Optimization and quality control of genome-wide Hi-C library preparation.

Highest-throughput chromosome conformation capture (Hi-C) is one of the key assays for genome- wide chromatin interaction studies. It is a time-consuming process that involves many steps and many different kinds of reagents, consumables, and equipments. At present, the reproducibility is unsatisfactory. By optimizing the key steps of the Hi-C experiment, such as crosslinking, pretreatment of digestion, inactivation of restriction enzyme, and in situ ligation etc., we established a robust Hi-C procedure and prepared two biological replicates of Hi-C libraries from the GM12878 cells. After preliminary quality control by Sanger sequencing, the two replicates were high-throughput sequenced. The bioinformatics analysis of the raw sequencing data revealed the mapping-ability and pair-mate rate of the raw data were around 90% and 72%, respectively. Additionally, after removal of self-circular ligations and dangling-end products, more than 96% of the valid pairs were reached. Genome-wide interactome profiling shows clear topological associated domains (TADs), which is consistent with previous reports. Further correlation analysis showed that the two biological replicates strongly correlate with each other in terms of both bin coverage and all bin pairs. All these results indicated that the optimized Hi-C procedure is robust and stable, which will be very helpful for the wide applications of the Hi-C assay.

Construction of CTCF degradation cell line by CRISPR/Cas9 mediated genome editing.

The CCCTC-binding factor (CTCF) is the main insulator protein described in vertebrates. It plays fundamental roles during diverse cellular processes. CTCF gene knockout mice led to death during embryonic development. To further explore the functions of CTCF, we employed a CRISPR/Cas9-based genome engineering strategy to in-frame insert the mitosis-special degradation domain (MD) of cyclin B into the upstream open reading frame of CTCF gene. Fusion protein is designed to degrade during mitosis leaded by MD. As a control group, mutation of a single arginine (R42A) within the destruction box inactivates the MD leading to constitutive expression of MD*-CTCF. The homozygous clones were obtained via the screening by puromycin when coexpressed with puromycin resistence gene. The protein level of CTCF in MD-CTCF cell line was about 10% of wild-type cells throughout cell cycles by the analyses of Western blotting and immunofluorescence. There was no significant difference between MD*-CTCF cell line and wild type. Flow cytometry results showed prolonged G1 phase in MD-CTCF cell line. Taken together, we demonstrated the feasibility of efficiently inserting MD domain into genome with the CRISPR/Cas9 technology and reported the first CTCF-specific degradation human cell line.

"Qufeng Tongluo" acupuncture prevents the progression of glomerulonephritis by decreasing renal sympathetic nerve activity.

ETHNOPHARMACOLOGICAL RELEVANCE: Although the exact mechanism(s) underlying acupuncture remain unknown, acupuncture and acupuncture-like somatic nerve stimulation have been used to treat different kidney diseases and several complications related to them.The aim of this preliminary study was to assess the effectiveness of acupuncture on glomerulonephritis (GN) according to the theory of "Wind-hided renal collaterals" previously proposed. MATERIAL AND METHODS: We used a New Zealand white rabbit model of cationized bovine serum albumin (cBSA)-induced glomerulonephritis and then administered them metoprolol, irbesartan or acupuncture to evaluate the effectiveness of acupuncture treatment and preliminarily explore its potential mechanism. RESULTS: After immunization, our results showed that compared to the cBSA+MET and cBSA+IRB medication groups, "Qufeng Tongluo" significantly lowered parameters of renal function and improved podocyte injury in the 3rd, 6th and 8th weeks of treatment. Moreover, acupuncture increased the protein expression of phosphorylated ERK1/2. CONCLUSIONS: Our study suggests that a potential mechanism by which acupuncture has an antihypertensive effect and can significantly halt deteriorating renal function due to cBSA GN might be mediated by inhibiting the Erk1/2 MAPK pathway to reduce renal sympathetic nerve activity (RSNA).

[Effect of Qufeng Tongluo Recipe on the expressions of connexin 36 protein and gene in rat mesangial cells].

OBJECTIVE: To determine the effect of Qufeng Tongluo Recipe (QFTLR) on the expressions of connexin 36 (Cx36) protein and gene in rat mesangial cells (MCs) and the proliferation of the MCs. METHODS: Serum samples containing Benazepril (Bena) and QFTLR were prepared in line with serum pharmacology methodology. The MCs cultured in vitro were divided into normal control and Lipopolysaccharide (LPS), Bena and QFTLR treated groups. The expressions of Cx36 protein and gene were detected by laser scanning confocal microscope (LSCM), Western blot, immunohistochemical assay and quantitative real time polymerase chain reaction (QRT-PCR) respectively. RESULTS: Compared with the control, higher level of Cx36 protein expression was found in the MCs than treated with LPS (P < 0.01). Both Bena and QFTLR lowered the level of Cx36 protein expression in the MCs treated with LPS significantly (P < 0.01 or P < 0.05). Similar results were found with the expression of Cx36 mRNA. CONCLUSION: QFTLR inhibits the proliferation of rat MCs, possibly through down-regulating the expressions of Cx36 protein and gene.

Qufeng Tongluo Prescription () inhibits mesangial cell proliferation and promotes apoptosis through regulating cell cycle progression.

OBJECTIVE: To study the effects and possible underlying mechanism of Qufeng Tongluo Prescription (, QFTL) on the regulation of mesangial cells (MCs) proliferation and apoptosis. METHODS: The MCs used in this experiment have undergone five passages induced by lipopolysaccharide (LPS). Changes in the proliferation, apoptosis, cell cycle regulatory proteins and mRNA expression levels of the MCs after administration of Benazepril or QFTL were measured by methyl thiazolyl tetrazolium (MTT) reduction assay, flow cytometry, Western blot and quantitative real-time polymerase chain reaction (qRT-PCR), respectively. RESULTS: The addition of Benazepril or QFTL serum inhibited LPS-induced MC proliferation after treatment for 24, 48 and 72 h, respectively (P<0.05 or P<0.01). Moreover, the inhibitory effect is more significant in the QFTL group at 48 h (P<0.05). Compared with the control group, LPS-induced cell proliferation decreased the number of cells in G1 phase versus cells in S and G2/M phases, while the addition of QFTL and Benazepril serum increased the ratio of cells at G1 phase (P<0.05 or P<0.01) to cells at S phase (P<0.01), implicating the cell cycle inhibition effect exerted by QFTL. LPS decreased the level of MC apoptosis, compared with the control group (P<0.05), while QFTL and Benazepril serum increased the level of MC apoptosis (P<0.01). Moreover, the difference between the QFTL group and the Benazepril group was statistically significant (P<0.01). Compared with the control group, the protein and mRNA expression levels of cylinD1, cyclin dependent kinase 2 (CDK2) and p21 were significantly increased (P<0.05 or P<0.01), p27 was decreased but with no statistical significance (P>0.05); After being treated with QFTL and Benazepril serum, the protein and mRNA expression levels of cylinD1, CDK2, p21 were decreased and p27 increased significantly (P<0.05 or P<0.01); Compared with the Benazepril group, QFTL show better effects on protein and mRNA expression levels of cylinD1, CDK2 (P<0.05 or P<0.01) and p21 protein expression (P<0.05). CONCLUSION: QFTL inhibits MCs proliferation, promotes MCs apoptosis through an underlying mechanism of down-regulating the protein and mRNA expression levels of cylinD1, CDK2, p21 and up-regulation of the expression level of p27.