein concentration as a biomarker of central nervous system injury, and plasma interleukin (IL)-6 and tumor necrosis factor (TNF)-α concentrations to judge the contribution of systemic inflammation to POCD.MethodsNinety patients aged 65–75 years scheduled for resection of an esophageal carcinoma were randomly assigned to one of three groups (n = 30) as follows: a group receiving sevoflurane anesthesia (Group S); a group receiving preoperative methylprednisolone before sevoflurane anesthesia (Group S + MP); and a control group maintained with intravenous propofol (Group C). The mini-mental state examination (MMSE) and Montreal cognitive assessment (MoCA) were used to measure patients’ cognitive function the day before surgery, and on the first, third and seventh postoperative days. The plasma concentrations of TNF-α, IL-6 and S-100β protein were measured 10 min before anesthesia, and on the first, third and seventh postoperative days.ResultsThere were no significant differences in the demographic or clinical characteristics, or perioperative hemodynamic status, of the three groups. The MMSE and MoCA scores were significantly lower in Group S than in the propofol control (Group C) and Group S + MP on the first, third and seventh postoperative days (P <0.05). Throughout the first postoperative week the plasma concentrations of TNF-α, IL-6, and S-100β protein were significantly elevated in Group S compared with Group C (P <0.05), but were significantly lower in Group S + MP than Group S (P <0.05).ConclusionsThe incidence of POCD was higher in elderly patients undergoing major surgery under inhalational anesthesia with sevoflurane than those maintained on intravenous propofol, and lower in elderly patients pro-treating with methylprednisolone. Furthermore, we found elevated plasma concentrations of S-100β protein, TNF-α and IL-6 in those receiving sevoflurane anesthesia.Trial registrationChiCTR-IOR-15007007 (02-09-2015).

BackgroundLong non-coding RNAs (lncRNAs) are not translated into proteins and were initially considered to be part of the ‘dark matter’ of the genome. Recently, it has been shown that lncRNAs play a role in the recruitment of chromatin modifying complexes and can influence gene expression. However, it is unknown if lncRNAs function in a similar way in cancer.ResultsHere, we show that the lncRNA ROR occupies and activates the TESC promoter by repelling the histone G9A methyltransferase and promoting the release of histone H3K9 methylation. Suppression of ROR in tumors results in silencing of TESC expression, and G9A-mediated histone H3K9 methylation in the TESC promoter is restored, which significantly reduces tumor growth and metastasis. Without ROR silencing, TESC knockdown presents consistent and significant reductions in tumor progression.ConclusionsOur results reveal a novel mechanism by which ROR may serve as a decoy oncoRNA that blocks binding surfaces, preventing the recruitment of histone modifying enzymes, thereby specifying a new pattern of histone modifications that promote tumorigenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0705-2) contains supplementary material, which is available to authorized users.

CCCTC binding factor (CTCF) mutants that cannot bind components of the polycomb repressive complex-2 (PRC2) do not form the chromatin loops that regulate monoallelic gene expression.

Long noncoding RNAs (lncRNAs) are proved to be critical regulators in numerous cellular processes. However, the potential involvement of lncRNAs in macroautophagy/autophagy is largely unknown. Autophagy is a highly regulated cellular degradation system, and its dysregulation is involved in many human diseases, including cancers. Here, we show that the lncRNA ZNNT1 is induced by PP242 and MTORC1 selective inhibitor rapamycin in uveal melanoma (UM) cells. Overexpression of ZNNT1 promotes autophagy by upregulating ATG12 expression, whereas knockdown of ZNNT1 attenuates PP242-induced autophagy. Overexpression of ZNNT1 inhibits tumorigenesis and the migration of UM cells, and knockdown of ATG12 can partially rescue the ZNNT1-induced inhibition of UM tumorigenesis. In summary, our study reveals that ZNNT1 acts as a potential tumor suppressor in UM by inducing autophagy.

Liver fibrosis is overly exuberant wound healing that leads to portal hypertension or liver cirrhosis. Recent studies have demonstrated the functions of bone morphogenetic protein 9 (BMP9) in liver fibrosis, and thus, targeting liver-specific BMP9 abnormalities will become an attractive approach for developing therapeutics to treat liver fibrosis. Here, we reveal that BMP9 serves as a valuable serum diagnostic indicator and efficient therapeutic target to attenuate liver fibrogenesis. Our analysis of biopsies from liver fibrotic patients revealed that higher BMP9 levels accompanied advanced stages of liver fibrosis. In mouse models, recombinant Bmp9 overexpression accelerated liver fibrosis, and adenovirus-mediated Bmp9 knockdown attenuated liver fibrogenesis. Intriguingly, BMP9 directly stimulated hepatic stellate cell activation via the SMAD signaling pathway to enhance hepatic fibrosis. Moreover, an inhibitory monoclonal antibody targeting Bmp9 was efficacious in treatment of mice with liver fibrosis. These observations delineate a novel model in which BMP9 directly drives SMAD/ID1 signaling in hepatic stellate cells, which modulates liver fibrogenesis development. Moreover, the findings unveil a promising surrogate biomarker for the diagnosis of hepatic fibrosis, thereby representing an efficient "BMP9 neutralization" approach in alleviating hepatic fibrosis.

Generation of induced pluripotent stem cells (iPSCs) from somatic cells by defined factors is a mechanism-unknown, yet extremely time-consuming process. Inefficient reprogramming leads to prolonged periods of in vitro iPSC selection, resulting in subtle genetic and epigenetic abnormalities. To facilitate pluripotent reprogramming, we have identified the thyroid hormone triiodothyronine (T3) as an endogenous factor that can enhance reprogramming of human dermal fibroblasts (HDF) and umbilical cord mesenchymal stem cells (UCMSC). This potentiation of iPSC induction is associated with metabolic remodeling activity, including up-regulation of key glycolytic genes, an increase in cell proliferation, and the induction of mesenchymal-epithelial transition (MET). We further identify the activation of the PI3K/AKT signal pathway by T3 as an underlying mechanism for the enhanced conversion to cell pluripotency in this model. These studies demonstrate that T3 enhances metabolic remodeling of donor cells in potentiating cell reprogramming.