FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data

Motivation: How chromatin folds in three-dimensional (3D) space is closely related to transcription regulation. As powerful tools to study such 3D chromatin conformation, the recently developed Hi-C technologies enable a genome-wide measurement of pair-wise chromatin interaction. However, methods for the detection of biologically meaningful chromatin interactions, i.e. peak calling, from Hi-C data, are still under development. In our previous work, we have developed a novel hidden Markov random field (HMRF) based Bayesian method, which through explicitly modeling the non-negligible spatial dependency among adjacent pairs of loci manifesting in high resolution Hi-C data, achieves substantially improved robustness and enhanced statistical power in peak calling. Superior to peak callers that ignore spatial dependency both methodologically and in performance, our previous Bayesian framework suffers from heavy computational costs due to intensive computation incurred by modeling the correlated peak status of neighboring loci pairs and the inference of hidden dependency structure

VAWCM-Instillation Improves Delayed Primary Fascial Closure of Open Septic Abdomen

Background. Failure to achieve delayed primary fascial closure (DPFC) is one of the main complications of open abdomen (OA), certainly when abdominal sepsis is present. This retrospective cohort study aims to evaluate the effect of combined therapy of vacuum-assisted mesh-mediated fascial traction and topical instillation (VAWCM-instillation) on DPFC in the open septic abdomen. Methods. The patients with abdominal sepsis who underwent OA using VAWCM were included and divided into the instillation and noninstillation (control) groups. The DPFC rate and other outcomes were compared between the two groups. Results. Between 2007 and 2013, 73 patients with open septic abdomen were treated with VAWCM-instillation and 61 cases with VAWCM-only. The DPFC rate in the instillation group was significantly increased (63% versus 41%, P=0.011). The mortality with OA was similar (24.6% versus 23%, P=0.817) between the two groups. However, time to DPFC (P=0.003) and length of stay in hospital (P=0.022) of the survivals were significantly decreased in the instillation group. In addition, VAWCM-instillation (OR 1.453, 95% CI 1.222–4.927, P=0.011) was an independent influencing factor related to successful DPFC. Conclusions. VAWCM-instillation could improve the DPFC rate but could not decrease the mortality in the patients with open septic abdomen

Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression: Cross-Platform Imputation of Methylation Profile

DNA methylation is a key epigenetic mark involved in both normal development and disease progression. Recent advances in high-throughput technologies have enabled genome-wide profiling of DNA methylation. However, DNA methylation profiling often employs different designs and platforms with varying resolution, which hinders joint analysis of methylation data from multiple platforms. In this study, we propose a penalized functional regression model to impute missing methylation data. By incorporating functional predictors, our model utilizes information from nonlocal probes to improve imputation quality. Here, we compared the performance of our functional model to linear regression and the best single probe surrogate in real data and via simulations. Specifically, we applied different imputation approaches to an acute myeloid leukemia dataset consisting of 194 samples and our method showed higher imputation accuracy, manifested, for example, by a 94% relative increase in information content and up to 86% more CpG sites passing post-imputation filtering. Our simulated association study further demonstrated that our method substantially improves the statistical power to identify trait-associated methylation loci. These findings indicate that the penalized functional regression model is a convenient and valuable imputation tool for methylation data, and it can boost statistical power in downstream epigenome-wide association study (EWAS)

HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants

Abstract Background Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases. However, most of them are located in the non-protein coding regions, and therefore it is challenging to hypothesize the functions of these non-coding GWAS variants. Recent large efforts such as the ENCODE and Roadmap Epigenomics projects have predicted a large number of regulatory elements. However, the target genes of these regulatory elements remain largely unknown. Chromatin conformation capture based technologies such as Hi-C can directly measure the chromatin interactions and have generated an increasingly comprehensive catalog of the interactome between the distal regulatory elements and their potential target genes. Leveraging such information revealed by Hi-C holds the promise of elucidating the functions of genetic variants in human diseases. Results In this work, we present HiView, the first integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. HiView is able to display Hi-C data and statistical evidence for chromatin interactions in genomic regions surrounding any given GWAS variant, enabling straightforward visualization and interpretation. Conclusions We believe that as the first GWAS variants-centered Hi-C genome browser, HiView is a useful tool guiding post-GWAS functional genomics studies. HiView is freely accessible at: http://www.unc.edu/~yunmli/HiView

The m6A Reader IGF2BP2 Regulates Macrophage Phenotypic Activation and Inflammatory Diseases by Stabilizing TSC1 and PPARγ.

peer reviewedPhenotypic polarization of macrophages is regulated by a milieu of cues in the local tissue microenvironment. Currently, little is known about how the intrinsic regulators modulate proinflammatory (M1) versus prohealing (M2) macrophages activation. Here, it is observed that insulin-like growth factor 2 messenger RNA (mRNA)-binding protein 2 (IGF2BP2)-deleted macrophages exhibit enhanced M1 phenotype and promote dextran sulfate sodium induced colitis development. However, the IGF2BP2-/- macrophages are refractory to interleukin-4 (IL-4) induced activation and alleviate cockroach extract induced pulmonary allergic inflammation. Molecular studies indicate that IGF2BP2 switches M1 macrophages to M2 activation by targeting tuberous sclerosis 1 via an N6-methyladenosine (m6A)-dependent manner. Additionally, it is also shown a signal transducer and activators of transcription 6 (STAT6)-high mobility group AT-hook 2-IGF2BP2-peroxisome proliferator activated receptor-γ axis involves in M2 macrophages differentiation. These findings highlight a key role of IGF2BP2 in regulation of macrophages activation and imply a potential therapeutic target of macrophages in the inflammatory diseases

Single-Atom Catalyst Aggregates: Size-Matching is Critical to Electrocatalytic Performance in Sulfur Cathodes

Electrocatalysis is critical to the performance displayed by sulfur cathodes. However, the constituent electrocatalysts and the sulfur reactants have vastly different molecular sizes, which ultimately restrict electrocatalysis efficiency and hamper device performance. Herein, the authors report that aggregates of cobalt single-atom catalysts (SACs) attached to graphene via porphyrins can overcome the challenges associated with the catalyst/reactant size mismatch. Atomic-resolution transmission electron microscopy and X-ray absorption spectroscopy measurements show that the Co atoms present in the SAC aggregates exist as single atoms with spatially resolved dimensions that are commensurate the sulfur species found in sulfur cathodes and thus fully accessible to enable 100% atomic utilization efficiency in electrocatalysis. Density functional theory calculations demonstrate that the Co SAC aggregates can interact with the sulfur species in a synergistic manner that enhances the electrocatalytic effect and promote the performance of sulfur cathodes. For example, Li-S cells prepared from the Co SAC aggregates exhibit outstanding capacity retention (i.e., 505 mA h g(-1) at 0.5 C after 600 cycles) and excellent rate capability (i.e., 648 mA h g(-1) at 6 C). An ultrahigh area specific capacity of 12.52 mA h cm(-2) is achieved at a high sulfur loading of 11.8 mg cm(-2)

Development of an Infectious Cell Culture System for Hepatitis C Virus Genotype 6a Clinical Isolate Using a Novel Strategy and Its Sensitivity to Direct-Acting Antivirals

Hepatitis C virus (HCV) is classified into seven major genotypes, and genotype 6 is commonly prevalent in Asia, thus reverse genetic system representing genotype 6 isolates in prevalence is required. Here, we developed an infectious clone for a Chinese HCV 6a isolate (CH6a) using a novel strategy. We determined CH6a consensus sequence from patient serum and assembled a CH6a full-length (CH6aFL) cDNA using overlapped PCR product-derived clones that shared the highest homology with the consensus. CH6aFL was non-infectious in hepatoma Huh7.5 cells. Next, we constructed recombinants containing Core-NS5A or 5′UTR-NS5A from CH6a and the remaining sequences from JFH1 (genotype 2a), and both were engineered with 7 mutations identified previously. However, they replicated inefficiently without virus spread in Huh7.5 cells. Addition of adaptive mutations from CH6a Core-NS2 recombinant, with JFH1 5′UTR and NS3-3′UTR, enhanced the viability of Core-NS5A recombinant and acquired replication-enhancing mutations. Combination of 22 mutations in CH6a recombinant with JFH1 5′UTR and 3′UTR (CH6aORF) enabled virus replication and recovered additional four mutations. Adding these four mutations, we generated two efficient recombinants containing 26 mutations (26m), CH6aORF_26m and CH6aFL_26m (designated “CH6acc”), releasing HCV of 104.3–104.5 focus-forming units (FFU)/ml in Huh7.5.1-VISI-mCherry and Huh7.5 cells. Seven newly identified mutations were important for HCV replication, assembly, and release. The CH6aORF_26m virus was inhibited in a dose- and genotype-dependent manner by direct-acting-antivirals targeting NS3/4A, NS5A, and NS5B. The CH6acc enriches the toolbox of HCV culture systems, and the strategy and mutations applied here will facilitate the culture development of other HCV isolates and related viruses